;;; ob-R.el --- org-babel functions for R code evaluation
-;; Copyright (C) 2009, 2010 Free Software Foundation, Inc.
+;; Copyright (C) 2009-2016 Free Software Foundation, Inc.
-;; Author: Eric Schulte, Dan Davison
+;; Author: Eric Schulte
+;; Dan Davison
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: http://orgmode.org
-;; Version: 7.7
;; This file is part of GNU Emacs.
;;; 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 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)
+(declare-function org-remove-if-not "org" (predicate seq))
+
+(defconst org-babel-header-args:R
+ '((width . :any)
+ (height . :any)
+ (bg . :any)
+ (units . :any)
+ (pointsize . :any)
+ (antialias . :any)
+ (quality . :any)
+ (compression . :any)
+ (res . :any)
+ (type . :any)
+ (family . :any)
+ (title . :any)
+ (fonts . :any)
+ (version . :any)
+ (paper . :any)
+ (encoding . :any)
+ (pagecentre . :any)
+ (colormodel . :any)
+ (useDingbats . :any)
+ (horizontal . :any)
+ (results . ((file list vector table scalar verbatim)
+ (raw org html latex code pp wrap)
+ (replace silent append prepend)
+ (output value graphics))))
"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.")
+(defcustom org-babel-R-command "R --slave --no-save"
+ "Name of command to use for executing R code."
+ :group 'org-babel
+ :version "24.1"
+ :type 'string)
-(defvar ess-local-process-name)
+(defvar ess-local-process-name) ; dynamically scoped
(defun org-babel-edit-prep:R (info)
(let ((session (cdr (assoc :session (nth 2 info)))))
(when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
- (save-match-data (org-babel-R-initiate-session session nil))
- (setq ess-local-process-name (match-string 1 session)))))
+ (save-match-data (org-babel-R-initiate-session session nil)))))
(defun org-babel-expand-body:R (body params &optional graphics-file)
"Expand BODY according to PARAMS, return the expanded body."
(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.
This function is called by `org-babel-execute-src-block'."
(save-excursion
- (let* ((result-type (cdr (assoc :result-type params)))
+ (let* ((result-params (cdr (assoc :result-params params)))
+ (result-type (cdr (assoc :result-type params)))
(session (org-babel-R-initiate-session
(cdr (assoc :session params)) params))
(colnames-p (cdr (assoc :colnames params)))
(full-body (org-babel-expand-body:R body params graphics-file))
(result
(org-babel-R-evaluate
- session full-body result-type
+ session full-body result-type result-params
(or (equal "yes" colnames-p)
(org-babel-pick-name
(cdr (assoc :colname-names params)) colnames-p))
;; helper functions
(defun org-babel-variable-assignments:R (params)
- "Return list of R statements assigning the block's variables"
+ "Return list of R statements assigning the block's variables."
(let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
(mapcar
(lambda (pair)
(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)
+ (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 (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")))
+ (insert
+ (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
+ "\n"))
+ (let ((file (org-babel-process-file-name transition-file 'noquote))
+ (header (if (or (eq (nth 1 value) 'hline) colnames-p)
+ "TRUE" "FALSE"))
+ (row-names (if rownames-p "1" "NULL")))
+ (if (= max min)
+ (format "%s <- read.table(\"%s\",
+ header=%s,
+ row.names=%s,
+ sep=\"\\t\",
+ as.is=TRUE)" name file header row-names)
+ (format "%s <- read.table(\"%s\",
+ header=%s,
+ row.names=%s,
+ sep=\"\\t\",
+ as.is=TRUE,
+ fill=TRUE,
+ col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
+ name file header row-names max))))
(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
-(defvar ess-ask-for-ess-directory nil)
+(defvar ess-ask-for-ess-directory) ; dynamically scoped
(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))))))
+ (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
+ (not (cdr (assoc :dir params))))))
(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)
(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
(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")
- (: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"))
+ (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 ",%s=%s"
+ (format ",%s=%S"
(substring (symbol-name (car pair)) 1)
(cdr pair)) ""))
params ""))
(defvar org-babel-R-write-object-command "{function(object,transfer.file){object;invisible(if(inherits(try({tfile<-tempfile();write.table(object,file=tfile,sep=\"\\t\",na=\"nil\",row.names=%s,col.names=%s,quote=FALSE);file.rename(tfile,transfer.file)},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)
+ (session body result-type result-params 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)
+ session body result-type result-params column-names-p row-names-p)
(org-babel-R-evaluate-external-process
- body result-type column-names-p row-names-p)))
+ body result-type result-params column-names-p row-names-p)))
(defun org-babel-R-evaluate-external-process
- (body result-type column-names-p row-names-p)
+ (body result-type result-params 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
+string. If RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
(case result-type
(value
(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)))
+ (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 column-names-p row-names-p)
+ (session body result-type result-params 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
+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))))
+ (process-name (get-buffer-process session)))
+ (ess-eval-visibly-p nil))
(ess-eval-buffer nil)))
(let ((tmp-file (org-babel-temp-file "R-")))
(org-babel-comint-eval-invisibly-and-wait-for-file
"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)))
+ (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
(mapconcat
#'org-babel-chomp
(mapcar
(lambda (line) ;; cleanup extra prompts left in output
(if (string-match
- "^\\([ ]*[>+][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
+ "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
(substring line (match-end 1))
line))
(org-babel-comint-with-output (session org-babel-R-eoe-output)