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;ELC
;;; Compiled
;;; in Emacs version 25.2.1
;;; with all optimizations.
;;; This file uses dynamic docstrings, first added in Emacs 19.29.
;;; This file does not contain utf-8 non-ASCII characters,
;;; and so can be loaded in Emacs versions earlier than 23.
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(require 'ob)
#@30 R-specific header arguments.
(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))) (#$ . 424))
(defvar org-babel-default-header-args:R nil)
#@46 Name of command to use for executing R code.
(custom-declare-variable 'org-babel-R-command "R --slave --no-save" '(#$ . 1032) :group 'org-babel :version "24.1" :type 'string)
(defalias 'org-babel-edit-prep:R #[(info) "\303\304\3058\"A\211\205 \306\307 \"\205 \310 \311\216\312 \313\"*)\207" [info session save-match-data-internal assoc :session 2 string-match "^\\*\\(.+?\\)\\*$" match-data #[nil "\301\302\"\207" [save-match-data-internal set-match-data evaporate] 3] org-babel-R-initiate-session nil] 5])
#@60 Expand BODY according to PARAMS, return the expanded body.
(defalias 'org-babel-expand-body:R #[(body params &optional graphics-file) "\206 \304 !\305\306\307\310\311 \"A\205 \310\311 \"AC\312 !\nC\310\313 \"A\205, \310\313 \"AC$\203? \307\314 \"C \315C#\202@ )\316#)\207" [graphics-file params body inside org-babel-R-graphical-output-file mapconcat identity append assoc :prologue org-babel-variable-assignments:R :epilogue org-babel-R-construct-graphics-device-call "dev.off()" "\n"] 9 (#$ . 1551)])
#@86 Execute a block of R code.
This function is called by `org-babel-execute-src-block'.
(defalias 'org-babel-execute:R #[(body params) "\212\306\307\"A\306\310\"A\311\306\312\"A\"\306\313\"A \306\314\"A \315! \316# \317 \n \f\320\232\206D \321\306\322\"A\f\"
\320\232\206R \321\306\323\"A
\"& ?\205^ . \207" [params result-params result-type session colnames-p rownames-p assoc :result-params :result-type org-babel-R-initiate-session :session :colnames :rownames org-babel-R-graphical-output-file org-babel-expand-body:R org-babel-R-evaluate "yes" org-babel-pick-name :colname-names :rowname-names graphics-file body full-body result] 10 (#$ . 2068)])
#@72 Prepare SESSION according to the header arguments specified in PARAMS.
(defalias 'org-babel-prep-session:R #[(session params) "\304 \"\305 !\212\306 \307\216\310!\204 \311\312\"\210q\210\313\314\n\"\210+*\207" [session params var-lines save-match-data-internal org-babel-R-initiate-session org-babel-variable-assignments:R match-data #[nil "\301\302\"\207" [save-match-data-internal set-match-data evaporate] 3] org-babel-comint-buffer-livep error "Buffer %s does not exist or has no process" mapc #[(var) "\302\210c\210\303\304\305\"\210\306 !\207" [var session 1 comint-send-input nil t org-babel-comint-wait-for-output] 3]] 3 (#$ . 2751)])
#@25 Load BODY into SESSION.
(defalias 'org-babel-load-session:R #[(session body params) "\305 \306\216\307 \n\"r q\210\310\311p!!b\210\312\f!c\210) +\207" [#1=#:wconfig session params buffer body current-window-configuration #[nil "\301!\207" [#1# set-window-configuration] 2] org-babel-prep-session:R process-mark get-buffer-process org-babel-chomp] 3 (#$ . 3412)])
#@62 Return list of R statements assigning the block's variables.
(defalias 'org-babel-variable-assignments:R #[(params) "\302\303\304\305\"\"\302\306\302\307\310\311 GS\"\"\")\207" [params vars mapcar cdr org-babel-get-header :var #[(pair) "\302@A\303\304 \"A\305\232\303\306 \"A\305\232$\207" [pair params org-babel-R-assign-elisp assoc :colnames "yes" :rownames] 7] #[(i) " 8@\303 8A\304\305\n\"A8A\304\306\n\"A8A#B\207" [i vars params org-babel-reassemble-table assoc :colname-names :rowname-names] 8] org-number-sequence 0] 7 (#$ . 3784)])
#@32 Quote field S for export to R.
(defalias 'org-babel-R-quote-tsv-field #[(s) ";\203 \301\302\303\304\301\"\305#\301Q\207\306\307\"\207" [s "\"" mapconcat identity split-string "\"\"" format "%S"] 6 (#$ . 4338)])
#@70 Construct R code assigning the elisp VALUE to a variable named NAME.
(defalias 'org-babel-R-assign-elisp #[(name value colnames-p rownames-p) "<\203\244 \306\307\310\311\"\"\211\203 \312\302 \"\202 \313 \203% \312\303 \"\202& \313\314\315! @<\2044 C\f\316\317\320!! #\321\216r
q\210\322\323\"\324\261\210)r
q\210\325\326\211#\326\313%\210,\327\f\330\"A@\331=\204k $\203o \332\202p \333%\203y \334\202z \335 & ' (\n U\203\224 \336\337)('&%\202\241 \336\340)('&\n&.\207\336\341)\342!#\207" [value lengths max min transition-file #1=#:temp-buffer mapcar length org-remove-if-not sequencep apply 0 org-babel-temp-file "R-import-" get-buffer-create generate-new-buffer-name " *temp file*" #[nil "\301!\205 \302!\207" [#1# buffer-name kill-buffer] 2] orgtbl-to-tsv (:fmt org-babel-R-quote-tsv-field) "\n" write-region nil org-babel-process-file-name noquote hline "TRUE" "FALSE" "1" "NULL" format "%s <- read.table(\"%s\",\n header=%s,\n row.names=%s,\n sep=\"\\t\",\n as.is=TRUE)" "%s <- read.table(\"%s\",\n header=%s,\n row.names=%s,\n sep=\"\\t\",\n as.is=TRUE,\n fill=TRUE,\n col.names = paste(\"V\", seq_len(%d), sep =\"\"))" "%s <- %s" org-babel-R-quote-tsv-field #2=#:temp-file colnames-p rownames-p row-names header file name] 8 (#$ . 4559)])
#@54 If there is not a current R process then create one.
(defalias 'org-babel-R-initiate-session #[(session params) "\304\230?\205Z \206\f \305\306\301!\205 \205 \307\310\n\"A?\311!\203( \202Y \312 \313\216\314!\2036 q\210\315\316!\210\317 \210\320\321!\203J \322!\202U ;\203S \202U \322 !\210p**\207" [session ess-ask-for-ess-directory params #1=#:wconfig "none" "*R*" boundp assoc :dir org-babel-comint-buffer-livep current-window-configuration #[nil "\301!\207" [#1# set-window-configuration] 2] get-buffer require ess R rename-buffer bufferp buffer-name] 4 (#$ . 6035)])
#@126 Associate R code buffer with an R session.
Make SESSION be the inferior ESS process associated with the
current code buffer.
(defalias 'org-babel-R-associate-session #[(session) "\302\303!!\304 \207" [session ess-local-process-name process-name get-buffer-process ess-make-buffer-current] 3 (#$ . 6630)])
#@55 Name of file to which R should send graphical output.
(defalias 'org-babel-R-graphical-output-file #[(params) "\301\302\236A\235\205
\303\236A\207" [params "graphics" :result-params :file] 3 (#$ . 6943)])
#@359 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")
(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")) (#$ . 7158))
#@44 Construct the call to the graphics device.
(defalias 'org-babel-R-construct-graphics-device-call #[(out-file params) "\306\307\310 \"\205
\311\312 \"\313\314\nP! \236\206 \315 \236 \316
\236A \317\211 \fA@\320\f8\321\322
\323#\324\325\n \203I \326\202J \323\206P \323&.\207" [allowed-args out-file device org-babel-R-graphics-devices device-info params (:width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal) string-match ".+\\.\\([^.]+\\)" match-string 1 intern ":" :png :R-dev-args nil 2 mapconcat #[(pair) "@ \235\203 \302\303\304@!\305\306OA#\207\307\207" [pair allowed-args format ",%s=%S" symbol-name 1 nil #1=""] 5] #1# format "%s(%s=\"%s\"%s%s%s)" "," extra-args filearg args] 9 (#$ . 7822)])
(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\")")
#@26 Evaluate R code in BODY.
(defalias 'org-babel-R-evaluate #[(session body result-type result-params column-names-p row-names-p) "\203 \306 \n \f
&\207\307 \n \f
%\207" [session body result-type result-params column-names-p row-names-p org-babel-R-evaluate-session org-babel-R-evaluate-external-process] 7 (#$ . 9170)])
#@202 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.
(defalias 'org-babel-R-evaluate-external-process #[(body result-type result-params column-names-p row-names-p) "\306\307\"\203\247 \310\311!\312\n\313 \f\203 \314\202 \315
\203( \f\203$ \316\202) \314\202) \315\313\317&\"\320 \321\"%\"\210\322' (\323(\235?\205\242 \324(\235\204\210 \325(\235\204\210 \326(\235\204\210 \327(\235\204\210 \330(\235\204\210 \331(\235\204\201 \332(\235\204\201 \333(\235\204\201 \334(\235\203\236 \335(\235\204\236 \336\337! )r)q\210\340\216\341 !\210\342 +\202\242 \343 \344\")
\")\207\306\345\"\205\263 \312\n&\"\207" [result-type tmp-file org-babel-R-command org-babel-R-write-object-command row-names-p column-names-p eql value org-babel-temp-file "R-" org-babel-eval format "TRUE" "FALSE" "NA" "{function ()\n{\n%s\n}}()" org-babel-process-file-name noquote org-babel-R-process-value-result "none" "scalar" "verbatim" "html" "code" "pp" "output" "raw" "org" "drawer" "table" generate-new-buffer " *temp*" #[nil "\301!\205 \302!\207" [#1=#:temp-buffer buffer-name kill-buffer] 2] insert-file-contents buffer-string org-babel-import-elisp-from-file (16) output body result-params #2=#:--params #1#] 10 (#$ . 9499)])
#@191 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.
(defalias 'org-babel-R-evaluate-session #[(session body result-type result-params column-names-p row-names-p) "\306\307\"\203\312 \310\311!r q\210\312\216\313\n!c\210\314\315 !!\316 \317\316!\210-\320\321! @\322 @\323AB\2038 \324\2029 \325C\203K B\203G \326\202L \324\202L \325\327\330@\331\"%#\210\332D E\333E\235?\205\304 \334E\235\204\250 \335E\235\204\250 \336E\235\204\250 \337E\235\204\250 \340E\235\204\250 \341E\235\204\241 \342E\235\204\241 \343E\235\204\241 \344E\235\203\277 \345E\235\204\277 \310\311! FrFq\210\346\216\347@!\210\350 +\202\304 \351@\352\")C\")\207\306\353\"\205h\354\313\355\356\316\357\360\357\361\212\362 G\363\216\364 !\204\354 \365\366 \"\210 q\210\367\316\211 H I J\370KBK\371\216\372\315p!!b\210`d L\211 ML{IML|\210*\354\313\nND\373#c\210\374 \210Ob\210\212\375\376P!\316\377#\205=\375Q\316\377#)\204L\201R \315p!!\210\202'\372\315p!!b\210Ic\210)\201S JQ\".\"\"\"!\373#\207" [result-type #1=#:temp-buffer body session ess-eval-visibly-p ess-local-process-name eql value generate-new-buffer " *temp*" #[nil "\301!\205 \302!\207" [#1# buffer-name kill-buffer] 2] org-babel-chomp process-name get-buffer-process nil ess-eval-buffer org-babel-temp-file "R-" org-babel-comint-eval-invisibly-and-wait-for-file format "TRUE" "FALSE" "NA" ".Last.value" org-babel-process-file-name noquote org-babel-R-process-value-result "none" "scalar" "verbatim" "html" "code" "pp" "output" "raw" "org" "drawer" "table" #[nil "\301!\205 \302!\207" [#2=#:temp-buffer buffer-name kill-buffer] 2] insert-file-contents buffer-string org-babel-import-elisp-from-file (16) output mapconcat butlast delq mapcar #[(line) "G\301V\205 \207" [line 0] 2] #[(line) "\301\302\"\203
\303\225\304O\207\207" [line string-match "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" 1 nil] 3] match-data #[nil "\301\302\"\207" [save-match-data-internal set-match-data evaporate] 3] org-babel-comint-buffer-livep error "Buffer %s does not exist or has no process" "" #[(text) " P\211\207" [string-buffer text] 2] #[nil "A\211\207" [comint-output-filter-functions] 2] process-mark "\n" inferior-ess-send-input re-search-forward regexp-quote t tmp-file org-babel-R-write-object-command row-names-p column-names-p result-params #3=#:--params #2# save-match-data-internal raw dangling-text string-buffer comint-output-filter-functions end start org-babel-R-eoe-indicator comint-last-input-end org-babel-R-eoe-output comint-prompt-regexp accept-process-output split-string] 14 (#$ . 10879)])
#@100 R-specific processing of return value.
Insert hline if column names in output have been requested.
(defalias 'org-babel-R-process-value-result #[(result column-names-p) "\203\f @\302 ABB\207 \207" [column-names-p result hline] 3 (#$ . 13609)])
(provide 'ob-R)
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