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author | Luke Shumaker <LukeShu@sbcglobal.net> | 2011-04-13 23:20:15 -0400 |
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committer | Luke Shumaker <LukeShu@sbcglobal.net> | 2011-04-13 23:20:15 -0400 |
commit | f7464fdd2e33e5dc6c159a4adc8f53902e6d4511 (patch) | |
tree | b1d65db982af54cc2088de3228174c4ea710c2f4 /.emacs.d/org-7.4/lisp/ob-R.el |
Initial commit of Luke Shumaker's "dot-files".
Diffstat (limited to '.emacs.d/org-7.4/lisp/ob-R.el')
-rw-r--r-- | .emacs.d/org-7.4/lisp/ob-R.el | 303 |
1 files changed, 303 insertions, 0 deletions
diff --git a/.emacs.d/org-7.4/lisp/ob-R.el b/.emacs.d/org-7.4/lisp/ob-R.el new file mode 100644 index 0000000..1f4fd87 --- /dev/null +++ b/.emacs.d/org-7.4/lisp/ob-R.el @@ -0,0 +1,303 @@ +;;; 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 |