;;; ob-R.el --- org-babel functions for R code evaluation
-;; Copyright (C) 2009-2012 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
;; Author: Eric Schulte
;; Dan Davison
;;; 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))
(or graphics-file (org-babel-R-graphical-output-file params))))
(mapconcat
#'identity
- ((lambda (inside)
- (if graphics-file
- (append
- (list (org-babel-R-construct-graphics-device-call
- graphics-file params))
- inside
- (list "dev.off()"))
- inside))
- (append (org-babel-variable-assignments:R params)
- (list body))) "\n")))
+ (let ((inside
+ (append
+ (when (cdr (assoc :prologue params))
+ (list (cdr (assoc :prologue params))))
+ (org-babel-variable-assignments:R params)
+ (list body)
+ (when (cdr (assoc :epilogue params))
+ (list (cdr (assoc :epilogue params)))))))
+ (if graphics-file
+ (append
+ (list (org-babel-R-construct-graphics-device-call
+ graphics-file params))
+ inside
+ (list "dev.off()"))
+ inside))
+ "\n")))
(defun org-babel-execute:R (body params)
"Execute a block of R code.
(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 ((max (apply #'max (mapcar #'length (org-remove-if-not
- #'sequencep value))))
- (min (apply #'min (mapcar #'length (org-remove-if-not
- #'sequencep value))))
- (transition-file (org-babel-temp-file "R-import-")))
- ;; ensure VALUE has an orgtbl structure (depth of at least 2)
+ (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
+ (max (if lengths (apply 'max lengths) 0))
+ (min (if lengths (apply 'min lengths) 0))
+ (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
(if (org-babel-comint-buffer-livep session)
session
(save-window-excursion
+ (when (get-buffer session)
+ ;; Session buffer exists, but with dead process
+ (set-buffer session))
(require 'ess) (R)
(rename-buffer
(if (bufferp session)
(and (member "graphics" (cdr (assq :result-params params)))
(cdr (assq :file params))))
+(defvar org-babel-R-graphics-devices
+ '((:bmp "bmp" "filename")
+ (:jpg "jpeg" "filename")
+ (:jpeg "jpeg" "filename")
+ (:tikz "tikz" "file")
+ (:tiff "tiff" "filename")
+ (:png "png" "filename")
+ (:svg "svg" "file")
+ (:pdf "pdf" "file")
+ (:ps "postscript" "file")
+ (:postscript "postscript" "file"))
+ "An alist mapping graphics file types to R functions.
+
+Each member of this list is a list with three members:
+1. the file extension of the graphics file, as an elisp :keyword
+2. the R graphics device function to call to generate such a file
+3. the name of the argument to this function which specifies the
+ file to write to (typically \"file\" or \"filename\")")
+
(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")
- (:tex . "tikz")
- (: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" "tikz")) "file" "filename"))
+ (let* ((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)))
+ (device-info (or (assq (intern (concat ":" device))
+ org-babel-R-graphics-devices)
+ (assq :png org-babel-R-graphics-devices)))
+ (extra-args (cdr (assq :R-dev-args params))) filearg args)
+ (setq device (nth 1 device-info))
+ (setq filearg (nth 2 device-info))
(setq args (mapconcat
(lambda (pair)
(if (member (car pair) allowed-args)
(format "{function ()\n{\n%s\n}}()" body)
(org-babel-process-file-name tmp-file 'noquote)))
(org-babel-R-process-value-result
- (if (or (member "scalar" result-params)
- (member "verbatim" result-params))
- (with-temp-buffer
- (insert-file-contents tmp-file)
- (buffer-string))
+ (org-babel-result-cond result-params
+ (with-temp-buffer
+ (insert-file-contents tmp-file)
+ (buffer-string))
(org-babel-import-elisp-from-file tmp-file '(16)))
column-names-p)))
(output (org-babel-eval org-babel-R-command body))))
+(defvar ess-eval-visibly-p)
+
(defun org-babel-R-evaluate-session
(session body result-type result-params column-names-p row-names-p)
"Evaluate BODY in SESSION.
"FALSE")
".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
(org-babel-R-process-value-result
- (if (or (member "scalar" result-params)
- (member "verbatim" result-params))
- (with-temp-buffer
- (insert-file-contents tmp-file)
- (buffer-string))
+ (org-babel-result-cond result-params
+ (with-temp-buffer
+ (insert-file-contents tmp-file)
+ (buffer-string))
(org-babel-import-elisp-from-file tmp-file '(16)))
column-names-p)))
(output