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-;;; ob-R.el --- org-babel functions for R code evaluation
-
-;; Copyright (C) 2009, 2010 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)
-
-;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237
-
-;;; ob-R.el ends here