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- ;;; ess-jags-d.el --- ESS[JAGS] dialect -*- lexical-binding: t; -*-
-
- ;; Copyright (C) 2008-2011 Rodney Sparapani
-
- ;; Author: Rodney Sparapani
- ;; Created: 13 March 2008
- ;; Maintainer: ESS-help <ess-help@r-project.org>
-
- ;; 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.
- ;;
- ;; A copy of the GNU General Public License is available at
- ;; https://www.r-project.org/Licenses/
-
- ;;; Code:
-
- (require 'ess-bugs-d)
- (require 'ess-utils)
- (require 'ess-inf)
- (require 'ess-mode)
-
- (defvar ess-jags-command "jags" "Default JAGS program in PATH.")
- (make-local-variable 'ess-jags-command)
-
- (defvar ess-jags-monitor '("") "Default list of variables to monitor.")
- (make-local-variable 'ess-jags-monitor)
-
- (defvar ess-jags-thin 1 "Default thinning parameter.")
- (make-local-variable 'ess-jags-thin)
-
- (defvar ess-jags-chains 1 "Default number of chains.")
- (make-local-variable 'ess-jags-chains)
-
- (defvar ess-jags-burnin 10000 "Default burn-in.")
- (make-local-variable 'ess-jags-burnin)
-
- (defvar ess-jags-update 10000 "Default number of updates after burnin.")
- (make-local-variable 'ess-jags-update)
-
- (defvar ess-jags-system t "Default whether JAGS recognizes the system command.")
-
- (defvar ess-jags-font-lock-keywords
- (list
- ;; .jag files
- (cons "#.*\n" font-lock-comment-face)
-
- (cons "^[ \t]*\\(model\\|var\\)\\>"
- font-lock-keyword-face)
-
- (cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisq\\|"
- "dexp\\|dirch\\|exp\\|\\(gen[.]\\)?gamma\\|hyper\\|"
- "interval\\|lnorm\\|logis\\|mnorm\\|mt\\|multi\\|"
- "negbin\\|norm\\(mix\\)?\\|par\\|pois\\|sum\\|t\\|"
- "unif\\|weib\\|wish\\)[ \t\n]*(")
- font-lock-constant-face)
-
- (cons (concat "\\<\\(abs\\|cos\\|dim\\|\\(i\\)?cloglog\\|equals\\|"
- "exp\\|for\\|inprod\\|interp[.]line\\|inverse\\|length\\|"
- "\\(i\\)?logit\\|logdet\\|logfact\\|loggam\\|max\\|mean\\|"
- "mexp\\|min\\|phi\\|pow\\|probit\\|prod\\|rank\\|round\\|"
- "sd\\|sin\\|sort\\|sqrt\\|step\\|sum\\|t\\|trunc\\|T\\)[ \t\n]*(")
- font-lock-function-name-face)
-
- ;; .jmd files
- (cons (concat "\\<\\(adapt\\|cd\\|clear\\|coda\\|data\\|dir\\|"
- "exit\\|in\\(itialize\\)?\\|load\\|model\\|monitors\\|parameters\\|"
- "pwd\\|run\\|s\\(amplers\\|ystem\\)\\|to\\|update\\)[ \t\n]")
- font-lock-keyword-face)
-
- (cons "\\<\\(compile\\|monitor\\)[, \t\n]"
- font-lock-keyword-face)
-
- (cons "[, \t\n]\\(by\\|chain\\|nchains\\|stem\\|thin\\|type\\)[ \t\n]*("
- font-lock-function-name-face)
- )
- "ESS[JAGS]: Font lock keywords."
- )
-
- (defun ess-jags-switch-to-suffix (suffix &optional jags-chains jags-monitor jags-thin
- jags-burnin jags-update)
- "ESS[JAGS]: 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 ".jag" suffix) (progn
- (insert "var ;\n")
- (insert "model {\n")
- (insert " for (i in 1:N) {\n \n")
- (insert " }\n")
- (insert "}\n")
- (insert "#Local Variables" ":\n")
- (insert "#ess-jags-chains:1\n")
- (insert "#ess-jags-monitor:(\"\")\n")
- (insert "#ess-jags-thin:1\n")
- (insert "#ess-jags-burnin:10000\n")
- (insert "#ess-jags-update:10000\n")
- (insert "#End:\n")
- ))
-
- (if (equal ".jmd" suffix) (let
- ((ess-jags-temp-chains "") (ess-jags-temp-monitor "") (ess-jags-temp-chain ""))
-
- (if jags-chains (setq ess-jags-chains jags-chains))
- (if jags-monitor (setq ess-jags-monitor jags-monitor))
- (if jags-thin (setq ess-jags-thin jags-thin))
-
- (setq ess-jags-temp-chains
- (concat "compile, nchains(" (format "%d" ess-jags-chains) ")\n"))
-
- (setq jags-chains ess-jags-chains)
-
- (while (< 0 jags-chains)
- (setq ess-jags-temp-chains
- (concat ess-jags-temp-chains
- "parameters ## \"" ess-bugs-file-root
- ".##" (format "%d" jags-chains) "\", chain("
- (format "%d" jags-chains) ")\n"))
- (setq jags-chains (- jags-chains 1)))
-
- (setq ess-jags-temp-monitor "")
-
- (while (and (listp ess-jags-monitor) (consp ess-jags-monitor))
- (if (not (string-equal "" (car ess-jags-monitor)))
- (setq ess-jags-temp-monitor
- (concat ess-jags-temp-monitor "monitor "
- (car ess-jags-monitor) ", thin(" (format "%d" ess-jags-thin) ")\n")))
- (setq ess-jags-monitor (cdr ess-jags-monitor)))
-
- (insert "model in \"" ess-bugs-file-root ".jag\"\n")
- (insert "data in \"" ess-bugs-file-root ".jdt\"\n")
- (insert (ess-replace-in-string ess-jags-temp-chains "##" "in"))
- (insert "initialize\n")
- ;(insert "update " (format "%d" (* jags-thin jags-burnin)) "\n")
- (insert "update " (format "%d" jags-burnin) "\n")
- (insert ess-jags-temp-monitor)
- (insert "update " (format "%d" (* jags-thin jags-update)) "\n")
- (insert (ess-replace-in-string
- (ess-replace-in-string ess-jags-temp-chains
- "compile, nchains([0-9]+)" "#") "##" "to"))
- (insert "coda "
- ;(if ess-microsoft-p (if (w32-shell-dos-semantics) "*" "\\*") "\\*")
- "*, stem(\"" ess-bugs-file-root "\")\n")
-
- (if ess-jags-system (progn
- (insert "system rm -f " ess-bugs-file-root ".ind\n")
- (insert "system ln -s " ess-bugs-file-root "index.txt " ess-bugs-file-root ".ind\n")
-
- (setq jags-chains ess-jags-chains)
-
- (while (< 0 jags-chains)
- (setq ess-jags-temp-chain (format "%d" jags-chains))
-
- ;.txt not recognized by BOA and impractical to over-ride
- (insert "system rm -f " ess-bugs-file-root ess-jags-temp-chain ".out\n")
- (insert "system ln -s " ess-bugs-file-root "chain" ess-jags-temp-chain ".txt "
- ess-bugs-file-root ess-jags-temp-chain ".out\n")
- (setq jags-chains (- jags-chains 1)))))
-
- (insert "exit\n")
- (insert "Local Variables" ":\n")
- (insert "ess-jags-chains:" (format "%d" ess-jags-chains) "\n")
- (insert "ess-jags-command:\"jags\"\n")
- (insert "End:\n")
- ))
- ))
- )
-
- (defun ess-jags-na-jmd (jags-command)
- "ESS[JAGS]: Perform the Next-Action for .jmd."
- ;(ess-save-and-set-local-variables)
- (if (equal 0 (buffer-size)) (ess-jags-switch-to-suffix ".jmd")
- ;else
- (shell)
- (ess-sleep)
-
- (if (when (fboundp 'w32-shell-dos-semantics)
- (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 "cd \"" ess-bugs-file-dir "\"")
- (comint-send-input)
-
- ; (let ((ess-jags-temp-chains ""))
- ;
- ; (while (< 0 jags-chains)
- ; (setq ess-jags-temp-chains
- ; (concat (format "%d " jags-chains) ess-jags-temp-chains))
- ; (setq jags-chains (- jags-chains 1)))
-
- (insert ess-bugs-batch-pre-command " " jags-command " "
- ess-bugs-file-root ".jmd "
-
- (if (or (equal shell-file-name "/bin/csh")
- (equal shell-file-name "/bin/tcsh")
- (equal shell-file-name "/bin/zsh")
- (equal shell-file-name "/bin/bash"))
- (concat ">& " ess-bugs-file-root ".jog ")
- ;else
- "> " ess-bugs-file-root ".jog 2>&1 ")
-
- ; ;.txt not recognized by BOA and impractical to over-ride
- ; "&& (rm -f " ess-bugs-file-root ".ind; "
- ; "ln -s " ess-bugs-file-root "index.txt " ess-bugs-file-root ".ind; "
- ; "for i in " ess-jags-temp-chains "; do; "
- ; "rm -f " ess-bugs-file-root "$i.out; "
- ; "ln -s " ess-bugs-file-root "chain$i.txt " ess-bugs-file-root "$i.out; done) "
-
- ess-bugs-batch-post-command)
-
- (comint-send-input)
- ))
-
- (defun ess-jags-na-bug ()
- "ESS[JAGS]: Perform Next-Action for .jag"
-
- (if (equal 0 (buffer-size)) (ess-jags-switch-to-suffix ".jag")
- ;else
- (ess-save-and-set-local-variables)
- (ess-jags-switch-to-suffix ".jmd"
- ess-jags-chains ess-jags-monitor ess-jags-thin ess-jags-burnin ess-jags-update))
- )
-
- ;;;###autoload
- (define-derived-mode ess-jags-mode ess-bugs-mode "ESS[JAGS]"
- "Major mode for JAGS."
- (setq-local comment-start "#")
- (setq font-lock-defaults '(ess-jags-font-lock-keywords nil t))
- (setq ess-language "S") ; mimic S for ess-smart-underscore
- (unless (and (fboundp 'w32-shell-dos-semantics)
- (w32-shell-dos-semantics))
- (add-hook 'comint-output-filter-functions 'ess-bugs-exit-notify-sh))
- )
-
- ;;;###autoload
- (add-to-list 'auto-mode-alist '("\\.[Jj][Aa][Gg]\\'" . ess-jags-mode))
-
- (provide 'ess-jags-d)
-
- ;;; ess-jags-d.el ends here
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