157 lines
7.3 KiB
EmacsLisp
157 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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(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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(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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(result-params (split-string (or (cdr (assoc :results params)) "")))
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(result-type (cond ((member "output" result-params) 'output)
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((member "value" result-params) 'value)
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(t 'value)))
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(session (org-babel-R-initiate-session (cdr (assoc :session params))))
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results)
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;; ;;; debugging statements
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;; (message (format "result-type=%S" result-type))
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;; (message (format "body=%S" body))
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;; (message (format "session=%S" session))
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;; (message (format "result-params=%S" result-params))
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;; evaluate body and convert the results to ruby
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(setq results (org-babel-R-evaluate session full-body result-type))
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(setq results (if (member "scalar" result-params)
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results
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(let ((tmp-file (make-temp-file "org-babel-R")))
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(with-temp-file tmp-file (insert results))
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(org-babel-import-elisp-from-file tmp-file))))
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(if (and (member "vector" result-params) (not (listp results)))
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(list (list results))
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results))))
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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 (R) (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."
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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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;; (message "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)
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(shell-command-to-string (format "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)))
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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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;; (message "R --no-save < '%s'" in-tmp-file)
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(shell-command (format "R --no-save < '%s'" in-tmp-file))))
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(with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
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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 (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 (let ((broke nil))
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(delete nil (mapcar (lambda (el)
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(if (or broke
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(and (string-match (regexp-quote org-babel-R-eoe-output) 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-trim (with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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(t (reverse results)))))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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