forked from mirrors/org-mode
adding support for R source code blocks
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01401748e4
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fc21c4b559
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@ -35,7 +35,7 @@
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;; language specific files
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(require 'litorgy-script)
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(require 'litorgy-R)
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(require 'litorgy-lisp)
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(require 'litorgy-R)
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;;; init.el ends here
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@ -1,9 +1,9 @@
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;;; litorgy-R.el --- litorgy functions for R code evaluation
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;; Copyright (C) 2009 Eric Schulte, Dan Davison, Austin F. Frank
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;; Copyright (C) 2009 Eric Schulte
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;; Author: Eric Schulte, Dan Davison, Austin F. Frank
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;; Keywords: literate programming, reproducible research
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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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@ -31,16 +31,87 @@
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;;; Code:
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(require 'litorgy)
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(litorgy-add-interpreter "emacs-R")
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(litorgy-add-interpreter "R")
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(defun litorgy-execute:emacs-R (body params)
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"Execute a block of emacs-R code with litorgy. This
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function is called by `litorgy-execute-src-block'."
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(defun litorgy-execute:R (body params)
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"Execute a block of R code with litorgy. This function is
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called by `litorgy-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 (litorgy-reference-variables params))
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results)
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;;TODO: implement
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(error "`litorgy-execute:emacs-R' is not implemented"))))
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(litorgy-R-initiate-R-buffer)
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(litorgy-R-command-to-string body))))
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;; functions for evaluation of R code
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(defvar litorgy-R-buffer nil
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"Holds the buffer for the current R process")
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(defun litorgy-R-initiate-R-buffer ()
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"If there is not a current R process then create one."
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(unless (and (buffer-live-p litorgy-R-buffer) (get-buffer litorgy-R-buffer))
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(save-excursion
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(R)
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(setf litorgy-R-buffer (current-buffer))
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(litorgy-R-wait-for-output)
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(litorgy-R-input-command ""))))
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(defun litorgy-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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(litorgy-R-input-command command)
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(litorgy-R-last-output))
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(defun litorgy-R-input-command (command)
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"Pass COMMAND to the R process running in `litorgy-R-buffer'."
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(save-excursion
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(save-match-data
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(set-buffer litorgy-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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(litorgy-R-wait-for-output))))
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(defun litorgy-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 litorgy-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 litorgy-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 litorgy-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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(defun litorgy-R-table-or-results (results)
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"If the results look like a matrix, then convert them into an
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Emacs-lisp table otherwise return the results as a string."
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;; TODO: these simple assumptions will probably need some tweaking
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(when (string-match "[ \f\t\n\r\v]+" results)
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(concat "(" (mapconcat #'litorgy-R-tale-or-results
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(split-string results) " ") ")"))
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results)
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(provide 'litorgy-R)
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;;; litorgy-R.el ends here
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22
rorg.org
22
rorg.org
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@ -746,6 +746,8 @@ out...
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finally it should insert the transposed table into the buffer
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immediately following the block
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*** Emacs lisp
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#+begin_src emacs-lisp
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(defun transpose (table)
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(apply #'mapcar* #'list table))
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@ -763,6 +765,8 @@ out...
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(transpose table)
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#+end_src
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*** Ruby and Python
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#+begin_src ruby :var table=sandbox :replace t
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table.first.join(" - ")
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#+end_src
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@ -789,6 +793,24 @@ table
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| 1 | 2 | 3 |
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| 4 | "schulte" | 6 |
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*** R
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#+begin_src R :replace t
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a <- 9
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b <- 8
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#+end_src
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#+begin_src R :replace t
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x <- c(rnorm(10, mean=-3, sd=1), rnorm(10, mean=3, sd=1))
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x
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#+end_src
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: -2.059712 -1.299807 -2.518628 -4.319525 -1.944779 -5.345708 -3.921314
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: -2.841109 -0.963475 -2.465979 4.092037 1.299202 1.476687 2.128594
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: 3.200629 1.990952 1.888890 3.561541 3.818319 1.969161
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* COMMENT Commentary
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I'm seeing this as like commit notes, and a place for less formal
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