BUGS-users:
I have made some major changes to the emacs mode for BUGS called ess-bugs-mode
which will become part of Emacs Speaks Statistics (ESS) -- emacs modes for
statistical packages like SAS, R/S/S+ and Stata. This is the final beta before
the next release of ESS which is imminent. Most of the changes have to do with
convenience and giving the user configuration options. A few of the changes
were mitigated by extension-collisions. .log is a very common extension and so
is .cmd; these were replaced by .bog and .bmd so emacs can properly assume a
BUGS relationship. I have added "substitution parameters":
One-time substitution (.bug):
%MODEL replaced by the .bug filename w/out directory or extension
%DATA replaced by the .bug filename with the extension replaced by .dat
%INITS replaced by the .bug filename with the extension replaced by .in
Every-time substitution (.bug):
#%N "N = [0-9]+; #%N" where [0-9]+ is replaced by the number of records
in the file referenced by the "data.*in" statement (probably only
useful with rectangular data files)
#%MONITOR a list of variables to be monitored terminated by a colon
#%STATS a list of variables to be summarized terminated by a colon
Every-time substitution (.bmd):
#%MONITOR.*#%MONITOR
everything between the pair is replaced by "monitor( )"
statements with the variables listed by #%MONITOR in .bug; if there is
no #%MONITOR in .bug, then it defaults to the "var" statement
#%STATS.*#%STATS
everything between the pair is replaced by "stats( )"
statements with the variables listed by #%STATS in .bug; if there is
no #%STATS in .bug, then it defaults to the #%MONITOR list of variables
Many variables are now user-configurable via Customize:
ess-bugs-batch-command path to "backbugs" script (attached)
ess-bugs-batch-pre-command "start" for DOS; "nohup" for Unix
ess-bugs-batch-post-command " " for DOS; "&" for Unix
ess-bugs-default-bins "32"; # of bins for Metropolis sampling
ess-bugs-default-burn-in "500"
ess-bugs-default-update "1000"
ess-bugs-default-checkpoint "100"
ess-bugs-inits-suffix ".in"
ess-bugs-data-suffix ".dat"
Currently, 'Next-Action' is defined as F12. If you are in a .bug buffer that is
empty; press F12 and a template .bug file is generated. Once you are through
editing .bug; press F12 again to save .bug and take you to a .bmd file. If the
.bmd file is empty, then a template .bmd is created. Either way, the
appropriate "substitution"'s are performed. When you are through editing .bmd;
press F12 to save and submit. I have tested this mode under XEmacs on Solaris
and Emacs on Windows 98 with BUGS 0.603. Due to differences between
XEmacs/Emacs and Unix/Windows, the file ess-emcs.el will also be necessary
(attached).
Lastly, a note on the new version of DECODA which creates SAS datasets from CODA
data files. The old version was self-contained and did not require other SAS
macros. This is no longer the case. You can get the necessary Open-source SAS
Macro Library at ftp://ftp.mcw.edu/pub/pcor/sasmacro or
http://www.mcw.edu/pcor/sasmacro.tar.Z or http://www.mcw.edu/pcor/sasmacro.zip
The old version, while a brilliant example of concise SAS Datastep coding, was
inefficient. The new version, which is more verbose, is very efficient due to
the internal implementation of SAS; reading times are now competitive with CODA
and BOA.
Rodney Sparapani Medical College of Wisconsin
Sr. Biostatistician Patient Care & Outcomes Research (PCOR)
[log in to unmask] 8701 Watertown Plank Rd., Rm. H2775
(414) 456-8786 (FAX: 6689) PO Box 26509, Milwaukee, WI 53226-0509
@echo off
if not "%3"=="" goto 30
if not "%2"=="" goto 20
if not "%1"=="" goto 10
echo usage: backbugs [[number_of_bins] default_output_name] command_file
goto 40
:10
bugs0603.exe 32 bugs %1
del bugs.buf
goto 40
:20
bugs0603.exe 32 %1 %2
del %1.buf
goto 40
:30
bugs0603.exe %1 %2 %3
del %2.buf
:40
;;; essl-bug.el -- ESS BUGS customization
;; Copyright (C) 2001 Rodney Sparapani
;; Author: Rodney Sparapani <[log in to unmask]>
;; Maintainer: A.J. Rossini <[log in to unmask]>
;; Created: 27 February 2001
;; Modified: $Date: 2001/07/27 18:12:14 $
;; Version: $Revision: 1.10 $
;; RCS: $Id: essl-bug.el,v 1.10 2001/07/27 18:12:14 ess Exp $
;; Keywords: BUGS, bugs, BACKBUGS, backbugs.
;; 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 'font-lock)
(require 'comint)
(require 'ess-emcs)
(if (assoc "\\.bug\\'" auto-mode-alist) nil
(setq auto-mode-alist
(append
'(("\\.bug\\'" . ess-bugs-mode)
("\\.BUG\\'" . ess-bugs-mode)
("\\.bmd\\'" . ess-bugs-mode)
("\\.BMD\\'" . ess-bugs-mode)
("\\.bog\\'" . ess-bugs-mode)
("\\.BOG\\'" . ess-bugs-mode)
)
auto-mode-alist)
)
)
(defcustom ess-bugs-batch-command
(convert-standard-filename (concat ess-lisp-directory "/../etc/" "backbugs"))
"ESS[BUGS]: Set to name and location of ESS \"backbugs\" script."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-batch-pre-command
(if (w32-shell-dos-semantics) "start" "nohup")
"ESS[BUGS]: Modifiers at the beginning of the backbugs command line."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-batch-post-command
(if (w32-shell-dos-semantics) " " "&")
"ESS[BUGS]: Modifiers at the end of the backbugs command line."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-default-bins "32"
"ESS[BUGS]: number of bins to use in the Griddy algorithm (Metropolis sampling)."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-default-burn-in "500"
"ESS[BUGS]: burn-in iterations to discard."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-default-update "1000"
"ESS[BUGS]: iterations to store."
: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-file "."
"ESS[BUGS]: BUGS file with PATH.")
(defvar ess-bugs-file-root "."
"ESS[BUGS]: Root of BUGS file.")
(defvar ess-bugs-file-suffix "."
"ESS[BUGS]: Suffix of BUGS file.")
(defvar ess-bugs-file-dir "."
"ESS[BUGS]: Directory of BUGS file.")
(defvar ess-bugs-file-data "."
"ESS[BUGS]: BUGS data file.")
(defcustom ess-bugs-inits-suffix ".in"
"ESS[BUGS]: BUGS init file suffix."
:group 'ess-bugs
:type 'string
)
(defcustom ess-bugs-data-suffix ".dat"
"ESS[BUGS]: BUGS data file suffix."
:group 'ess-bugs
:type 'string
)
(defvar ess-bugs-monitor-vars " "
"ESS[BUGS]: List of BUGS variables to be written out to a file.")
(defvar ess-bugs-stats-vars " "
"ESS[BUGS]: List of BUGS variables to be summarized with statistics.")
(defvar ess-bugs-mode-hook nil
"ESS[BUGS]: List of functions to call upon entering mode.")
(defvar ess-bugs-mode-map nil
"ESS[BUGS]: Keymap for mode.")
(if ess-bugs-mode-map nil
(setq ess-bugs-mode-map (make-keymap))
(define-key ess-bugs-mode-map [f2] 'ess-revert)
(define-key ess-bugs-mode-map [f12] 'ess-bugs-next-action)
)
(defvar ess-bugs-syntax-table nil
"ESS[BUGS]: Syntax table for mode.")
(if ess-bugs-syntax-table nil
(setq ess-bugs-syntax-table (make-syntax-table))
(modify-syntax-entry ?\\ "." ess-bugs-syntax-table)
(modify-syntax-entry ?# "<" ess-bugs-syntax-table)
(modify-syntax-entry ?\n ">" ess-bugs-syntax-table)
(modify-syntax-entry ?( "()" ess-bugs-syntax-table)
(modify-syntax-entry ?) ")(" ess-bugs-syntax-table)
(modify-syntax-entry ?. "w" ess-bugs-syntax-table)
)
(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\\>" font-lock-keyword-face)
(cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisq\\|"
"dexp\\|dirch\\|exp\\|gamma\\|lnorm\\|logis\\|"
"mnorm\\|multi\\|negbin\\|norm\\|par\\|pois\\|"
"t\\|unif\\|weib\\|wish\\)[ \t\n]*(")
font-lock-reference-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)
;; .dat files
;;(cons (concat "\\<\\(c\\|list\\)[ \t\n]*(")
;; font-lock-function-name-face)
)
"ESS[BUGS]: Font lock keywords."
)
(defun ess-bugs-file ()
"ESS[BUGS]: Set `ess-bugs-file', `ess-bugs-file-root', `ess-bugs-file-suffix'"
" and `ess-bugs-file-dir'."
(interactive)
(let ((ess-bugs-temp-string (buffer-name)))
(setq ess-bugs-file (expand-file-name ess-bugs-temp-string))
(setq ess-bugs-file-dir
(convert-standard-filename (file-name-directory ess-bugs-file)))
(setq ess-bugs-file-root
(file-name-nondirectory (file-name-sans-extension ess-bugs-file)))
(if (fboundp 'file-name-extension)
(setq ess-bugs-file-suffix (file-name-extension ess-bugs-temp-string))
;;else
(setq ess-bugs-temp-string (split-string ess-bugs-temp-string "[.]"))
(setq ess-bugs-file-suffix
(nth (- (length ess-bugs-temp-string) 1) ess-bugs-temp-string)))
(setq ess-bugs-file-suffix
(nth 0 (split-string (concat "." ess-bugs-file-suffix) "[<]")))
)
)
(defun ess-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 (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) (progn
(insert (concat "compile(\"" ess-bugs-file-dir ess-bugs-file-root ".bug\")\n"))
(insert (concat "save(\"" ess-bugs-file-dir ess-bugs-file-root ".in0\")\n"))
(insert (concat "update(" ess-bugs-default-burn-in ")\n"))
(insert (concat "save(\"" ess-bugs-file-dir ess-bugs-file-root ".in1\")\n"))
(insert "#%MONITOR\n\n#%MONITOR\n")
(insert (concat "checkpoint(" ess-bugs-default-checkpoint ")\n"))
(insert (concat "update(" ess-bugs-default-update ")\n"))
(insert (concat "save(\"" ess-bugs-file-dir ess-bugs-file-root ".in2\")\n"))
(insert "#%STATS\n\n#%STATS\n")
(insert "q(\"" ess-bugs-file-dir ess-bugs-file-root ".bog\")\n")
))
))
)
(defun ess-exit-notify-sh (string)
"Detect completion or failure of submitted job and notify the user."
(let* ((exit-done "\\[[0-9]+\\]\\ *\\+*\\ *\\(Exit\\|Done\\).*$")
(beg (string-match exit-done string)))
(if beg
(message (substring string beg (match-end 0))))))
(defun ess-revert ()
"ESS: Revert from disk if file and buffer modification times are different."
(interactive)
(if (not(verify-visited-file-modtime (current-buffer)))
(revert-buffer t t)))
(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 " "
ess-bugs-default-bins " " ess-bugs-file-root " " ess-bugs-file " "
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-switch-to-suffix ".bug")
(save-excursion
(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 ess-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))))
(if (search-forward "%INITS" nil t)
(replace-match
(concat ess-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))
(goto-char (point-min))
(if (search-forward "%MONITOR" 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
"[, \t\n#]+\\([a-zA-Z0-9.]+\\)\\(\\(\\[\\)[a-zA-Z0-9]*\\(\\]\\)\\)?"
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) ")\n"))
)
(setq ess-bugs-monitor-vars
(concat "#%MONITOR\n" ess-bugs-monitor-vars "#%MONITOR\n"))
(goto-char (point-min))
(if (search-forward "%STATS" 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
"[, \t\n#]+\\([a-zA-Z0-9.]+\\)\\(\\(\\[\\)[a-zA-Z0-9]*\\(\\]\\)\\)?"
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) ")\n"))
)
(setq ess-bugs-stats-vars (concat "#%STATS\n" ess-bugs-stats-vars "#%STATS\n"))
)
;; replace-in-string may not be available, work-around necessary; see below
;; (setq ess-bugs-stats-vars
;; (replace-in-string ess-bugs-monitor-vars "#%MONITOR" "#%STATS"))
;; (setq ess-bugs-stats-vars
;; (replace-in-string ess-bugs-stats-vars "monitor" "stats" t))
;;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-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))
(run-hooks 'ess-bugs-mode-hook)
(if (not (w32-shell-dos-semantics))
(add-hook 'comint-output-filter-functions 'ess-exit-notify-sh))
)
(provide 'essl-bug)
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