您最多选择25个主题
主题必须以字母或数字开头，可以包含连字符 (-)，并且长度不得超过35个字符
254 行
14 KiB
254 行
14 KiB
;;; 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
|