;;; ob-R.el --- org-babel functions for R code evaluation ;; Copyright (C) 2009-2014 Free Software Foundation, Inc. ;; Author: Eric Schulte ;; Dan Davison ;; Keywords: literate programming, reproducible research, R, statistics ;; Homepage: http://orgmode.org ;; 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 . ;;; Commentary: ;; Org-Babel support for evaluating R code ;;; Code: (require 'ob) (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)) (declare-function org-remove-if-not "org" (predicate seq)) (declare-function org-every "org" (pred 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.") (defconst ob-R-safe-header-args (append org-babel-safe-header-args '(:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal)) "Header args which are safe for R babel blocks. See `org-babel-safe-header-args' for documentation of the format of this variable.") (defvar org-babel-default-header-args:R '()) (put 'org-babel-default-header-args:R 'safe-local-variable (org-babel-header-args-safe-fn ob-R-safe-header-args)) (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) ; 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))))) (defconst ob-R-transfer-variable-table-with-header "%s <- local({ con <- textConnection( %S ) res <- read.table( con, header = %s, row.names = %s, sep = \"\\t\", as.is = TRUE ) close(con) res })" "R code used to transfer a table defined as a variable from org to R. This function is used when the table contains a header.") (defconst ob-R-transfer-variable-table-without-header "%s <- local({ con <- textConnection( %S ) res <- read.table( con, header = %s, row.names = %s, sep = \"\\t\", as.is = TRUE, fill = TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ) close(con) res })" "R code used to transfer a table defined as a variable from org to R. This function is used when the table does not contain a header.") (defun org-babel-expand-body:R (body params &optional graphics-file) "Expand BODY according to PARAMS, return the expanded body." (mapconcat 'identity (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))))) "\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-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))) (rownames-p (cdr (assoc :rownames params))) (graphics-file (and (member "graphics" (assq :result-params params)) (org-babel-graphical-output-file params))) (full-body (let ((inside (list (org-babel-expand-body:R body params graphics-file)))) (mapconcat 'identity (if graphics-file (append (list (org-babel-R-construct-graphics-device-call graphics-file params)) inside (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()")) inside) "\n"))) (result (org-babel-R-evaluate session full-body result-type result-params (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))))) (if graphics-file nil 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* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value))) (max (if lengths (apply 'max lengths) 0)) (min (if lengths (apply 'min lengths) 0))) ;; Ensure VALUE has an orgtbl structure (depth of at least 2). (unless (listp (car value)) (setq value (list value))) (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) (header (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")) (row-names (if rownames-p "1" "NULL"))) (if (= max min) (format ob-R-transfer-variable-table-with-header name file header row-names) (format ob-R-transfer-variable-table-without-header name file header row-names max)))) (cond ((integerp value) (format "%s <- %s" name (concat (number-to-string value) "L"))) ((floatp value) (format "%s <- %s" name value)) ((stringp value) (format "%s <- %S" name (org-no-properties value))) (t (format "%s <- %S" name (prin1-to-string value)))))) (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 (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 session) (if (stringp session) session (buffer-name)))) (current-buffer)))))) (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)) (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* ((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" (substring (symbol-name (car pair)) 1) (cdr pair)) "")) params "")) (format "%s(%s=\"%s\"%s%s%s); tryCatch({" 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){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 result-params column-names-p row-names-p) "Evaluate R code in BODY." (if session (org-babel-R-evaluate-session session body result-type result-params column-names-p row-names-p) (org-babel-R-evaluate-external-process body result-type result-params column-names-p row-names-p))) (defun org-babel-R-evaluate-external-process (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 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-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) (defvar ess-execute-in-process-buffer) (defun org-babel-R-evaluate-session (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 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-visibly-p nil)) (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-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 (let* ((sentinel-file (org-babel-temp-file "R-"))) ;; This code borrowed from ;; `org-babel-comint-eval-invisibly-and-wait-for-file' (unless (org-babel-comint-buffer-livep session) (error "Buffer %s does not exist or has no process" session)) (if (file-exists-p sentinel-file) (delete-file sentinel-file)) (with-current-buffer session (let ((ess-execute-in-process-buffer nil)) (ess-execute (format " .org.old.opts <- options(prompt = \"# Org babel prompt\\n\", continue = \"# Org babel prompt\\n\") cat(\"# Org babel begin output\n\") %s cat(\"# Org babel end output\n\") options(.org.old.opts) rm(.org.old.opts) file.create(%S) " (org-babel-chomp body) (if (tramp-tramp-file-p sentinel-file) (tramp-file-name-localname (tramp-dissect-file-name sentinel-file)) sentinel-file)) nil "org-babel-R-output")) ;; From Tramp 2.1.19 the following cache flush is not necessary (if (file-remote-p default-directory) (let (v) (with-parsed-tramp-file-name default-directory nil (tramp-flush-directory-property v ""))))) (while (not (file-exists-p sentinel-file)) (sit-for 0.25)) ;; End borrowed code. (with-current-buffer "*org-babel-R-output*" (goto-char (point-min)) (search-forward "# Org babel begin output") (delete-region (point-min) (1+ (point))) (goto-char (point-max)) (search-backward "# Org babel end output") (delete-region (point) (point-max)) (goto-char (point-min)) (flush-lines "^$") (flush-lines "^# Org babel prompt$") (delete-trailing-whitespace) (buffer-string)))))) (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