lisp/ob-R.el

   1 ;;; ob-R.el --- org-babel functions for R code evaluation
   2
   3 ;; Copyright (C) 2009-2015 Free Software Foundation, Inc.
   4
   5 ;; Author: Eric Schulte
   6 ;;      Dan Davison
   7 ;; Keywords: literate programming, reproducible research, R, statistics
   8 ;; Homepage: http://orgmode.org
   9
  10 ;; This file is part of GNU Emacs.
  11
  12 ;; GNU Emacs is free software: you can redistribute it and/or modify
  13 ;; it under the terms of the GNU General Public License as published by
  14 ;; the Free Software Foundation, either version 3 of the License, or
  15 ;; (at your option) any later version.
  16
  17 ;; GNU Emacs is distributed in the hope that it will be useful,
  18 ;; but WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;; GNU General Public License for more details.
  21
  22 ;; You should have received a copy of the GNU General Public License
  23 ;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 ;;; Commentary:
  26
  27 ;; Org-Babel support for evaluating R code
  28
  29 ;;; Code:
  30 (require 'ob)
  31 (eval-when-compile (require 'cl))
  32
  33 (declare-function orgtbl-to-tsv "org-table" (table params))
  34 (declare-function R "ext:essd-r" (&optional start-args))
  35 (declare-function inferior-ess-send-input "ext:ess-inf" ())
  36 (declare-function ess-make-buffer-current "ext:ess-inf" ())
  37 (declare-function ess-eval-buffer "ext:ess-inf" (vis))
  38 (declare-function ess-wait-for-process "ext:ess-inf"
  39                   (proc &optional sec-prompt wait force-redisplay))
  40 (declare-function org-number-sequence "org-compat" (from &optional to inc))
  41 (declare-function org-remove-if-not "org" (predicate seq))
  42 (declare-function org-every "org" (pred seq))
  43
  44 (defconst org-babel-header-args:R
  45   '((width               . :any)
  46     (height              . :any)
  47     (bg                  . :any)
  48     (units               . :any)
  49     (pointsize           . :any)
  50     (antialias           . :any)
  51     (quality             . :any)
  52     (compression         . :any)
  53     (res                 . :any)
  54     (type                . :any)
  55     (family              . :any)
  56     (title               . :any)
  57     (fonts               . :any)
  58     (version             . :any)
  59     (paper               . :any)
  60     (encoding            . :any)
  61     (pagecentre          . :any)
  62     (colormodel          . :any)
  63     (useDingbats         . :any)
  64     (horizontal          . :any)
  65     (results             . ((file list vector table scalar verbatim)
  66                             (raw html latex org code pp drawer)
  67                             (replace silent none append prepend)
  68                             (output value graphics))))
  69   "R-specific header arguments.")
  70
  71 (defconst ob-R-safe-header-args
  72   (append org-babel-safe-header-args
  73           '(:width :height :bg :units :pointsize :antialias :quality
  74                    :compression :res :type :family :title :fonts
  75                    :version :paper :encoding :pagecentre :colormodel
  76                    :useDingbats :horizontal))
  77   "Header args which are safe for R babel blocks.
  78
  79 See `org-babel-safe-header-args' for documentation of the format of
  80 this variable.")
  81
  82 (defvar org-babel-default-header-args:R '())
  83 (put 'org-babel-default-header-args:R 'safe-local-variable
  84      (org-babel-header-args-safe-fn ob-R-safe-header-args))
  85
  86 (defcustom org-babel-R-command "R --slave --no-save"
  87   "Name of command to use for executing R code."
  88   :group 'org-babel
  89   :version "24.1"
  90   :type 'string)
  91
  92 (defvar ess-current-process-name) ; dynamically scoped
  93 (defvar ess-local-process-name)   ; dynamically scoped
  94 (defun org-babel-edit-prep:R (info)
  95   (let ((session (cdr (assoc :session (nth 2 info)))))
  96     (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
  97       (save-match-data (org-babel-R-initiate-session session nil)))))
  98
  99 ;; The usage of utils::read.table() ensures that the command
 100 ;; read.table() can be found even in circumstances when the utils
 101 ;; package is not in the search path from R.
 102 (defconst ob-R-transfer-variable-table-with-header
 103   "%s <- local({
 104      con <- textConnection(
 105        %S
 106      )
 107      res <- utils::read.table(
 108        con,
 109        header    = %s,
 110        row.names = %s,
 111        sep       = \"\\t\",
 112        as.is     = TRUE
 113      )
 114      close(con)
 115      res
 116    })"
 117   "R code used to transfer a table defined as a variable from org to R.
 118
 119 This function is used when the table contains a header.")
 120
 121 (defconst ob-R-transfer-variable-table-without-header
 122   "%s <- local({
 123      con <- textConnection(
 124        %S
 125      )
 126      res <- utils::read.table(
 127        con,
 128        header    = %s,
 129        row.names = %s,
 130        sep       = \"\\t\",
 131        as.is     = TRUE,
 132        fill      = TRUE,
 133        col.names = paste(\"V\", seq_len(%d), sep =\"\")
 134      )
 135      close(con)
 136      res
 137    })"
 138   "R code used to transfer a table defined as a variable from org to R.
 139
 140 This function is used when the table does not contain a header.")
 141
 142 (defun org-babel-expand-body:R (body params &optional graphics-file)
 143   "Expand BODY according to PARAMS, return the expanded body."
 144   (mapconcat 'identity
 145              (append
 146               (when (cdr (assoc :prologue params))
 147                 (list (cdr (assoc :prologue params))))
 148               (org-babel-variable-assignments:R params)
 149               (list body)
 150               (when (cdr (assoc :epilogue params))
 151                 (list (cdr (assoc :epilogue params)))))
 152              "\n"))
 153
 154 (defun org-babel-execute:R (body params)
 155   "Execute a block of R code.
 156 This function is called by `org-babel-execute-src-block'."
 157   (save-excursion
 158     (let* ((result-params (cdr (assoc :result-params params)))
 159            (result-type (cdr (assoc :result-type params)))
 160            (session (org-babel-R-initiate-session
 161                      (cdr (assoc :session params)) params))
 162            (colnames-p (cdr (assoc :colnames params)))
 163            (rownames-p (cdr (assoc :rownames params)))
 164            (graphics-file (and (member "graphics" (assq :result-params params))
 165                                (org-babel-graphical-output-file params)))
 166            (full-body
 167             (let ((inside
 168                    (list (org-babel-expand-body:R body params graphics-file))))
 169               (mapconcat 'identity
 170                          (if graphics-file
 171                              (append
 172                               (list (org-babel-R-construct-graphics-device-call
 173                                      graphics-file params))
 174                               inside
 175                               (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()"))
 176                            inside)
 177                          "\n")))
 178            (result
 179             (org-babel-R-evaluate
 180              session full-body result-type result-params
 181              (or (equal "yes" colnames-p)
 182                  (org-babel-pick-name
 183                   (cdr (assoc :colname-names params)) colnames-p))
 184              (or (equal "yes" rownames-p)
 185                  (org-babel-pick-name
 186                   (cdr (assoc :rowname-names params)) rownames-p)))))
 187       (if graphics-file nil result))))
 188
 189 (defun org-babel-prep-session:R (session params)
 190   "Prepare SESSION according to the header arguments specified in PARAMS."
 191   (let* ((session (org-babel-R-initiate-session session params))
 192          (var-lines (org-babel-variable-assignments:R params)))
 193     (org-babel-comint-in-buffer session
 194       (mapc (lambda (var)
 195               (end-of-line 1) (insert var) (comint-send-input nil t)
 196               (org-babel-comint-wait-for-output session)) var-lines))
 197     session))
 198
 199 (defun org-babel-load-session:R (session body params)
 200   "Load BODY into SESSION."
 201   (save-window-excursion
 202     (let ((buffer (org-babel-prep-session:R session params)))
 203       (with-current-buffer buffer
 204         (goto-char (process-mark (get-buffer-process (current-buffer))))
 205         (insert (org-babel-chomp body)))
 206       buffer)))
 207
 208 ;; helper functions
 209
 210 (defun org-babel-variable-assignments:R (params)
 211   "Return list of R statements assigning the block's variables."
 212   (let ((vars (mapcar 'cdr (org-babel-get-header params :var))))
 213     (mapcar
 214      (lambda (pair)
 215        (org-babel-R-assign-elisp
 216         (car pair) (cdr pair)
 217         (equal "yes" (cdr (assoc :colnames params)))
 218         (equal "yes" (cdr (assoc :rownames params)))))
 219      (mapcar
 220       (lambda (i)
 221         (cons (car (nth i vars))
 222               (org-babel-reassemble-table
 223                (cdr (nth i vars))
 224                (cdr (nth i (cdr (assoc :colname-names params))))
 225                (cdr (nth i (cdr (assoc :rowname-names params)))))))
 226       (org-number-sequence 0 (1- (length vars)))))))
 227
 228 (defun org-babel-R-quote-tsv-field (s)
 229   "Quote field S for export to R."
 230   (if (stringp s)
 231       (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
 232     (format "%S" s)))
 233
 234 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
 235   "Construct R code assigning the elisp VALUE to a variable named NAME."
 236   (if (listp value)
 237       (let* ((lengths (mapcar 'length (org-remove-if-not 'sequencep value)))
 238              (max (if lengths (apply 'max lengths) 0))
 239              (min (if lengths (apply 'min lengths) 0)))
 240         ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
 241         (unless (listp (car value)) (setq value (list value)))
 242         (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
 243               (header (if (or (eq (nth 1 value) 'hline) colnames-p)
 244                           "TRUE" "FALSE"))
 245               (row-names (if rownames-p "1" "NULL")))
 246           (if (= max min)
 247               (format ob-R-transfer-variable-table-with-header
 248                       name file header row-names)
 249             (format ob-R-transfer-variable-table-without-header
 250                     name file header row-names max))))
 251     (cond ((integerp value) (format "%s <- %s" name (concat (number-to-string value) "L")))
 252           ((floatp   value) (format "%s <- %s" name value))
 253           ((stringp  value) (format "%s <- %S" name (org-no-properties value)))
 254           (t                (format "%s <- %S" name (prin1-to-string value))))))
 255
 256
 257 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 258 (defun org-babel-R-initiate-session (session params)
 259   "If there is not a current R process then create one."
 260   (unless (string= session "none")
 261     (let ((session (or session "*R*"))
 262           (ess-ask-for-ess-directory
 263            (and (boundp 'ess-ask-for-ess-directory)
 264                 ess-ask-for-ess-directory
 265                 (not (cdr (assoc :dir params))))))
 266       (if (org-babel-comint-buffer-livep session)
 267           session
 268         (save-window-excursion
 269           (when (get-buffer session)
 270             ;; Session buffer exists, but with dead process
 271             (set-buffer session))
 272           (require 'ess) (R)
 273           (let ((R-proc (get-process (or ess-local-process-name
 274                                          ess-current-process-name))))
 275             (while (process-get R-proc 'callbacks)
 276               (ess-wait-for-process R-proc)))
 277           (rename-buffer
 278            (if (bufferp session)
 279                (buffer-name session)
 280              (if (stringp session)
 281                  session
 282                (buffer-name))))
 283           (current-buffer))))))
 284
 285 (defun org-babel-R-associate-session (session)
 286   "Associate R code buffer with an R session.
 287 Make SESSION be the inferior ESS process associated with the
 288 current code buffer."
 289   (setq ess-local-process-name
 290         (process-name (get-buffer-process session)))
 291   (ess-make-buffer-current))
 292
 293 (defvar org-babel-R-graphics-devices
 294   '((:bmp "bmp" "filename")
 295     (:jpg "jpeg" "filename")
 296     (:jpeg "jpeg" "filename")
 297     (:tikz "tikz" "file")
 298     (:tiff "tiff" "filename")
 299     (:png "png" "filename")
 300     (:svg "svg" "file")
 301     (:pdf "pdf" "file")
 302     (:ps "postscript" "file")
 303     (:postscript "postscript" "file"))
 304   "An alist mapping graphics file types to R functions.
 305
 306 Each member of this list is a list with three members:
 307 1. the file extension of the graphics file, as an elisp :keyword
 308 2. the R graphics device function to call to generate such a file
 309 3. the name of the argument to this function which specifies the
 310    file to write to (typically \"file\" or \"filename\")")
 311
 312 (defun org-babel-R-construct-graphics-device-call (out-file params)
 313   "Construct the call to the graphics device."
 314   (let* ((allowed-args '(:width :height :bg :units :pointsize
 315                                 :antialias :quality :compression :res
 316                                 :type :family :title :fonts :version
 317                                 :paper :encoding :pagecentre :colormodel
 318                                 :useDingbats :horizontal))
 319          (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
 320                       (match-string 1 out-file)))
 321          (device-info (or (assq (intern (concat ":" device))
 322                                 org-babel-R-graphics-devices)
 323                           (assq :png org-babel-R-graphics-devices)))
 324         (extra-args (cdr (assq :R-dev-args params))) filearg args)
 325     (setq device (nth 1 device-info))
 326     (setq filearg (nth 2 device-info))
 327     (setq args (mapconcat
 328                 (lambda (pair)
 329                   (if (member (car pair) allowed-args)
 330                       (format ",%s=%S"
 331                               (substring (symbol-name (car pair)) 1)
 332                               (cdr pair)) ""))
 333                 params ""))
 334     (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
 335             device filearg out-file args
 336             (if extra-args "," "") (or extra-args ""))))
 337
 338 (defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'")
 339 (defconst org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
 340
 341 (defconst org-babel-R-write-object-command "{
 342     function(object,transfer.file) {
 343         object
 344         invisible(
 345             if (
 346                 inherits(
 347                     try(
 348                         {
 349                             tfile<-tempfile()
 350                             write.table(object, file=tfile, sep=\"\\t\",
 351                                         na=\"nil\",row.names=%s,col.names=%s,
 352                                         quote=FALSE)
 353                             file.rename(tfile,transfer.file)
 354                         },
 355                         silent=TRUE),
 356                     \"try-error\"))
 357                 {
 358                     if(!file.exists(transfer.file))
 359                         file.create(transfer.file)
 360                 }
 361             )
 362     }
 363 }(object=%s,transfer.file=\"%s\")"
 364   "A template for an R command to evaluate a block of code and write the result to a file.
 365
 366 Has four %s escapes to be filled in:
 367 1. Row names, \"TRUE\" or \"FALSE\"
 368 2. Column names, \"TRUE\" or \"FALSE\"
 369 3. The code to be run (must be an expression, not a statement)
 370 4. The name of the file to write to")
 371
 372 (defun org-babel-R-evaluate
 373   (session body result-type result-params column-names-p row-names-p)
 374   "Evaluate R code in BODY."
 375   (if session
 376       (org-babel-R-evaluate-session
 377        session body result-type result-params column-names-p row-names-p)
 378     (org-babel-R-evaluate-external-process
 379      body result-type result-params column-names-p row-names-p)))
 380
 381 (defun org-babel-R-evaluate-external-process
 382   (body result-type result-params column-names-p row-names-p)
 383   "Evaluate BODY in external R process.
 384 If RESULT-TYPE equals `output' then return standard output as a
 385 string.  If RESULT-TYPE equals `value' then return the value of the
 386 last statement in BODY, as elisp."
 387   (case result-type
 388     (value
 389      (let ((tmp-file (org-babel-temp-file "R-")))
 390        (org-babel-eval org-babel-R-command
 391                        (format org-babel-R-write-object-command
 392                                (if row-names-p "TRUE" "FALSE")
 393                                (if column-names-p
 394                                    (if row-names-p "NA" "TRUE")
 395                                  "FALSE")
 396                                (format "{function ()\n{\n%s\n}}()" body)
 397                                (org-babel-process-file-name tmp-file 'noquote)))
 398        (org-babel-R-process-value-result
 399         (org-babel-result-cond result-params
 400           (with-temp-buffer
 401             (insert-file-contents tmp-file)
 402             (buffer-string))
 403           (org-babel-import-elisp-from-file tmp-file '(16)))
 404         column-names-p)))
 405     (output (org-babel-eval org-babel-R-command body))))
 406
 407 (defvar ess-eval-visibly-p)
 408
 409 (defun org-babel-R-evaluate-session
 410   (session body result-type result-params column-names-p row-names-p)
 411   "Evaluate BODY in SESSION.
 412 If RESULT-TYPE equals `output' then return standard output as a
 413 string.  If RESULT-TYPE equals `value' then return the value of the
 414 last statement in BODY, as elisp."
 415   (case result-type
 416     (value
 417      (with-temp-buffer
 418        (insert (org-babel-chomp body))
 419        (let ((ess-local-process-name
 420               (process-name (get-buffer-process session)))
 421              (ess-eval-visibly-p nil))
 422          (ess-eval-buffer nil)))
 423      (let ((tmp-file (org-babel-temp-file "R-")))
 424        (org-babel-comint-eval-invisibly-and-wait-for-file
 425         session tmp-file
 426         (format org-babel-R-write-object-command
 427                 (if row-names-p "TRUE" "FALSE")
 428                 (if column-names-p
 429                     (if row-names-p "NA" "TRUE")
 430                   "FALSE")
 431                 ".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
 432        (org-babel-R-process-value-result
 433         (org-babel-result-cond result-params
 434           (with-temp-buffer
 435             (insert-file-contents tmp-file)
 436             (buffer-string))
 437           (org-babel-import-elisp-from-file tmp-file '(16)))
 438         column-names-p)))
 439     (output
 440      (mapconcat
 441       'org-babel-chomp
 442       (butlast
 443        (delq nil
 444              (mapcar
 445               (lambda (line) (when (> (length line) 0) line))
 446               (mapcar
 447                (lambda (line) ;; cleanup extra prompts left in output
 448                  (if (string-match
 449                       "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
 450                      (substring line (match-end 1))
 451                    line))
 452                (org-babel-comint-with-output (session org-babel-R-eoe-output)
 453                  (insert (mapconcat 'org-babel-chomp
 454                                     (list body org-babel-R-eoe-indicator)
 455                                     "\n"))
 456                  (inferior-ess-send-input)))))) "\n"))))
 457
 458 (defun org-babel-R-process-value-result (result column-names-p)
 459   "R-specific processing of return value.
 460 Insert hline if column names in output have been requested."
 461   (if column-names-p
 462       (cons (car result) (cons 'hline (cdr result)))
 463     result))
 464
 465 (provide 'ob-R)
 466
 467
 468
 469 ;;; ob-R.el ends here