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|
;;; ob-R.el --- org-babel functions for R code evaluation
;; Copyright (C) 2009-2011 Free Software Foundation, Inc.
;; Author: Eric Schulte, Dan Davison
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: http://orgmode.org
;; Version: 7.4
;; This file is part of GNU Emacs.
;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.
;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;; GNU General Public License for more details.
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
;;; Commentary:
;; Org-Babel support for evaluating R code
;;; Code:
(require 'ob)
(require 'ob-ref)
(require 'ob-comint)
(require 'ob-eval)
(eval-when-compile (require 'cl))
(declare-function orgtbl-to-tsv "org-table" (table params))
(declare-function R "ext:essd-r" (&optional start-args))
(declare-function inferior-ess-send-input "ext:ess-inf" ())
(declare-function ess-make-buffer-current "ext:ess-inf" ())
(declare-function ess-eval-buffer "ext:ess-inf" (vis))
(declare-function org-number-sequence "org-compat" (from &optional to inc))
(defconst org-babel-header-arg-names:R
'(width height bg units pointsize antialias quality compression
res type family title fonts version paper encoding
pagecentre colormodel useDingbats horizontal)
"R-specific header arguments.")
(defvar org-babel-default-header-args:R '())
(defvar org-babel-R-command "R --slave --no-save"
"Name of command to use for executing R code.")
(defun org-babel-expand-body:R (body params)
"Expand BODY according to PARAMS, return the expanded body."
(let ((out-file (cdr (assoc :file params))))
(mapconcat
#'identity
((lambda (inside)
(if out-file
(append
(list (org-babel-R-construct-graphics-device-call out-file params))
inside
(list "dev.off()"))
inside))
(append (org-babel-variable-assignments:R params)
(list body))) "\n")))
(defun org-babel-execute:R (body params)
"Execute a block of R code.
This function is called by `org-babel-execute-src-block'."
(save-excursion
(let* ((result-type (cdr (assoc :result-type params)))
(session (org-babel-R-initiate-session
(cdr (assoc :session params)) params))
(colnames-p (cdr (assoc :colnames params)))
(rownames-p (cdr (assoc :rownames params)))
(out-file (cdr (assoc :file params)))
(full-body (org-babel-expand-body:R body params))
(result
(org-babel-R-evaluate
session full-body result-type
(or (equal "yes" colnames-p)
(org-babel-pick-name
(cdr (assoc :colname-names params)) colnames-p))
(or (equal "yes" rownames-p)
(org-babel-pick-name
(cdr (assoc :rowname-names params)) rownames-p)))))
(message "result is %S" result)
(or out-file result))))
(defun org-babel-prep-session:R (session params)
"Prepare SESSION according to the header arguments specified in PARAMS."
(let* ((session (org-babel-R-initiate-session session params))
(var-lines (org-babel-variable-assignments:R params)))
(org-babel-comint-in-buffer session
(mapc (lambda (var)
(end-of-line 1) (insert var) (comint-send-input nil t)
(org-babel-comint-wait-for-output session)) var-lines))
session))
(defun org-babel-load-session:R (session body params)
"Load BODY into SESSION."
(save-window-excursion
(let ((buffer (org-babel-prep-session:R session params)))
(with-current-buffer buffer
(goto-char (process-mark (get-buffer-process (current-buffer))))
(insert (org-babel-chomp body)))
buffer)))
;; helper functions
(defun org-babel-variable-assignments:R (params)
"Return list of R statements assigning the block's variables"
(let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
(mapcar
(lambda (pair)
(org-babel-R-assign-elisp
(car pair) (cdr pair)
(equal "yes" (cdr (assoc :colnames params)))
(equal "yes" (cdr (assoc :rownames params)))))
(mapcar
(lambda (i)
(cons (car (nth i vars))
(org-babel-reassemble-table
(cdr (nth i vars))
(cdr (nth i (cdr (assoc :colname-names params))))
(cdr (nth i (cdr (assoc :rowname-names params)))))))
(org-number-sequence 0 (1- (length vars)))))))
(defun org-babel-R-quote-tsv-field (s)
"Quote field S for export to R."
(if (stringp s)
(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
(format "%S" s)))
(defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
"Construct R code assigning the elisp VALUE to a variable named NAME."
(if (listp value)
(let ((transition-file (org-babel-temp-file "R-import-")))
;; ensure VALUE has an orgtbl structure (depth of at least 2)
(unless (listp (car value)) (setq value (list value)))
(with-temp-file transition-file
(insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
(insert "\n"))
(format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
name (org-babel-process-file-name transition-file 'noquote)
(if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
(if rownames-p "1" "NULL")))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
(defvar ess-ask-for-ess-directory nil)
(defun org-babel-R-initiate-session (session params)
"If there is not a current R process then create one."
(unless (string= session "none")
(let ((session (or session "*R*"))
(ess-ask-for-ess-directory
(and ess-ask-for-ess-directory (not (cdr (assoc :dir params))))))
(if (org-babel-comint-buffer-livep session)
session
(save-window-excursion
(require 'ess) (R)
(rename-buffer
(if (bufferp session)
(buffer-name session)
(if (stringp session)
session
(buffer-name))))
(current-buffer))))))
(defvar ess-local-process-name nil)
(defun org-babel-R-associate-session (session)
"Associate R code buffer with an R session.
Make SESSION be the inferior ESS process associated with the
current code buffer."
(setq ess-local-process-name
(process-name (get-buffer-process session)))
(ess-make-buffer-current))
(defun org-babel-R-construct-graphics-device-call (out-file params)
"Construct the call to the graphics device."
(let ((devices
'((:bmp . "bmp")
(:jpg . "jpeg")
(:jpeg . "jpeg")
(:tiff . "tiff")
(:png . "png")
(:svg . "svg")
(:pdf . "pdf")
(:ps . "postscript")
(:postscript . "postscript")))
(allowed-args '(:width :height :bg :units :pointsize
:antialias :quality :compression :res
:type :family :title :fonts :version
:paper :encoding :pagecentre :colormodel
:useDingbats :horizontal))
(device (and (string-match ".+\\.\\([^.]+\\)" out-file)
(match-string 1 out-file)))
(extra-args (cdr (assq :R-dev-args params))) filearg args)
(setq device (or (and device (cdr (assq (intern (concat ":" device))
devices))) "png"))
(setq filearg
(if (member device '("pdf" "postscript" "svg")) "file" "filename"))
(setq args (mapconcat
(lambda (pair)
(if (member (car pair) allowed-args)
(format ",%s=%s"
(substring (symbol-name (car pair)) 1)
(cdr pair)) ""))
params ""))
(format "%s(%s=\"%s\"%s%s%s)"
device filearg out-file args
(if extra-args "," "") (or extra-args ""))))
(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
(defvar org-babel-R-write-object-command "{function(object, transfer.file) {invisible(if(inherits(try(write.table(object, file=transfer.file, sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE), silent=TRUE),\"try-error\")) {if(!file.exists(transfer.file)) file.create(transfer.file)})}}(object=%s, transfer.file=\"%s\")")
(defun org-babel-R-evaluate
(session body result-type column-names-p row-names-p)
"Evaluate R code in BODY."
(if session
(org-babel-R-evaluate-session
session body result-type column-names-p row-names-p)
(org-babel-R-evaluate-external-process
body result-type column-names-p row-names-p)))
(defun org-babel-R-evaluate-external-process
(body result-type column-names-p row-names-p)
"Evaluate BODY in external R process.
If RESULT-TYPE equals 'output then return standard output as a
string. If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
(case result-type
(value
(let ((tmp-file (org-babel-temp-file "R-")))
(org-babel-eval org-babel-R-command
(format org-babel-R-write-object-command
(if row-names-p "TRUE" "FALSE")
(if column-names-p
(if row-names-p "NA" "TRUE")
"FALSE")
(format "{function ()\n{\n%s\n}}()" body)
(org-babel-process-file-name tmp-file 'noquote)))
(org-babel-R-process-value-result
(org-babel-import-elisp-from-file tmp-file '(16)) column-names-p)))
(output (org-babel-eval org-babel-R-command body))))
(defun org-babel-R-evaluate-session
(session body result-type column-names-p row-names-p)
"Evaluate BODY in SESSION.
If RESULT-TYPE equals 'output then return standard output as a
string. If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
(case result-type
(value
(with-temp-buffer
(insert (org-babel-chomp body))
(let ((ess-local-process-name
(process-name (get-buffer-process session))))
(ess-eval-buffer nil)))
(let ((tmp-file (org-babel-temp-file "R-")))
(org-babel-comint-eval-invisibly-and-wait-for-file
session tmp-file
(format org-babel-R-write-object-command
(if row-names-p "TRUE" "FALSE")
(if column-names-p
(if row-names-p "NA" "TRUE")
"FALSE")
".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
(org-babel-R-process-value-result
(org-babel-import-elisp-from-file tmp-file '(16)) column-names-p)))
(output
(mapconcat
#'org-babel-chomp
(butlast
(delq nil
(mapcar
(lambda (line) (when (> (length line) 0) line))
(mapcar
(lambda (line) ;; cleanup extra prompts left in output
(if (string-match
"^\\([ ]*[>+][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
(substring line (match-end 1))
line))
(org-babel-comint-with-output (session org-babel-R-eoe-output)
(insert (mapconcat #'org-babel-chomp
(list body org-babel-R-eoe-indicator)
"\n"))
(inferior-ess-send-input)))))) "\n"))))
(defun org-babel-R-process-value-result (result column-names-p)
"R-specific processing of return value.
Insert hline if column names in output have been requested."
(if column-names-p
(cons (car result) (cons 'hline (cdr result)))
result))
(provide 'ob-R)
;;; ob-R.el ends here
|
