Mercurial > emacs
annotate lisp/org/ob-R.el @ 110682:ba6a1c230532
gnus-html.el (gnus-html-prefetch-images): Adjust regexp to avoid regexp backtrace overflows.
author | Katsumi Yamaoka <yamaoka@jpl.org> |
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date | Fri, 01 Oct 2010 13:33:03 +0000 |
parents | 063e94b66261 |
children | 5cb272c831e8 |
rev | line source |
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109462
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1 ;;; ob-R.el --- org-babel functions for R code evaluation |
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2 |
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3 ;; Copyright (C) 2009, 2010 Free Software Foundation, Inc. |
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4 |
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5 ;; Author: Eric Schulte, Dan Davison |
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6 ;; Keywords: literate programming, reproducible research, R, statistics |
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7 ;; Homepage: http://orgmode.org |
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8 ;; Version: 7.01 |
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9 |
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10 ;; This file is part of GNU Emacs. |
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11 |
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12 ;; GNU Emacs is free software: you can redistribute it and/or modify |
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13 ;; it under the terms of the GNU General Public License as published by |
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14 ;; the Free Software Foundation, either version 3 of the License, or |
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15 ;; (at your option) any later version. |
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16 |
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17 ;; GNU Emacs is distributed in the hope that it will be useful, |
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18 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of |
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19 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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20 ;; GNU General Public License for more details. |
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21 |
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22 ;; You should have received a copy of the GNU General Public License |
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23 ;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>. |
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24 |
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25 ;;; Commentary: |
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26 |
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27 ;; Org-Babel support for evaluating R code |
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28 |
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29 ;;; Code: |
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30 (require 'ob) |
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31 (require 'ob-ref) |
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32 (require 'ob-comint) |
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33 (require 'ob-eval) |
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34 (eval-when-compile (require 'cl)) |
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35 |
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36 (declare-function orgtbl-to-tsv "org-table" (table params)) |
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37 (declare-function R "ext:essd-r" (&optional start-args)) |
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38 (declare-function inferior-ess-send-input "ext:ess-inf" ()) |
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39 |
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40 (defconst org-babel-header-arg-names:R |
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41 '(width height bg units pointsize antialias quality compression |
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42 res type family title fonts version paper encoding |
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43 pagecentre colormodel useDingbats horizontal) |
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44 "R-specific header arguments.") |
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45 |
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46 (defvar org-babel-default-header-args:R '()) |
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47 |
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48 (defvar org-babel-R-command "R --slave --no-save" |
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49 "Name of command to use for executing R code.") |
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50 |
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51 (defun org-babel-expand-body:R (body params &optional processed-params) |
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52 "Expand BODY according to PARAMS, return the expanded body." |
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53 (let* ((processed-params (or processed-params |
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54 (org-babel-process-params params))) |
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55 (vars (mapcar |
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56 (lambda (i) |
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57 (cons (car (nth i (nth 1 processed-params))) |
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58 (org-babel-reassemble-table |
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59 (cdr (nth i (nth 1 processed-params))) |
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60 (cdr (nth i (nth 4 processed-params))) |
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61 (cdr (nth i (nth 5 processed-params)))))) |
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62 (number-sequence 0 (1- (length (nth 1 processed-params)))))) |
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63 (out-file (cdr (assoc :file params)))) |
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64 (mapconcat ;; define any variables |
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65 #'org-babel-trim |
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66 ((lambda (inside) |
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67 (if out-file |
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68 (append |
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69 (list (org-babel-R-construct-graphics-device-call out-file params)) |
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70 inside |
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71 (list "dev.off()")) |
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72 inside)) |
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73 (append |
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74 (mapcar |
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75 (lambda (pair) |
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76 (org-babel-R-assign-elisp |
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77 (car pair) (cdr pair) |
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78 (equal "yes" (cdr (assoc :colnames params))) |
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79 (equal "yes" (cdr (assoc :rownames params))))) |
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80 vars) |
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81 (list body))) "\n"))) |
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82 |
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83 (defun org-babel-execute:R (body params) |
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84 "Execute a block of R code. |
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85 This function is called by `org-babel-execute-src-block'." |
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86 (save-excursion |
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87 (let* ((processed-params (org-babel-process-params params)) |
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88 (result-type (nth 3 processed-params)) |
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89 (session (org-babel-R-initiate-session |
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90 (first processed-params) params)) |
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91 (colnames-p (cdr (assoc :colnames params))) |
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92 (rownames-p (cdr (assoc :rownames params))) |
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93 (out-file (cdr (assoc :file params))) |
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94 (full-body (org-babel-expand-body:R body params processed-params)) |
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95 (result |
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96 (org-babel-R-evaluate |
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97 session full-body result-type |
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98 (or (equal "yes" colnames-p) |
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99 (org-babel-pick-name (nth 4 processed-params) colnames-p)) |
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100 (or (equal "yes" rownames-p) |
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101 (org-babel-pick-name (nth 5 processed-params) rownames-p))))) |
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102 (message "result is %S" result) |
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103 (or out-file result)))) |
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104 |
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105 (defun org-babel-prep-session:R (session params) |
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106 "Prepare SESSION according to the header arguments specified in PARAMS." |
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107 (let* ((session (org-babel-R-initiate-session session params)) |
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108 (vars (org-babel-ref-variables params)) |
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109 (var-lines |
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110 (mapcar |
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111 (lambda (pair) (org-babel-R-assign-elisp |
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112 (car pair) (cdr pair) |
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113 (equal (cdr (assoc :colnames params)) "yes") |
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114 (equal (cdr (assoc :rownames params)) "yes"))) |
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115 vars))) |
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116 (org-babel-comint-in-buffer session |
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117 (mapc (lambda (var) |
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118 (end-of-line 1) (insert var) (comint-send-input nil t) |
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119 (org-babel-comint-wait-for-output session)) var-lines)) |
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120 session)) |
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121 |
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122 (defun org-babel-load-session:R (session body params) |
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123 "Load BODY into SESSION." |
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124 (save-window-excursion |
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125 (let ((buffer (org-babel-prep-session:R session params))) |
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126 (with-current-buffer buffer |
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127 (goto-char (process-mark (get-buffer-process (current-buffer)))) |
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128 (insert (org-babel-chomp body))) |
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129 buffer))) |
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130 |
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131 ;; helper functions |
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132 |
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133 (defun org-babel-R-quote-tsv-field (s) |
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134 "Quote field S for export to R." |
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135 (if (stringp s) |
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136 (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"") |
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137 (format "%S" s))) |
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138 |
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139 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p) |
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140 "Construct R code assigning the elisp VALUE to a variable named NAME." |
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141 (if (listp value) |
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142 (let ((transition-file (make-temp-file "org-babel-R-import"))) |
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143 ;; ensure VALUE has an orgtbl structure (depth of at least 2) |
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144 (unless (listp (car value)) (setq value (list value))) |
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145 (with-temp-file (org-babel-maybe-remote-file transition-file) |
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146 (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) |
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147 (insert "\n")) |
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148 (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)" |
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149 name transition-file |
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150 (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE") |
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151 (if rownames-p "1" "NULL"))) |
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152 (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))) |
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153 |
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154 (defun org-babel-R-initiate-session (session params) |
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155 "If there is not a current R process then create one." |
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156 (unless (string= session "none") |
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157 (let ((session (or session "*R*")) |
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158 (ess-ask-for-ess-directory (not (cdr (assoc :dir params))))) |
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159 (if (org-babel-comint-buffer-livep session) |
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160 session |
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161 (save-window-excursion |
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162 (require 'ess) (R) |
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163 (rename-buffer |
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164 (if (bufferp session) |
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165 (buffer-name session) |
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166 (if (stringp session) |
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167 session |
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168 (buffer-name)))) |
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169 (current-buffer)))))) |
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170 |
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171 (defun org-babel-R-construct-graphics-device-call (out-file params) |
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172 "Construct the call to the graphics device." |
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173 (let ((devices |
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174 '((:bmp . "bmp") |
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175 (:jpg . "jpeg") |
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176 (:jpeg . "jpeg") |
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177 (:tiff . "tiff") |
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178 (:png . "png") |
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179 (:svg . "svg") |
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180 (:pdf . "pdf") |
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181 (:ps . "postscript") |
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182 (:postscript . "postscript"))) |
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183 (allowed-args '(:width :height :bg :units :pointsize |
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184 :antialias :quality :compression :res |
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185 :type :family :title :fonts :version |
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186 :paper :encoding :pagecentre :colormodel |
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187 :useDingbats :horizontal)) |
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188 (device (and (string-match ".+\\.\\([^.]+\\)" out-file) |
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189 (match-string 1 out-file))) |
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190 (extra-args (cdr (assq :R-dev-args params))) filearg args) |
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191 (setq device (or (and device (cdr (assq (intern (concat ":" device)) |
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192 devices))) "png")) |
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193 (setq filearg |
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194 (if (member device '("pdf" "postscript" "svg")) "file" "filename")) |
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195 (setq args (mapconcat |
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196 (lambda (pair) |
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197 (if (member (car pair) allowed-args) |
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198 (format ",%s=%s" |
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199 (substring (symbol-name (car pair)) 1) |
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200 (cdr pair)) "")) |
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201 params "")) |
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202 (format "%s(%s=\"%s\"%s%s%s)" |
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203 device filearg out-file args |
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204 (if extra-args "," "") (or extra-args "")))) |
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205 |
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206 (defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'") |
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207 (defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"") |
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208 (defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n} |
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209 write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)") |
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210 (defvar org-babel-R-wrapper-lastvar "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)") |
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211 |
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212 (defun org-babel-R-evaluate |
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213 (session body result-type column-names-p row-names-p) |
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214 "Pass BODY to the R process in SESSION. |
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215 If RESULT-TYPE equals 'output then return a list of the outputs |
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216 of the statements in BODY, if RESULT-TYPE equals 'value then |
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217 return the value of the last statement in BODY, as elisp." |
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218 (if (not session) |
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219 ;; external process evaluation |
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220 (case result-type |
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221 (output (org-babel-eval org-babel-R-command body)) |
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222 (value |
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223 (let ((tmp-file (make-temp-file "org-babel-R-results-"))) |
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224 (org-babel-eval org-babel-R-command |
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225 (format org-babel-R-wrapper-method |
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226 body tmp-file |
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227 (if row-names-p "TRUE" "FALSE") |
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228 (if column-names-p |
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229 (if row-names-p "NA" "TRUE") |
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230 "FALSE"))) |
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231 (org-babel-R-process-value-result |
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232 (org-babel-import-elisp-from-file |
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233 (org-babel-maybe-remote-file tmp-file)) column-names-p)))) |
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234 ;; comint session evaluation |
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235 (case result-type |
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236 (value |
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237 (let ((tmp-file (make-temp-file "org-babel-R")) |
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238 broke) |
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239 (org-babel-comint-with-output (session org-babel-R-eoe-output) |
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240 (insert (mapconcat |
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241 #'org-babel-chomp |
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242 (list |
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243 body |
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244 (format org-babel-R-wrapper-lastvar |
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245 tmp-file |
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246 (if row-names-p "TRUE" "FALSE") |
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247 (if column-names-p |
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248 (if row-names-p "NA" "TRUE") |
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249 "FALSE")) |
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250 org-babel-R-eoe-indicator) "\n")) |
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251 (inferior-ess-send-input)) |
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252 (org-babel-R-process-value-result |
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253 (org-babel-import-elisp-from-file |
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254 (org-babel-maybe-remote-file tmp-file)) column-names-p))) |
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255 (output |
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256 (mapconcat |
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257 #'org-babel-chomp |
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258 (butlast |
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259 (delq nil |
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260 (mapcar |
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261 #'identity |
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262 (org-babel-comint-with-output (session org-babel-R-eoe-output) |
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263 (insert (mapconcat #'org-babel-chomp |
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264 (list body org-babel-R-eoe-indicator) |
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265 "\n")) |
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266 (inferior-ess-send-input)))) 2) "\n"))))) |
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267 |
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268 (defun org-babel-R-process-value-result (result column-names-p) |
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269 "R-specific processing of return value. |
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270 Insert hline if column names in output have been requested." |
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271 (if column-names-p |
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272 (cons (car result) (cons 'hline (cdr result))) |
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273 result)) |
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274 |
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275 (provide 'ob-R) |
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276 |
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277 ;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237 |
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278 |
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279 ;;; ob-R.el ends here |