diff options
Diffstat (limited to 'elpa/org-9.5.2/ob-R.el')
| -rw-r--r-- | elpa/org-9.5.2/ob-R.el | 570 |
1 files changed, 570 insertions, 0 deletions
diff --git a/elpa/org-9.5.2/ob-R.el b/elpa/org-9.5.2/ob-R.el new file mode 100644 index 0000000..169e1d6 --- /dev/null +++ b/elpa/org-9.5.2/ob-R.el @@ -0,0 +1,570 @@ +;;; ob-R.el --- Babel Functions for R -*- lexical-binding: t; -*- + +;; Copyright (C) 2009-2021 Free Software Foundation, Inc. + +;; Author: Eric Schulte +;; Dan Davison +;; Maintainer: Jeremie Juste +;; Keywords: literate programming, reproducible research, R, statistics +;; Homepage: https://orgmode.org + +;; 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 <https://www.gnu.org/licenses/>. + +;;; Commentary: + +;; Org-Babel support for evaluating R code + +;;; Code: + +(require 'cl-lib) +(require 'ob) + +(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 ess-wait-for-process "ext:ess-inf" + (&optional proc sec-prompt wait force-redisplay)) + +;; FIXME: Temporary declaration to silence the byte-compiler +(defvar user-inject-src-param) +(defvar ess-eval-visibly-tmp) +(defvar ess-eval-visibly) +(defvar ess-inject-source) +(defvar user-inject-src-param) + +(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 html latex org code pp drawer) + (replace silent none append prepend) + (output value graphics)))) + "R-specific header arguments.") + +(defconst ob-R-safe-header-args + (append org-babel-safe-header-args + '(:width :height :bg :units :pointsize :antialias :quality + :compression :res :type :family :title :fonts + :version :paper :encoding :pagecentre :colormodel + :useDingbats :horizontal)) + "Header args which are safe for R babel blocks. + +See `org-babel-safe-header-args' for documentation of the format of +this variable.") + +(defvar org-babel-default-header-args:R '()) +(put 'org-babel-default-header-args:R 'safe-local-variable + (org-babel-header-args-safe-fn ob-R-safe-header-args)) + +(defcustom org-babel-R-command "R --slave --no-save" + "Name of command to use for executing R code." + :group 'org-babel + :version "24.1" + :type 'string) + +(defvar ess-current-process-name) ; dynamically scoped +(defvar ess-local-process-name) ; dynamically scoped +(defun org-babel-edit-prep:R (info) + (let ((session (cdr (assq :session (nth 2 info))))) + (when (and session + (string-prefix-p "*" session) + (string-suffix-p "*" session)) + (org-babel-R-initiate-session session nil)))) + +;; The usage of utils::read.table() ensures that the command +;; read.table() can be found even in circumstances when the utils +;; package is not in the search path from R. +(defconst ob-R-transfer-variable-table-with-header + "%s <- local({ + con <- textConnection( + %S + ) + res <- utils::read.table( + con, + header = %s, + row.names = %s, + sep = \"\\t\", + as.is = TRUE + ) + close(con) + res + })" + "R code used to transfer a table defined as a variable from org to R. + +This function is used when the table contains a header.") + +(defconst ob-R-transfer-variable-table-without-header + "%s <- local({ + con <- textConnection( + %S + ) + res <- utils::read.table( + con, + header = %s, + row.names = %s, + sep = \"\\t\", + as.is = TRUE, + fill = TRUE, + col.names = paste(\"V\", seq_len(%d), sep =\"\") + ) + close(con) + res + })" + "R code used to transfer a table defined as a variable from org to R. + +This function is used when the table does not contain a header.") + +(defun org-babel-expand-body:R (body params &optional _graphics-file) + "Expand BODY according to PARAMS, return the expanded body." + (mapconcat 'identity + (append + (when (cdr (assq :prologue params)) + (list (cdr (assq :prologue params)))) + (org-babel-variable-assignments:R params) + (list body) + (when (cdr (assq :epilogue params)) + (list (cdr (assq :epilogue params))))) + "\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-params (cdr (assq :result-params params))) + (result-type (cdr (assq :result-type params))) + (async (org-babel-comint-use-async params)) + (session (org-babel-R-initiate-session + (cdr (assq :session params)) params)) + (graphics-file (and (member "graphics" (assq :result-params params)) + (org-babel-graphical-output-file params))) + (colnames-p (unless graphics-file (cdr (assq :colnames params)))) + (rownames-p (unless graphics-file (cdr (assq :rownames params)))) + (full-body + (let ((inside + (list (org-babel-expand-body:R body params graphics-file)))) + (mapconcat 'identity + (if graphics-file + (append + (list (org-babel-R-construct-graphics-device-call + graphics-file params)) + inside + (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()")) + inside) + "\n"))) + (result + (org-babel-R-evaluate + session full-body result-type result-params + (or (equal "yes" colnames-p) + (org-babel-pick-name + (cdr (assq :colname-names params)) colnames-p)) + (or (equal "yes" rownames-p) + (org-babel-pick-name + (cdr (assq :rowname-names params)) rownames-p)) + async))) + (if graphics-file nil 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 (org-babel--get-vars params))) + (mapcar + (lambda (pair) + (org-babel-R-assign-elisp + (car pair) (cdr pair) + (equal "yes" (cdr (assq :colnames params))) + (equal "yes" (cdr (assq :rownames params))))) + (mapcar + (lambda (i) + (cons (car (nth i vars)) + (org-babel-reassemble-table + (cdr (nth i vars)) + (cdr (nth i (cdr (assq :colname-names params)))) + (cdr (nth i (cdr (assq :rowname-names params))))))) + (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* ((lengths (mapcar 'length (cl-remove-if-not 'sequencep value))) + (max (if lengths (apply 'max lengths) 0)) + (min (if lengths (apply 'min lengths) 0))) + ;; Ensure VALUE has an orgtbl structure (depth of at least 2). + (unless (listp (car value)) (setq value (list value))) + (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) + (header (if (or (eq (nth 1 value) 'hline) colnames-p) + "TRUE" "FALSE")) + (row-names (if rownames-p "1" "NULL"))) + (if (= max min) + (format ob-R-transfer-variable-table-with-header + name file header row-names) + (format ob-R-transfer-variable-table-without-header + name file header row-names max)))) + (cond ((integerp value) (format "%s <- %s" name (concat (number-to-string value) "L"))) + ((floatp value) (format "%s <- %s" name value)) + ((stringp value) (format "%s <- %S" name (org-no-properties value))) + (t (format "%s <- %S" name (prin1-to-string value)))))) + + +(defvar ess-ask-for-ess-directory) ; dynamically scoped +(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 (boundp 'ess-ask-for-ess-directory) + ess-ask-for-ess-directory + (not (cdr (assq :dir params)))))) + (if (org-babel-comint-buffer-livep session) + session + (save-window-excursion + (when (get-buffer session) + ;; Session buffer exists, but with dead process + (set-buffer session)) + (require 'ess) (R) + (let ((R-proc (get-process (or ess-local-process-name + ess-current-process-name)))) + (while (process-get R-proc 'callbacks) + (ess-wait-for-process R-proc))) + (rename-buffer + (if (bufferp session) + (buffer-name session) + (if (stringp session) + session + (buffer-name)))) + (current-buffer)))))) + +(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)) + +(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")) + "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\")") + +(defun org-babel-R-construct-graphics-device-call (out-file params) + "Construct the call to the graphics device." + (let* ((allowed-args '(:width :height :bg :units :pointsize + :antialias :quality :compression :res + :type :family :title :fonts :version + :paper :encoding :pagecentre :colormodel + :useDingbats :horizontal)) + (device (file-name-extension out-file)) + (device-info (or (assq (intern (concat ":" device)) + org-babel-R-graphics-devices) + (assq :png org-babel-R-graphics-devices))) + (extra-args (cdr (assq :R-dev-args params))) filearg args) + (setq device (nth 1 device-info)) + (setq filearg (nth 2 device-info)) + (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); tryCatch({" + device filearg out-file args + (if extra-args "," "") (or extra-args "")))) + +(defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'") +(defconst org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"") + +(defconst 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=\"\",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\")" + "Template for an R command to evaluate a block of code and write result to file. + +Has four %s escapes to be filled in: +1. Row names, \"TRUE\" or \"FALSE\" +2. Column names, \"TRUE\" or \"FALSE\" +3. The code to be run (must be an expression, not a statement) +4. The name of the file to write to") + +(defun org-babel-R-evaluate + (session body result-type result-params column-names-p row-names-p async) + "Evaluate R code in BODY." + (if session + (if async + (ob-session-async-org-babel-R-evaluate-session + session body result-type result-params column-names-p row-names-p) + (org-babel-R-evaluate-session + session body result-type result-params column-names-p row-names-p)) + (org-babel-R-evaluate-external-process + body result-type result-params column-names-p row-names-p))) + +(defun org-babel-R-evaluate-external-process + (body result-type result-params 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." + (cl-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-result-cond result-params + (with-temp-buffer + (insert-file-contents tmp-file) + (org-babel-chomp (buffer-string) "\n")) + (org-babel-import-elisp-from-file tmp-file '(16))) + column-names-p))) + (output (org-babel-eval org-babel-R-command body)))) + +(defvar ess-eval-visibly-p) + +(defun org-babel-R-evaluate-session + (session body result-type result-params 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." + (cl-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-visibly-p nil)) + (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-result-cond result-params + (with-temp-buffer + (insert-file-contents tmp-file) + (org-babel-chomp (buffer-string) "\n")) + (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 + "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)" + (car (split-string line "\n"))) + (substring line (match-end 1)) + line)) + (with-current-buffer session + (let ((comint-prompt-regexp (concat "^" comint-prompt-regexp))) + (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 + (condition-case nil + (cons (car result) (cons 'hline (cdr result))) + (error "Could not parse R result")) + result)) + + +;;; async evaluation + +(defconst ob-session-async-R-indicator "'ob_comint_async_R_%s_%s'") + +(defun ob-session-async-org-babel-R-evaluate-session + (session body result-type _ column-names-p row-names-p) + "Asynchronously evaluate BODY in SESSION. +Returns a placeholder string for insertion, to later be replaced +by `org-babel-comint-async-filter'." + (org-babel-comint-async-register + session (current-buffer) + "^\\(?:[>.+] \\)*\\[1\\] \"ob_comint_async_R_\\(.+?\\)_\\(.+\\)\"$" + 'org-babel-chomp + 'ob-session-async-R-value-callback) + (cl-case result-type + (value + (let ((tmp-file (org-babel-temp-file "R-"))) + (with-temp-buffer + (insert + (org-babel-chomp body)) + (let ((ess-local-process-name + (process-name (get-buffer-process session)))) + (ess-eval-buffer nil))) + (with-temp-buffer + (insert + (mapconcat + 'org-babel-chomp + (list (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)) + (format ob-session-async-R-indicator + "file" tmp-file)) + "\n")) + (let ((ess-local-process-name + (process-name (get-buffer-process session)))) + (ess-eval-buffer nil))) + tmp-file)) + (output + (let ((uuid (md5 (number-to-string (random 100000000)))) + (ess-local-process-name + (process-name (get-buffer-process session)))) + (with-temp-buffer + (insert (format ob-session-async-R-indicator + "start" uuid)) + (insert "\n") + (insert body) + (insert "\n") + (insert (format ob-session-async-R-indicator + "end" uuid)) + (setq ess-eval-visibly-tmp ess-eval-visibly) + (setq user-inject-src-param ess-inject-source) + (setq ess-eval-visibly nil) + (setq ess-inject-source 'function-and-buffer) + (ess-eval-buffer nil)) + (setq ess-eval-visibly ess-eval-visibly-tmp) + (setq ess-inject-source user-inject-src-param) + uuid)))) + +(defun ob-session-async-R-value-callback (params tmp-file) + "Callback for async value results. +Assigned locally to `ob-session-async-file-callback' in R +comint buffers used for asynchronous Babel evaluation." + (let* ((graphics-file (and (member "graphics" (assq :result-params params)) + (org-babel-graphical-output-file params))) + (colnames-p (unless graphics-file (cdr (assq :colnames params))))) + (org-babel-R-process-value-result + (org-babel-result-cond (assq :result-params params) + (with-temp-buffer + (insert-file-contents tmp-file) + (org-babel-chomp (buffer-string) "\n")) + (org-babel-import-elisp-from-file tmp-file '(16))) + (or (equal "yes" colnames-p) + (org-babel-pick-name + (cdr (assq :colname-names params)) colnames-p))))) + + + +;;; ob-session-async-R.el ends here + + +(provide 'ob-R) + +;;; ob-R.el ends here |