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|
;;; ess-bugs-d.el -- ESS[BUGS] dialect
;; Copyright (C) 2008-2009 Rodney Sparapani
;; Original Author: Rodney Sparapani
;; Created: 13 March 2008
;; Maintainers: ESS-help <ess-help@stat.math.ethz.ch>
;; This file is part of ESS
;; This file 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 2, or (at your option)
;; any later version.
;;
;; This file 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; see the file COPYING. If not, write to
;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
;;
;; In short: you may use this code any way you like, as long as you
;; don't charge money for it, remove this notice, or hold anyone liable
;; for its results.
;; Code:
(require 'ess-bugs-l)
(setq auto-mode-alist
(delete '("\\.[bB][uU][gG]\\'" . ess-jags-mode) auto-mode-alist))
(setq auto-mode-alist
(append '(("\\.[bB][uU][gG]\\'" . ess-bugs-mode)) auto-mode-alist))
(defcustom ess-bugs-batch-version "0.6"
"ESS[BUGS]: Major version of BUGS, i.e. 0.6 or 0.5"
:group 'ess-bugs
:type 'string
)
(setq ess-bugs-batch-command
(if (equal ess-bugs-batch-version "0.5") "backbug5" "backbugs"))
(defcustom ess-bugs-default-bins "32"
"ESS[BUGS]: Number of bins for the Griddy algorithm (Metropolis sampling)."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-default-checkpoint "100"
"ESS[BUGS]: Make a snapshot every this many iterations."
:group 'ess-bugs
:type 'string
)
(defvar ess-bugs-font-lock-keywords
(list
;; .bug files
(cons "#.*\n" font-lock-comment-face)
(cons "^[ \t]*\\(model\\|const\\|data\\|inits\\|var\\)\\>"
font-lock-keyword-face)
(cons "\\<in[ \t]+[1-9]\\>" font-lock-keyword-face)
(cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisqr\\|"
"dexp\\|dirch\\|exp\\|gamma\\|lnorm\\|logis\\|"
"mnorm\\|multi\\|negbin\\|norm\\|par\\|pois\\|"
"t\\|unif\\|weib\\|wish\\)[ \t\n]*(")
font-lock-constant-face)
(cons (concat "\\<\\(for\\|cloglog\\|equals\\|exp\\|inprod\\|"
"inverse\\|log\\(det\\|fact\\|gam\\|it\\)?\\|max\\|"
"mean\\|min\\|phi\\|pow\\|probit\\|sd\\|sqrt\\|"
"step\\|sum\\|I\\)[ \t\n]*(")
font-lock-function-name-face)
;; .bmd files
(cons (concat "\\<\\(clear\\|checkpoint\\|compile\\|data\\|"
"diag\\|help\\|inits\\|iter\\|model\\|monitor\\|"
"out\\|q\\|save\\|stats\\|update\\)[ \t\n]*(")
font-lock-function-name-face)
)
"ESS[BUGS]: Font lock keywords."
)
(defun ess-bugs-switch-to-suffix (suffix)
"ESS: Switch to file with suffix."
(find-file (concat ess-bugs-file-dir ess-bugs-file-root suffix))
(if (equal 0 (buffer-size)) (progn
(if (equal ".bug" suffix) (progn
(insert (concat "model %MODEL;\n"))
(insert (concat "const N = 0;#%N\n"))
(insert "var ;\n")
(insert "#%MONITOR;\n")
(insert "#%STATS;\n")
(insert (concat "data in \"%DATA\";\n"))
(insert (concat "inits in \"%INITS\";\n"))
(insert "{\n")
(insert " for (i in 1:N) {\n \n")
(insert " }\n")
(insert "}\n")
))
(if (equal ".bmd" suffix) (let
((tmp-bugs-file-dir (if (equal ess-bugs-batch-version "0.6") ess-bugs-file-dir)))
(insert (concat "compile(\"" tmp-bugs-file-dir ess-bugs-file-root ".bug\")\n"))
(insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in0\")\n"))
(insert (concat "update(" ess-bugs-default-burn-in ")\n"))
(insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in1\")\n"))
(insert "#%MONITOR\n\n#%MONITOR\n")
(if (equal ess-bugs-batch-version "0.6")
(insert (concat "checkpoint(" ess-bugs-default-checkpoint ")\n")))
(insert (concat "update(" ess-bugs-default-update ")\n"))
(insert (concat "save(\"" tmp-bugs-file-dir ess-bugs-file-root ".in2\")\n"))
(insert "#%STATS\n\n#%STATS\n")
(insert "q()\n")
;;(insert "q(\"" ess-bugs-file-dir ess-bugs-file-root ".bog\")\n")
))
))
)
(defun ess-bugs-next-action ()
"ESS[BUGS]: Perform the appropriate next action."
(interactive)
(ess-bugs-file)
(if (equal ".bug" ess-bugs-file-suffix) (ess-bugs-na-bug))
;;else
(if (equal ".bmd" ess-bugs-file-suffix) (ess-bugs-na-bmd))
)
(defun ess-bugs-na-bmd ()
"ESS[BUGS]: Perform the Next-Action for .bmd."
(save-buffer)
(shell)
(if (w32-shell-dos-semantics)
(if (string-equal ":" (substring ess-bugs-file 1 2))
(progn
(insert (substring ess-bugs-file 0 2))
(comint-send-input)
)
)
)
(insert (concat "cd \"" ess-bugs-file-dir "\""))
(comint-send-input)
(insert (concat ess-bugs-batch-pre-command " " ess-bugs-batch-command " "
(if (equal ess-bugs-batch-version "0.6") ess-bugs-default-bins)
" " ess-bugs-file-root " "
(if (equal ess-bugs-batch-version "0.6")
ess-bugs-file (concat ess-bugs-file-root ".bmd"))
" " ess-bugs-batch-post-command))
(comint-send-input)
)
(defun ess-bugs-na-bug ()
"ESS[BUGS]: Perform Next-Action for .bug"
(if (equal 0 (buffer-size)) (ess-bugs-switch-to-suffix ".bug")
(save-excursion (let
((tmp-bugs-file-dir (if (equal ess-bugs-batch-version "0.6") ess-bugs-file-dir)))
(goto-char (point-min))
(if (search-forward "%MODEL" nil t)
(replace-match ess-bugs-file-root t t))
(if (search-forward "%DATA" nil t) (progn
(setq ess-bugs-file-data
(concat tmp-bugs-file-dir ess-bugs-file-root ess-bugs-data-suffix))
(replace-match ess-bugs-file-data t t))
;;else
(if (search-forward-regexp "data.+in[ \t\n]+\"\\(.*\\)\"" nil t)
(setq ess-bugs-file-data (match-string 1))
;;else
(setq ess-bugs-file-data "...")
))
(if (search-forward "%INITS" nil t)
(replace-match
(concat tmp-bugs-file-dir ess-bugs-file-root ess-bugs-inits-suffix) t t))
(let ((ess-bugs-temp-string " ")
(ess-bugs-buffer-ptr nil))
(goto-char (point-min))
(if (search-forward-regexp
"N[ \t]*=[ \t]*[0-9]+[ \t]*;[ \t]*#[ \t]*%N" nil t) (progn
(save-excursion (save-match-data
(setq ess-bugs-buffer-ptr (find-buffer-visiting ess-bugs-file-data))
(if ess-bugs-buffer-ptr (set-buffer ess-bugs-buffer-ptr)
(set-buffer (create-file-buffer ess-bugs-file-data))
(insert-file-contents ess-bugs-file-data t))
(setq ess-bugs-temp-string
(concat "N = "
(int-to-string (count-lines (point-min) (point-max))) ";#%N"))
))
(replace-match ess-bugs-temp-string t t)
))
)
(let (
(ess-bugs-search-min nil)
(ess-bugs-search-max nil)
(ess-bugs-search-vars
"\\([a-zA-Z0-9.]+\\)\\(\\(\\[\\)[a-zA-Z0-9]*\\(,\\)?[a-zA-Z0-9]*\\(\\]\\)\\)?[ \t]*[,]?[ \t]*\\(#.*\\)?[\n]?"
))
(goto-char (point-min))
(if (search-forward-regexp "%MONITOR[ \t]+" nil t)
(setq ess-bugs-search-min (point))
;;else
(setq ess-bugs-search-min (search-forward "var"))
)
(setq ess-bugs-search-max (search-forward-regexp ";"))
(goto-char ess-bugs-search-min)
(setq ess-bugs-monitor-vars "")
(while (search-forward-regexp ess-bugs-search-vars ess-bugs-search-max t)
(setq ess-bugs-monitor-vars
(concat ess-bugs-monitor-vars "monitor("
(match-string 1) (match-string 3) (match-string 4) (match-string 5) ")\n"))
)
(setq ess-bugs-monitor-vars
(concat "#%MONITOR\n" ess-bugs-monitor-vars "#%MONITOR\n"))
(goto-char (point-min))
(if (search-forward-regexp "%STATS[ \t]+" nil t) (progn
(setq ess-bugs-search-min (point))
(setq ess-bugs-search-max (search-forward-regexp ";"))
(goto-char ess-bugs-search-min)
(setq ess-bugs-stats-vars "")
(while (search-forward-regexp ess-bugs-search-vars ess-bugs-search-max t)
(setq ess-bugs-stats-vars
(concat ess-bugs-stats-vars "stats("
(match-string 1) (match-string 3) (match-string 4) (match-string 5) ")\n"))
)
(setq ess-bugs-stats-vars (concat "#%STATS\n" ess-bugs-stats-vars "#%STATS\n"))
)
;;else
(setq ess-bugs-stats-vars ess-bugs-monitor-vars)
(while (string-match "#%MONITOR" ess-bugs-stats-vars)
(setq ess-bugs-stats-vars
(replace-match "#%STATS" t t ess-bugs-stats-vars)))
(while (string-match "monitor" ess-bugs-stats-vars)
(setq ess-bugs-stats-vars
(replace-match "stats" t t ess-bugs-stats-vars)))
)
)
))
(save-buffer)
(ess-bugs-switch-to-suffix ".bmd")
(save-excursion
(goto-char (point-min))
(if (search-forward-regexp "#%MONITOR\\(.\\|\n\\)*#%MONITOR\n" nil t)
(replace-match ess-bugs-monitor-vars t))
(if (search-forward-regexp "#%STATS\\(.\\|\n\\)*#%STATS\n" nil t)
(replace-match ess-bugs-stats-vars t))
)
)
)
(defun ess-bugs-mode ()
"ESS[BUGS]: Major mode for Classic BUGS."
(interactive)
(kill-all-local-variables)
(setq major-mode 'ess-bugs-mode)
(setq mode-name "ESS[BUGS]")
(use-local-map ess-bugs-mode-map)
(setq font-lock-auto-fontify t)
(make-local-variable 'font-lock-defaults)
(setq font-lock-defaults '(ess-bugs-font-lock-keywords nil t))
;; SJE: Basic comment functionality.
(setq comment-start "#")
(run-hooks 'ess-bugs-mode-hook)
(if (not (w32-shell-dos-semantics))
(add-hook 'comint-output-filter-functions 'ess-bugs-exit-notify-sh))
)
(setq features (delete 'ess-jags-d features))
(provide 'ess-bugs-d)
|
