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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, 0 insertions, 303 deletions
diff --git a/.emacs.d/org-7.4/lisp/ob-R.el b/.emacs.d/org-7.4/lisp/ob-R.el deleted file mode 100644 index 1f4fd87..0000000 --- a/.emacs.d/org-7.4/lisp/ob-R.el +++ /dev/null @@ -1,303 +0,0 @@ -;;; 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 |