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baa6e1d3d7
had to nest an argument in a trivial `or' to trick the compiler in the large ob-comint macro.
283 lines
9.9 KiB
EmacsLisp
283 lines
9.9 KiB
EmacsLisp
;;; ob-R.el --- org-babel functions for R code evaluation
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;; Copyright (C) 2009, 2010 Free Software Foundation, Inc.
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;; Author: Eric Schulte, Dan Davison
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;; Keywords: literate programming, reproducible research, R, statistics
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;; Homepage: http://orgmode.org
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;; Version: 0.01
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;; This file is part of GNU Emacs.
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;; GNU Emacs is free software: you can redistribute it and/or modify
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;; it under the terms of the GNU General Public License as published by
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;; the Free Software Foundation, either version 3 of the License, or
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;; (at your option) any later version.
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;; GNU Emacs is distributed in the hope that it will be useful,
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;; but WITHOUT ANY WARRANTY; without even the implied warranty of
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;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;; GNU General Public License for more details.
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;; You should have received a copy of the GNU General Public License
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;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
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;;; Commentary:
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;; Org-Babel support for evaluating R code
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;;; Code:
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(require 'ob)
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(require 'ob-ref)
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(require 'ob-comint)
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(require 'ob-eval)
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(eval-when-compile (require 'cl))
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(declare-function orgtbl-to-tsv "ob-table" (table params))
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(declare-function R "ext:essd-r" (&optional start-args))
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(declare-function inferior-ess-send-input "ext:ess-inf" ())
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(defconst org-babel-header-arg-names:R
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'(width height bg units pointsize antialias quality compression
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res type family title fonts version paper encoding
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pagecentre colormodel useDingbats horizontal)
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"R-specific header arguments.")
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(defvar org-babel-default-header-args:R '())
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(defvar org-babel-R-command "R --slave --no-save"
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"Name of command to use for executing R code.")
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(defun org-babel-expand-body:R (body params &optional processed-params)
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"Expand BODY according to PARAMS, return the expanded body."
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(let* ((processed-params (or processed-params
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(org-babel-process-params params)))
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(vars (mapcar
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(lambda (i)
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(cons (car (nth i (nth 1 processed-params)))
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(org-babel-reassemble-table
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(cdr (nth i (nth 1 processed-params)))
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(cdr (nth i (nth 4 processed-params)))
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(cdr (nth i (nth 5 processed-params))))))
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(number-sequence 0 (1- (length (nth 1 processed-params))))))
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(out-file (cdr (assoc :file params))))
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(mapconcat ;; define any variables
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#'org-babel-trim
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((lambda (inside)
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(if out-file
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(append
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(org-babel-R-construct-graphics-device-call out-file params)
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inside
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(list "dev.off()"))
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inside))
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(append
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(mapcar
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(lambda (pair)
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(org-babel-R-assign-elisp
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(car pair) (cdr pair)
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(equal "yes" (cdr (assoc :colnames params)))
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(equal "yes" (cdr (assoc :rownames params)))))
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vars)
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(list body))) "\n")))
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(defun org-babel-execute:R (body params)
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"Execute a block of R code with org-babel. This function is
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called by `org-babel-execute-src-block'."
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(message "executing R source code block...")
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(save-excursion
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(let* ((processed-params (org-babel-process-params params))
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(result-type (nth 3 processed-params))
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(session (org-babel-R-initiate-session
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(first processed-params) params))
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(colnames-p (cdr (assoc :colnames params)))
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(rownames-p (cdr (assoc :rownames params)))
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(out-file (cdr (assoc :file params)))
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(full-body (org-babel-expand-body:R body params processed-params))
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(result
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(org-babel-R-evaluate
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session full-body result-type
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(or (equal "yes" colnames-p)
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(org-babel-pick-name (nth 4 processed-params) colnames-p))
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(or (equal "yes" rownames-p)
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(org-babel-pick-name (nth 5 processed-params) rownames-p)))))
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(message "result is %S" result)
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(or out-file result))))
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(defun org-babel-prep-session:R (session params)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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(let* ((session (org-babel-R-initiate-session session params))
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(vars (org-babel-ref-variables params))
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(var-lines
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(mapcar
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(lambda (pair) (org-babel-R-assign-elisp
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(car pair) (cdr pair)
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(equal (cdr (assoc :colnames params)) "yes")
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(equal (cdr (assoc :rownames params)) "yes")))
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vars)))
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(org-babel-comint-in-buffer session
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(mapc (lambda (var)
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(end-of-line 1) (insert var) (comint-send-input nil t)
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(org-babel-comint-wait-for-output session)) var-lines))
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session))
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(defun org-babel-load-session:R (session body params)
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"Load BODY into SESSION."
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(save-window-excursion
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(let ((buffer (org-babel-prep-session:R session params)))
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(with-current-buffer buffer
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert (org-babel-chomp body)))
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buffer)))
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;; helper functions
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(defun org-babel-R-quote-tsv-field (s)
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"Quote field S for export to R."
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(if (stringp s)
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(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
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(format "%S" s)))
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(defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
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"Construct R code assigning the elisp VALUE to a variable named NAME."
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(if (listp value)
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(let ((transition-file (make-temp-file "org-babel-R-import")))
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;; ensure VALUE has an orgtbl structure (depth of at least 2)
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(unless (listp (car value)) (setq value (list value)))
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(with-temp-file (org-babel-maybe-remote-file transition-file)
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(insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
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(insert "\n"))
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(format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)"
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name transition-file
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(if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE")
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(if rownames-p "1" "NULL")))
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(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
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(defun org-babel-R-initiate-session (session params)
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"If there is not a current R process then create one."
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(unless (string= session "none")
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(let ((session (or session "*R*"))
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(ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))
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(if (org-babel-comint-buffer-livep session)
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session
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(save-window-excursion
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(require 'ess) (R)
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(rename-buffer
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(if (bufferp session)
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(buffer-name session)
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(if (stringp session)
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session
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(buffer-name))))
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(current-buffer))))))
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(defun org-babel-R-construct-graphics-device-call (out-file params)
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"Construct the call to the graphics device."
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(let ((devices
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'((:bmp . "bmp")
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(:jpg . "jpeg")
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(:jpeg . "jpeg")
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(:tiff . "tiff")
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(:png . "png")
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(:svg . "svg")
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(:pdf . "pdf")
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(:ps . "postscript")
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(:postscript . "postscript")))
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(allowed-args '(:width :height :bg :units :pointsize
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:antialias :quality :compression :res
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:type :family :title :fonts :version
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:paper :encoding :pagecentre :colormodel
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:useDingbats :horizontal))
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(device (and (string-match ".+\\.\\([^.]+\\)" out-file)
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(match-string 1 out-file)))
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(extra-args (cdr (assq :R-dev-args params))) filearg args)
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(setq device (or (and device (cdr (assq (intern (concat ":" device))
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devices))) "png"))
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(setq filearg
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(if (member device '("pdf" "postscript" "svg")) "file" "filename"))
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(setq args (mapconcat
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(lambda (pair)
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(if (member (car pair) allowed-args)
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(format ",%s=%s"
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(substring (symbol-name (car pair)) 1)
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(cdr pair)) ""))
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params ""))
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(format "%s(%s=\"%s\"%s%s%s)"
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device filearg out-file args
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(if extra-args "," "") (or extra-args ""))))
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(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
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(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
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(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
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write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")
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(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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(defun org-babel-R-evaluate
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(session body result-type column-names-p row-names-p)
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"Pass BODY to the R process in SESSION. If RESULT-TYPE equals
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'output then return a list of the outputs of the statements in
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BODY, if RESULT-TYPE equals 'value then return the value of the
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last statement in BODY, as elisp."
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(if (not session)
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;; external process evaluation
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(case result-type
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(output (org-babel-eval org-babel-R-command body))
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(value
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(let ((tmp-file (make-temp-file "org-babel-R-results-")))
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(org-babel-eval org-babel-R-command
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(format org-babel-R-wrapper-method
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body tmp-file
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(if row-names-p "TRUE" "FALSE")
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(if column-names-p
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(if row-names-p "NA" "TRUE")
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"FALSE")))
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(org-babel-R-process-value-result
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(org-babel-import-elisp-from-file
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(org-babel-maybe-remote-file tmp-file)) column-names-p))))
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;; comint session evaluation
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(case result-type
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(value
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(let ((tmp-file (make-temp-file "org-babel-R"))
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broke)
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(org-babel-comint-with-output (session org-babel-R-eoe-output)
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(insert (mapconcat
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#'org-babel-chomp
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(list
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body
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(format org-babel-R-wrapper-lastvar
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tmp-file
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(if row-names-p "TRUE" "FALSE")
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(if column-names-p
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(if row-names-p "NA" "TRUE")
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"FALSE"))
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org-babel-R-eoe-indicator) "\n"))
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(inferior-ess-send-input))
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(org-babel-R-process-value-result
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(org-babel-import-elisp-from-file
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(org-babel-maybe-remote-file tmp-file)) column-names-p)))
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(output
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(mapconcat
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#'org-babel-chomp
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(butlast
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(delq nil
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(mapcar
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#'identity
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(org-babel-comint-with-output (session org-babel-R-eoe-output)
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(insert (mapconcat #'org-babel-chomp
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(list body org-babel-R-eoe-indicator)
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"\n"))
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(inferior-ess-send-input)))) 2) "\n")))))
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(defun org-babel-R-process-value-result (result column-names-p)
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"R-specific processing of return value prior to return to
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org-babel. Insert hline if column names in output have been
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requested."
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(if column-names-p
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(cons (car result) (cons 'hline (cdr result)))
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result))
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(provide 'ob-R)
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;; arch-tag: cd4c7298-503b-450f-a3c2-f3e74b630237
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;;; ob-R.el ends here
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