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196 lines
7.3 KiB
EmacsLisp
196 lines
7.3 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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(defvar org-babel-R-func-name "org_babel_R_main"
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"This is the main function which wraps each R source code
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block.")
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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'."
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(message "executing R source code block...")
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(save-window-excursion
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(let ((vars (org-babel-ref-variables params))
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results)
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(org-babel-R-initiate-R-buffer)
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(mapc (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars)
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(org-babel-R-input-command
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(format "%s <- function ()\n{\n%s\n}" org-babel-R-func-name body))
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(org-babel-R-to-elisp org-babel-R-func-name))))
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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 in the current
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R process in `org-babel-R-buffer'."
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(unless org-babel-R-buffer (error "No active R buffer"))
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(org-babel-R-input-command
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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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has-header)
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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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(setq has-header (and (symbolp (cadr value)) (equal (cadr value) 'hline)))
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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=%s, sep=\"\\t\", as.is=TRUE)"
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name transition-file (if has-header "TRUE" "FALSE")))
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(format "%s <- %s" name (org-babel-R-quote-tsv-field value)))))
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(defun org-babel-R-to-elisp (func-name)
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"Return the result of calling the function named FUNC-NAME in
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`org-babel-R-buffer' as Emacs lisp."
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(let ((tmp-file (make-temp-file "org-babel-R")) result)
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(org-babel-R-input-command
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(format "write.table(%s(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
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func-name tmp-file))
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(with-temp-buffer
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(condition-case nil
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(progn
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(org-table-import tmp-file nil)
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(delete-file tmp-file)
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(setq result (mapcar (lambda (row)
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(mapcar #'org-babel-R-read row))
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(org-table-to-lisp)))
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;; (setq result (org-babel-R-set-header-row result))
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)
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(error nil))
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(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
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(if (consp (car result))
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(if (null (cdr (car result)))
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(caar result)
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result)
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(car result))
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result))))
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(defun org-babel-R-set-header-row (table)
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"Check whether the table appears to have (a) genuine
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user-supplied column names, or (b) default column names added
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automatically by R. In case (a), maintain the first row of the
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table as a header row and insert an hline. In case (b), remove
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the first row and return the org table without an hline."
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(if (or (string-equal (caar table) "V1")
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(string-equal (caar table) "x"))
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;; write.table(1, col.names=TRUE) makes a colname called "x". I
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;; think shows that this approach is too much of a hack: we
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;; can't take some totally different action just because we see
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;; an "x" there that might or might not be a automatic name.
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;; The first row looks like it contains default column names
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;; added by R. This condition could be improved so that it
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;; checks whether the first row is ("V1" "V2" ... "V$n") where
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;; $n is the number of columns.
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(cdr table)
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(cons (car table) (cons 'hline (cdr table)))))
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(defun org-babel-R-read (cell)
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"Strip nested \"s from around strings in exported R values."
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(org-babel-read (or (and (stringp cell)
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(string-match "\\\"\\(.+\\)\\\"" cell)
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(match-string 1 cell))
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cell)))
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;; functions for evaluation of R code
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(defvar org-babel-R-buffer nil
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"Holds the buffer for the current R process")
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(defun org-babel-R-initiate-R-buffer ()
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"If there is not a current R process then create one."
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;; DED: Ideally I think we should use ESS mechanisms for this sort
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;; of thing. See ess-force-buffer-current.
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(unless (and (buffer-live-p org-babel-R-buffer) (get-buffer org-babel-R-buffer))
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(save-excursion
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(R)
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(setf org-babel-R-buffer (current-buffer))
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(org-babel-R-wait-for-output)
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(org-babel-R-input-command ""))))
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(defun org-babel-R-command-to-string (command)
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"Send a command to R, and return the results as a string."
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(org-babel-R-input-command command)
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(org-babel-R-last-output))
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(defun org-babel-R-input-command (command)
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"Pass COMMAND to the R process running in `org-babel-R-buffer'."
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert command)
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(comint-send-input)
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(org-babel-R-wait-for-output))))
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(defun org-babel-R-wait-for-output ()
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"Wait until output arrives"
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(while (progn
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(goto-char comint-last-input-end)
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(not (re-search-forward comint-prompt-regexp nil t)))
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(accept-process-output (get-buffer-process (current-buffer)))))))
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(defun org-babel-R-last-output ()
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"Return the last R output as a string"
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(forward-line 0)
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(let ((raw (buffer-substring comint-last-input-end (- (point) 1)))
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output output-flag)
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(mapconcat
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(lambda (el)
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(if (stringp el)
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(format "%s" el)
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(format "%S" el)))
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(delq nil
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(mapcar
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(lambda (line)
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(unless (string-match "^>" line)
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(and (string-match "\\[[[:digit:]]+\\] *\\(.*\\)$" line)
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(match-string 1 line))))
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;; drop first, because it's the last line of input
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(cdr (split-string raw "[\n\r]")))) "\n")))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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