;;; ob-R.el --- org-babel functions for R code evaluation
-;; Copyright (C) 2009, 2010 Free Software Foundation, Inc.
+;; 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: 7.01
+;; Version: 7.4
;; This file is part of GNU Emacs.
(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
(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 &optional processed-params)
+(defun org-babel-expand-body:R (body params)
"Expand BODY according to PARAMS, return the expanded body."
- (let* ((processed-params (or processed-params
- (org-babel-process-params params)))
- (vars (mapcar
- (lambda (i)
- (cons (car (nth i (nth 1 processed-params)))
- (org-babel-reassemble-table
- (cdr (nth i (nth 1 processed-params)))
- (cdr (nth i (nth 4 processed-params)))
- (cdr (nth i (nth 5 processed-params))))))
- (number-sequence 0 (1- (length (nth 1 processed-params))))))
- (out-file (cdr (assoc :file params))))
- (mapconcat ;; define any variables
- #'org-babel-trim
+ (let ((out-file (cdr (assoc :file params))))
+ (mapconcat
+ #'identity
((lambda (inside)
(if out-file
(append
inside
(list "dev.off()"))
inside))
- (append
- (mapcar
- (lambda (pair)
- (org-babel-R-assign-elisp
- (car pair) (cdr pair)
- (equal "yes" (cdr (assoc :colnames params)))
- (equal "yes" (cdr (assoc :rownames params)))))
- vars)
- (list body))) "\n")))
+ (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* ((processed-params (org-babel-process-params params))
- (result-type (nth 3 processed-params))
+ (let* ((result-type (cdr (assoc :result-type params)))
(session (org-babel-R-initiate-session
- (first processed-params) params))
+ (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 processed-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 (nth 4 processed-params) colnames-p))
+ (org-babel-pick-name
+ (cdr (assoc :colname-names params)) colnames-p))
(or (equal "yes" rownames-p)
- (org-babel-pick-name (nth 5 processed-params) 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))
- (vars (org-babel-ref-variables params))
- (var-lines
- (mapcar
- (lambda (pair) (org-babel-R-assign-elisp
- (car pair) (cdr pair)
- (equal (cdr (assoc :colnames params)) "yes")
- (equal (cdr (assoc :rownames params)) "yes")))
- vars)))
+ (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)
;; 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)
(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 (make-temp-file "org-babel-R-import")))
+ (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 (org-babel-maybe-remote-file transition-file)
+ (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 transition-file
+ 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 (not (cdr (assoc :dir params)))))
+ (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
(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
(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-wrapper-method "main <- function ()\n{\n%s\n}
-write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
-(defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
+(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)
- "Pass BODY to the R process in SESSION.
-If RESULT-TYPE equals 'output then return a list of the outputs
-of the statements in BODY, if RESULT-TYPE equals 'value then
-return the value of the last statement in BODY, as elisp."
- (if (not session)
- ;; external process evaluation
- (case result-type
- (output (org-babel-eval org-babel-R-command body))
- (value
- (let ((tmp-file (make-temp-file "org-babel-R-results-")))
- (org-babel-eval org-babel-R-command
- (format org-babel-R-wrapper-method
- body tmp-file
- (if row-names-p "TRUE" "FALSE")
- (if column-names-p
- (if row-names-p "NA" "TRUE")
- "FALSE")))
- (org-babel-R-process-value-result
- (org-babel-import-elisp-from-file
- (org-babel-maybe-remote-file tmp-file)) column-names-p))))
- ;; comint session evaluation
- (case result-type
- (value
- (let ((tmp-file (make-temp-file "org-babel-R"))
- broke)
- (org-babel-comint-with-output (session org-babel-R-eoe-output)
- (insert (mapconcat
- #'org-babel-chomp
- (list
- body
- (format org-babel-R-wrapper-lastvar
- tmp-file
- (if row-names-p "TRUE" "FALSE")
- (if column-names-p
- (if row-names-p "NA" "TRUE")
- "FALSE"))
- org-babel-R-eoe-indicator) "\n"))
- (inferior-ess-send-input))
- (org-babel-R-process-value-result
- (org-babel-import-elisp-from-file
- (org-babel-maybe-remote-file tmp-file)) column-names-p)))
- (output
- (mapconcat
- #'org-babel-chomp
- (butlast
- (delq nil
- (mapcar
- #'identity
- (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)))) 2) "\n")))))
+ "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.
(provide 'ob-R)
-;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237
;;; ob-R.el ends here