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I added a couple of things listed below. I happy with the way this is
progressing so far. It's nice to work on a project where everyone uses org-mode. additions: - proposal for how we should implement the R-source-code blocks - example of source code evaluation using org-eval-light.el - notes section on evaluation of R code - some scattered thoughts/suggestions
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Eric Schulte
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existing_tools/org-eval-light.el
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existing_tools/org-eval-light.el
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;;; org-eval-light.el --- Display result of evaluating code in various languages (light)
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;; Copyright (C) 2008 Free Software Foundation, Inc.
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;; Author: Carsten Dominik <carsten at orgmode dot org>,
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;; Eric Schulte <schulte dot eric at gmail dot com>
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;; Keywords: outlines, hypermedia, calendar, wp, literate programming,
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;; reproducible research
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;; Homepage: http://orgmode.org
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;; Version: 0.04
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;; This file is not yet part of GNU Emacs.
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;; GNU Emacs 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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;; GNU Emacs 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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;; 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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;; This file is based off of org-eval, with the following changes.
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;;
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;; 1) forms are only executed manually, (allowing for the execution of
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;; an entire subtree of forms)
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;; 2) use the org-mode style src blocks, rather than the muse style
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;; <code></code> blocks
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;; 3) forms are not replaced by their outputs, but rather the output
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;; is placed in the buffer immediately following the src block
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;; commented by `org-eval-light-make-region-example' (when
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;; evaluated with a prefix argument no output is placed in the
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;; buffer)
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;; 4) add defadvice to org-ctrl-c-ctrl-c so that when called inside of
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;; a source block it will call `org-eval-light-current-snippet'
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;;; Code:
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(require 'org)
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(defgroup org-eval-light nil
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"Options concerning including output from commands into the Org-mode buffer."
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:tag "Org Eval"
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:group 'org)
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(defvar org-eval-light-example-size-cutoff 10
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"The number of lines under which an example is considered
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'small', and is exported with the '^:' syntax instead of in a
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large example block")
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(defvar org-eval-light-regexp nil)
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(defun org-eval-light-set-interpreters (var value)
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(set-default var value)
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(setq org-eval-light-regexp
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(concat "#\\+begin_src \\("
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(mapconcat 'regexp-quote value "\\|")
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"\\)\\([^\000]+?\\)#\\+end_src")))
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(defcustom org-eval-light-interpreters '("lisp" "emacs-lisp" "ruby" "shell")
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"Interpreters allows for evaluation tags.
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This is a list of program names (as strings) that can evaluate code and
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insert the output into an Org-mode buffer. Valid choices are
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lisp Interpret Emacs Lisp code and display the result
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shell Pass command to the shell and display the result
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perl The perl interpreter
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python Thy python interpreter
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ruby The ruby interpreter"
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:group 'org-eval-light
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:set 'org-eval-light-set-interpreters
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:type '(set :greedy t
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(const "lisp")
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(const "emacs-lisp")
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(const "perl")
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(const "python")
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(const "ruby")
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(const "shell")))
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;;; functions
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(defun org-eval-light-inside-snippet ()
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(interactive)
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(save-excursion
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(let ((case-fold-search t)
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(start-re "^#\\+begin_src\\( \\([^ \t\n]+\\)\\)?.*\n")
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(end-re "\n#\\+end_src")
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(pos (point))
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beg end)
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(if (and (setq beg (re-search-backward start-re nil t))
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(setq end (re-search-forward end-re nil t))
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(<= beg pos) (>= end pos))
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t))))
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(defun org-eval-light-make-region-example (beg end)
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"Comment out region using either the '^:' or the BEGIN_EXAMPLE
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syntax based on the size of the region as compared to
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`org-eval-light-example-size-cutoff'."
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(interactive "*r")
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(let ((size (abs (- (line-number-at-pos end)
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(line-number-at-pos beg)))))
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(if (= size 0)
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(let ((result (buffer-substring beg end)))
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(delete-region beg end)
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(insert (concat ": " result)))
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(if (<= size org-eval-light-example-size-cutoff)
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(save-excursion
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(goto-char beg)
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(dotimes (n size)
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(move-beginning-of-line 1) (insert ": ") (forward-line 1)))
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(let ((result (buffer-substring beg end)))
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(delete-region beg end)
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(insert (concat "#+BEGIN_EXAMPLE\n" result "#+END_EXAMPLE\n")))))))
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(defun org-eval-light-current-snippet (&optional arg)
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"Execute the current #+begin_src #+end_src block, and dump the
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results into the buffer immediately following the src block,
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commented by `org-eval-light-make-region-example'."
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(interactive "P")
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(let ((line (org-current-line))
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(case-fold-search t)
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(info (org-edit-src-find-region-and-lang))
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beg end lang result)
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(setq beg (nth 0 info)
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end (nth 1 info)
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lang (nth 2 info))
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(unless (member lang org-eval-light-interpreters)
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(error "Language is not in `org-eval-light-interpreters': %s" lang))
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(goto-line line)
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(setq result (org-eval-light-code lang (buffer-substring beg end)))
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(unless arg
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(save-excursion
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(re-search-forward "^#\\+end_src" nil t) (open-line 1) (forward-char 2)
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(let ((beg (point))
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(end (progn (insert result)
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(point))))
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(message (format "from %S %S" beg end))
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(org-eval-light-make-region-example beg end))))))
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(defun org-eval-light-eval-subtree (&optional arg)
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"Replace EVAL snippets in the entire subtree."
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(interactive "P")
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(save-excursion
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(org-narrow-to-subtree)
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(goto-char (point-min))
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(while (re-search-forward org-eval-light-regexp nil t)
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(org-eval-light-current-snippet arg))
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(widen)))
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(defun org-eval-light-code (interpreter code)
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(cond
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((member interpreter '("lisp" "emacs-lisp"))
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(org-eval-light-lisp (concat "(progn\n" code "\n)")))
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((equal interpreter "shell")
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(shell-command-to-string code))
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((member interpreter '("perl" "python" "ruby"))
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(org-eval-light-run (executable-find interpreter) code))
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(t (error "Cannot evaluate code type %s" interpreter))))
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(defun org-eval-light-lisp (form)
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"Evaluate the given form and return the result as a string."
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(require 'pp)
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(save-match-data
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(condition-case err
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(let ((object (eval (read form))))
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(cond
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((stringp object) object)
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((and (listp object)
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(not (eq object nil)))
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(let ((string (pp-to-string object)))
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(substring string 0 (1- (length string)))))
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((numberp object)
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(number-to-string object))
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((eq object nil) "")
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(t
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(pp-to-string object))))
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(error
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(org-display-warning (format "%s: Error evaluating %s: %s"
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"???" form err))
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"; INVALID LISP CODE"))))
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(defun org-eval-light-run (cmd code)
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(with-temp-buffer
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(insert code)
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(shell-command-on-region (point-min) (point-max) cmd nil 'replace)
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(buffer-string)))
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(defadvice org-ctrl-c-ctrl-c (around org-cc-eval-source activate)
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(if (org-eval-light-inside-snippet)
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(call-interactively 'org-eval-light-current-snippet)
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ad-do-it))
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(provide 'org-eval-light)
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;;; org-eval-light.el ends here
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109
rorg.org
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rorg.org
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#+TITLE: rorg --- R and org-mode
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#+SEQ_TODO: TODO PROPOSED | DONE DROPPED MAYBE
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* Commentary
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** Eric <2009-02-06 Fri 15:41>
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I think we're getting close to a comprehensive set of objectives
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(although since you two are the real R user's I leave that decision up
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to you). Once we've agreed on a set of objectives and agreed on at
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least to broad strokes of implementation, I think we should start
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listing out and assigning tasks.
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* Objectives
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** Send data to R from org
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@ -20,14 +31,26 @@
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files. Org tables are first exported to a temporary csv file
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using [[file:existing_tools/org-R.el::defun%20org%20R%20export%20to%20csv%20csv%20file%20options][org-R-export-to-csv]].
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**** org-exp-blocks
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org-exp-blocks uses [[org-interblock-R-command-to-string]] to send
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commands to an R process running in a comint buffer through ESS.
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org-exp-blocks has no support for dumping table data to R process, or
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vice versa.
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**** RweaveOrg
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NA
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** evaluate R code from org and deal with output appropriately
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** Evaluate R code from org and deal with output appropriately
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*** vector output
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When R code evaluation generates vectors and 2-dimensional arrays,
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this should be formatted appropriately in org buffers (orgtbl-mode) as well
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as in export targets (html, latex)
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Agreed, if we can convert the vector data to lists then we can use
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the many orgtbl-to-* functions to convert the list to whatever
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output format we desire. See `orgtbl-to-orgtbl, `orgtbl-to-latex',
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`orgtbl-to-html', `orgtbl-to-csv', etc...
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**** Implementations
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***** org-R
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org-R converts R output (vectors, or matrices / 2d-arrays) to an
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@ -45,13 +68,28 @@
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org file This should have the automatic consequence that it is
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included appropriately in subsequent export targets (html,
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latex).
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**** Implementations
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***** org-R
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org-R does (1) if no output file is specified and (2) otherwise
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***** org-exp-blocks
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org-exp-blocks tries to do 2, but I don't think that part was
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every really working
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***** RweaveOrg
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** Evaluate R code on export
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At first I was leaning towards leaving the exporting to Sweave, but it
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seems that once we have evaluation or R working, it will not be
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difficult to implement full evaluation of R blocks, one-liners, and
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creation of R graphics on export directly in elisp.
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I think that this would be worth the effort since it would eliminate
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the need for using Sweave, and would allow for exportation to any
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target format supported by org-mode.
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* Notes
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** Special editing and evaluation of source code in R blocks
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Unfortunately org-mode how two different block types, both useful.
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@ -64,6 +102,58 @@
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Note that upper and lower case are not relevant in block headings.
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*** PROPOSED R-block proposal
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I (Eric) propose that we use the syntax of source code blocks as they
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currently exist in org-mode with the addition of *evaluation*,
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*header-arguments*, *exportation*, *single-line-blocks*, and
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*references-to-table-data*.
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1) *evaluation*: These blocks can be evaluated through =\C-c\C-c= with
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a slight addition to the code already present and working in
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[[file:existing_tools/org-eval-light.el][org-eval-light.el]]. All we should need to add for R support would
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be an appropriate entry in [[org-eval-light-interpreters]] with a
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corresponding evaluation function. For an example usinga
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org-eval-light see [[* src block evaluation w/org-eval-light]].
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2) *header-arguments*: These can be implemented along the lines of
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Austin's header arguments in [[file:existing_tools/RweaveOrg/org-sweave.el][org-sweave.el]].
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3) *exportation*: Should be as similar as possible to that done by
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Sweave, and hopefully can re-use some of the code currently present
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in [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]].
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4) *single-line-blocks*: It seems that it is useful to be able to
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place a single line of R code on a line by itself. Should we add
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syntax for this similar to Dan's =#+R:= lines? I would lean
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towards something here that can be re-used for any type of source
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code in the same manner as the =#+begin_src R= blocks, maybe
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=#+src_R=?
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5) *references-to-table-data*: I get this impression that this is
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vital to the efficient use of R code in an org file, so we should
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come up with a way to reference table data from a single-line-block
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or from an R source-code block. It looks like Dan has already done
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this in [[file:existing_tools/org-R.el][org-R.el]].
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What do you think? Does this accomplish everything we want to be able
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to do with embedded R source code blocks?
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**** src block evaluation w/org-eval-light
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here's an example using org-eval-light.el
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first load the org-eval-light.el file
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[[elisp:(load (expand-file-name "org-eval-light.el" (expand-file-name "existing_tools" (file-name-directory buffer-file-name))))]]
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then press =\C-c\C-c= inside of the following src code snippet. The
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results should appear in a comment immediately following the source
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code block. It shouldn't be too hard to add R support to this
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function through the `org-eval-light-interpreters' variable.
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#+begin_src shell
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date
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#+end_src
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*** Source code blocks
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Org has an extremely useful method of editing source code and
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examples in their native modes. In the case of R code, we want to
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@ -104,8 +194,23 @@ a
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have the advantage of accepting options to the Sweave preprocessor
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following the #+BEGIN_R declaration.
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** Interaction with the R process
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We should take care to implement this in such a way that all of the
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different components which have to interactive with R including:
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- evaluation of source code blocks
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- automatic evaluation on export
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- evaluation of \R{} snippets
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- evaluation of single source code lines
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- sending/recieving vector data
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I think we currently have two implementation of interaction with R
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processes; [[file:existing_tools/org-R.el][org-R.el]] and [[file:existing_tools/exp-blocks/org-exp-blocks.el ][org-exp-blocks.el]]. We should be sure to take
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the best of each of these approaches.
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* Tasks
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* tasks
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* buffer dictionary
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LocalWords: DBlocks dblocks
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