Thread: [Bugs-r-devel] SF.net SVN: bugs-r:[161] trunk/R2OpenBUGS

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Revision: 161
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=161&view=rev
Author:   snthomas99
Date:     2010-08-06 14:07:38 +0000 (Fri, 06 Aug 2010)

Log Message:
-----------
updates to documentation and some bug fixes

Modified Paths:
--------------
    trunk/R2OpenBUGS/DESCRIPTION
    trunk/R2OpenBUGS/NAMESPACE
    trunk/R2OpenBUGS/R/bugs.R
    trunk/R2OpenBUGS/R/bugs.script.R
    trunk/R2OpenBUGS/man/R2WinBUGS-package.Rd
    trunk/R2OpenBUGS/man/bugs.Rd
    trunk/R2OpenBUGS/man/bugs.run.Rd
    trunk/R2OpenBUGS/man/bugs.script.Rd

Removed Paths:
-------------
    trunk/R2OpenBUGS/R/openbugs.R
    trunk/R2OpenBUGS/man/openbugs.Rd

Modified: trunk/R2OpenBUGS/DESCRIPTION
===================================================================

--- trunk/R2OpenBUGS/DESCRIPTION	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/DESCRIPTION	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,21 +1,19 @@
-Package: R2WinBUGS
-Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2010-03-18
-Version: 2.1-17
-Author: originally written by Andrew Gelman <ge...@st...>;
+Package: R2OpenBUGS
+Title: Running OpenBUGS from R / S-PLUS
+Date: 2010-08-5
+Version: 1.0-0
+Author: originally written as R2WinBUGS by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.
  With considerable contributions by Gregor Gorjanc <gre...@bf...>
  and Jouni Kerman <ke...@st...>.
- Ported to S-PLUS by Insightful Corp.
+ Ported to S-PLUS by Insightful Corp.  Adapted to R2OpenBUGS from R2WinBUGS by Neal Thomas.
 Description: Using this package,
  it is possible to call a BUGS model, summarize inferences and
  convergence in a table and graph, and save the simulations in arrays for easy access
- in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
- functionality is not yet available.
-Depends: R (>= 2.5.0), coda (>= 0.11-0)
-Suggests: BRugs (>= 0.3-2)
-SystemRequirements: WinBUGS 1.4
+ in R / S-PLUS. 
+Depends: R (>= 2.9.2), coda (>= 0.11-0)
+SystemRequirements: OpenBUGS >=3.1
 URL: http://www.stat.columbia.edu/~gelman/bugsR/
 Maintainer: Uwe Ligges <li...@st...>
 License: GPL-2

Modified: trunk/R2OpenBUGS/NAMESPACE
===================================================================
--- trunk/R2OpenBUGS/NAMESPACE	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/NAMESPACE	2010-08-06 14:07:38 UTC (rev 161)
@@ -9,7 +9,6 @@
        read.bugs,
        bugs.log,
        monitor,
-       openbugs,
        as.bugs.array,
        write.model)
 

Modified: trunk/R2OpenBUGS/R/bugs.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.R	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/R/bugs.R	2010-08-06 14:07:38 UTC (rev 161)
@@ -17,15 +17,16 @@
   if(.Platform$OS.type != "windows" & useWINE==FALSE){
     if(debug)stop("The debug option is not available with linux/unix")
     if(save.history)("History plots (save.history) is not available with linux/unix")
-  }else{
-    if(!file.exists(OpenBUGS.pgm))
-      stop("OpenBUGS executable was not found" )
   }
 
   if (missing(OpenBUGS.pgm) && 
         !is.null(bugs.pgm <- getOption("R2OpenBUGS.pgm"))) { # requested by Jouni Kerman
       OpenBUGS.pgm<- bugs.pgm
   }
+
+    if((.Platform$OS.type == "windows" | useWINE) & !file.exists(OpenBUGS.pgm))
+      stop("OpenBUGS executable was not found" )
+
   ## Is OpenBUGS.pgm defined in Windows (where second character is :
   ## i.e. C:\Program...) or Unix style path?
   if(useWINE && (substr(OpenBUGS.pgm, 2, 2) == ":")) {

Modified: trunk/R2OpenBUGS/R/bugs.script.R
===================================================================
--- trunk/R2OpenBUGS/R/bugs.script.R	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/R/bugs.script.R	2010-08-06 14:07:38 UTC (rev 161)
@@ -36,7 +36,7 @@
     function(x, useWINE, newWINE, WINEPATH) 
     {native2win(x, useWINE=useWINE, newWINE=newWINE, WINEPATH=WINEPATH)})
 
-  initlist <- paste("modelInits(", 1:n.chains, ", '", inits, "')\n", sep="")
+  initlist <- paste("modelInits(", "'", inits, "',",1:n.chains,")\n", sep="")
 
   savelist <- paste("samplesSet(", parameters.to.save, ")\n", sep="")
   summarylist <- paste("summarySet(", parameters.to.save, ")\n", sep="")

Deleted: trunk/R2OpenBUGS/R/openbugs.R
===================================================================
--- trunk/R2OpenBUGS/R/openbugs.R	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/R/openbugs.R	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,114 +0,0 @@
-openbugs <- function(data, inits, parameters.to.save, model.file="model.txt",
-  n.chains = 3, n.iter = 2000, n.burnin = floor(n.iter/2),
-  n.thin = max(1, floor(n.chains *(n.iter - n.burnin) / n.sims)), n.sims = 1000,
-  DIC = TRUE, bugs.directory = "c:/Program Files/OpenBUGS/",
-  working.directory=NULL, digits = 5, over.relax = FALSE, seed=NULL)
-{
-  if(!is.R())
-    stop("OpenBUGS is not yet available in S-PLUS")
-  if(!require("BRugs"))
-    stop("BRugs is required")
-
-  ## switching from bugs() to BRugsFit() notation
-  modelFile <- model.file
-  numChains <- n.chains
-  nBurnin <- n.burnin
-  nIter <- n.iter - n.burnin
-  nThin <- n.thin
-  if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
-  parametersToSave <- parameters.to.save
-
-  ## Move to working drirectory or temporary directory when NULL
-  if(is.null(working.directory)) {
-    working.directory <- tempdir()
-    inTempDir <- TRUE
-  }
-  savedWD <- getwd()
-  setwd(working.directory)
-  on.exit(setwd(savedWD))
-
-  if(inTempDir && basename(model.file) == model.file)
-    try(file.copy(file.path(savedWD, model.file), model.file, overwrite = TRUE))
-  if(!file.exists(modelFile)) {
-    stop(modelFile, " does not exist")
-  }
-  if(file.info(modelFile)$isdir) {
-    stop(modelFile, " is a directory, but a file is required")
-  }
-  ## kludge to add carriage-returns (line-feeds?) to the model file
-  if(!length(grep("\r\n", readChar(modelFile, 10^3)))) {
-    message("Carriage returns added to model file ", modelFile)
-    model <- readLines(modelFile)
-    try(writeLines(model, modelFile))
-  }
-  BRugs::modelCheck(modelFile)
-  if(!(is.vector(data) && is.character(data) && all(file.exists(data)))) {
-    data <- BRugs::bugsData(data, digits = digits)
-  }
-  if(inTempDir && all(basename(data) == data))
-    try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
-  BRugs::modelData(data)
-  BRugs::modelCompile(numChains)
-  if(!is.null(seed)) BRugs::modelSetRN(seed)
-  if(missing(inits) || is.null(inits)) {
-    BRugs::modelGenInits()
-  } else {
-    if(is.list(inits) || is.function(inits) || (is.character(inits) &&
-      !any(file.exists(inits)))) {
-      inits <- BRugs::bugsInits(inits = inits, numChains = numChains,
-                                digits = digits)
-    }
-    if(inTempDir && all(basename(inits) == inits))
-        try(file.copy(file.path(savedWD, inits), inits, overwrite = TRUE))
-    BRugs::modelInits(inits)
-    BRugs::modelGenInits()
-  }
-  BRugs::samplesSetThin(nThin)
-  ## set the adaptive phases
-
-## We do no longer have any Registry.txt file availabe,
-## hence not resetting the adaptive phase any more.
-## People should move to BRugs directly.
-#  adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
-#                                    "Registry.txt", package="BRugs"),
-#                        what="character", quiet = TRUE)
-#  factories <- sub(".adaptivePhase", "",
-#                   adaptivelines[grep("adaptivePhase",adaptivelines)])
-#  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
-  if(getOption("BRugsVerbose")){
-    cat("Sampling has been started ...\n")
-    flush.console()
-  }
-  BRugs::modelUpdate(nBurnin, overRelax = over.relax)
-  ## BRugs::samplesSetThin(nThin)
-  if(DIC) {
-    BRugs::dicSet()
-    on.exit(BRugs::dicClear(), add = TRUE)
-  }
-  BRugs::samplesSet(parametersToSave)
-  BRugs::modelUpdate(nIter, overRelax = over.relax)
-  params <- sort.name(BRugs::samplesMonitors("*"), parametersToSave)
-  samples <- sapply(params, BRugs::samplesSample)
-  n.saved.per.chain <- nrow(samples)/numChains
-  samples.array <- array(samples, c(n.saved.per.chain, numChains, ncol(samples)))
-  dimnames(samples.array)[[3]] <- dimnames(samples)[[2]]
-  if(DIC) {
-    DICOutput <- BRugs::dicStats()
-  } else {
-    DICOutput <- NULL
-  }
-  bugs.output <- as.bugs.array(sims.array=samples.array,
-                               model.file=modelFile, program="OpenBUGS",
-                               DIC=DIC, DICOutput=DICOutput,
-                               n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin)
-  bugs.output
-}
-
-## sorter called by openbugs() to save the parameters in the specified order
-sort.name <- function(a, b){
-  ## sort the scalar parameter names in the vector "a" according to the
-  ## ordering of their stems in the shorter vector "b"
-  bracket.pos <- regexpr("\\[", a)
-  a.stem <- substr(a, 1, ifelse(bracket.pos>0, bracket.pos-1, nchar(a)))
-  a[order(match(a.stem, b))]
-}

Modified: trunk/R2OpenBUGS/man/R2WinBUGS-package.Rd
===================================================================
--- trunk/R2OpenBUGS/man/R2WinBUGS-package.Rd	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/man/R2WinBUGS-package.Rd	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,37 +1,35 @@
-\name{R2WinBUGS-package}
-\alias{R2WinBUGS-package}
-\alias{R2WinBUGS}
+\name{R2OpenBUGS-package}
+\alias{R2OpenBUGS-package}
+\alias{R2OpenBUGS}
 
 \docType{package}
 
-\title{Running WinBUGS and OpenBUGS from R / S-PLUS}
+\title{Running OpenBUGS from R / S-PLUS}
 
 \description{
 
-\pkg{R2WinBUGS} package provides possiblity to call a \pkg{BUGS} model,
+\pkg{R2OpenBUGS} Call a \pkg{BUGS} model,
 summarize inferences and convergence in a table and graph, and save the
-simulations in arrays for easy access in \R / S-PLUS. In S-PLUS, the
-\pkg{OpenBUGS} functionality and the windows emulation functionality is
-not yet available. The main command is \code{\link{bugs}}.
+simulations in arrays for easy access in \R / S-PLUS.  The main command is \code{\link{bugs}}.
 
 }
 
 \details{
 
-The following are sources of information on \pkg{R2WinBUGS} package:
+The following are sources of information on \pkg{R2OpenBUGS} package:
 \tabular{ll}{
-  DESCRIPTION file\tab \code{library(help="R2WinBUGS")}\cr
+  DESCRIPTION file\tab \code{library(help="R2OpenBUGS")}\cr
   \tab \cr
-  This file\tab        \code{package?R2WinBUGS}\cr
+  This file\tab        \code{package?R2OpenBUGS}\cr
   \tab \cr
-  Vignette\tab         \code{vignette("R2WinBUGS")}\cr
+  Vignette\tab         \code{vignette("R2OpenBUGS")}\cr
   \tab \cr
   Some help files\tab  \code{\link{bugs}}\cr
   \tab                 \code{\link{write.model}}\cr
   \tab                 \code{\link{print.bugs}}\cr
   \tab                 \code{\link{plot.bugs}}\cr
   \tab \cr
-  News\tab             \code{file.show(system.file("NEWS", package="R2WinBUGS"))}\cr
+  News\tab             \code{file.show(system.file("NEWS", package="R2OpenBUGS"))}\cr
 }
 
 }

Modified: trunk/R2OpenBUGS/man/bugs.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.Rd	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/man/bugs.Rd	2010-08-06 14:07:38 UTC (rev 161)
@@ -3,21 +3,22 @@
 \title{Run WinBUGS and OpenBUGS from R or S-PLUS}
 
 \description{The \code{bugs} function takes data and starting values as
-  input.  It automatically writes a \pkg{WinBUGS} script, calls the model, and
+  input.  It automatically writes a \pkg{OpenBUGS} script, calls the model, and
   saves the simulations for easy access in \R or S-PLUS.}
 
 \usage{
-bugs(data, inits, parameters.to.save, model.file="model.bug",
-    n.chains=3, n.iter=2000, n.burnin=floor(n.iter/2),
-    n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)),
-    n.sims = 1000, bin=(n.iter - n.burnin) / n.thin,
+bugs(data, inits, parameters.to.save, n.iter, model.file="model.bug",
+    n.chains=3, n.burnin=floor(n.iter / 2), n.thin=1, 
     debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
-    bugs.directory="c:/Program Files/WinBUGS14/",
-    program=c("WinBUGS", "OpenBUGS", "winbugs", "openbugs"),
-    working.directory=NULL, clearWD=FALSE,
-    useWINE=.Platform$OS.type != "windows", WINE=NULL,
-    newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
-    save.history=!summary.only, over.relax = FALSE)
+    OpenBUGS.pgm=ifelse(.Platform$OS.type == "windows" | useWINE==TRUE,
+      paste("C:/Program Files/OpenBUGS/OpenBUGS",
+      version,"/OpenBUGS.exe",sep=""),"OpenBUGS"), 
+    version='311',
+    working.directory=NULL,
+    clearWD=FALSE, useWINE=FALSE, WINE=NULL,
+    newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE,
+    save.history=(.Platform$OS.type == "windows" | useWINE==TRUE), 
+    over.relax = FALSE) 
 }
 
 \arguments{
@@ -38,7 +39,7 @@
     parameters to save which should be monitored}
   \item{model.file}{file containing the model written in \pkg{WinBUGS} code.
     The extension can be either \file{.bug} or \file{.txt}.
-    If the extension is \file{.bug} and \code{program=="WinBUGS"},
+    If the extension is \file{.bug} and \code{program=="OpenBUGS"},
     a copy of the file with extension \file{.txt} will be created
     in the \code{bugs()} call and removed afterwards. Note that
     similarly named \file{.txt} files will be overwritten.
@@ -50,41 +51,37 @@
   \item{n.burnin}{length of burn in, i.e. number of iterations to
     discard at the beginning. Default is \code{n.iter/2}, that is,
     discarding the first half of the simulations.}
-  \item{n.thin}{thinning rate. Must be a positive integer.  Set
-    \code{n.thin} > 1 to save memory and computation time if
-    \code{n.iter} is large.  Default is \code{max(1, floor(n.chains *
-    (n.iter-n.burnin) / 1000))} which will only thin if there are at
-    least 2000 simulations.}
-  \item{n.sims}{The approximate number of simulations to keep after thinning.}
-  \item{bin}{number of iterations between saving of results
-    (i.e. the coda files are saved after each \code{bin} iterations);
-    default is to save only at the end.}
-  \item{debug}{if \code{FALSE} (default), \pkg{WinBUGS} is closed automatically
-    when the script has finished running, otherwise \pkg{WinBUGS} remains open
-    for further investigation}
+  \item{n.thin}{Thinning rate. Must be a positive integer. The default is 
+    \code{n.thin} = 1. The thinning is implemented in the OpenBUGS update phase, so
+    thinned samples are never stored, and they are not counted in \ocde{n.burnin} or
+    \oode{n.iter}.  Setting \ocde{n.thin}=2, doubles the number of iterations OpenBUGS 
+    performs, but does not change \ocde{n.iter} or \ocde{n.burnin}.  Thinning implemented
+    in this manner is not captured in summaries created by packages such as \pkg{coda}.}
+  \item{debug}{if \code{FALSE} (default), \pkg{OpenBUGS} is closed automatically
+    when the script has finished running, otherwise \pkg{OpenBUGS} remains open
+    for further investigation.  The debug option is not available for linux execution.}
   \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD,
-    and DIC. This is done in \pkg{WinBUGS} directly using the rule \code{pD =
+    and DIC. This is done in \pkg{OpenBUGS} directly using the rule \code{pD =
     Dbar - Dhat}.  If there are less iterations than required for the
     adaptive phase, the rule \code{pD=var(deviance) / 2} is used.}
-  \item{digits}{number of significant digits used for \pkg{WinBUGS} input, see
+  \item{digits}{number of significant digits used for \pkg{OpenBUGS} input, see
     \code{\link{formatC}}}
   \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
     is returned, if \code{TRUE} file names of \pkg{WinBUGS} output are
     returned for easy access by the \pkg{coda} package through function
-    \code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).
+    \code{\link{read.bugs}}.
     A \code{bugs} object can be converted to an \code{mcmc.list} object as 
     used by the \pkg{coda} package with the method \code{\link[coda]{as.mcmc.list}} 
-    (for which a method is provided by R2WinBUGS).}
-  \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable.
-    If the global option \code{R2WinBUGS.bugs.directory} is not \code{NULL}, 
+    (for which a method is provided by R2OpenBUGS).}
+  \item{OpenBUGS.pgm}{ For Windows or WINE execution, the full path to the OpenBUGS
+    executable.  For linux execution, the full path to the OpenBUGS shell script (not
+    required if OpenBUGS is in the user's PATH variable).  
+    If the global option \code{R2OpenBUGS.bugs.directory} is not \code{NULL}, 
     it will be used as the default.}
-  \item{program}{the program to use, either
-    \code{winbugs}/\code{WinBUGS} or \code{openbugs}/\code{OpenBUGS},
-    the latter makes use of function \code{\link{openbugs}} and requires
-    the CRAN package \pkg{BRugs}. The \code{openbugs}/\code{OpenBUGS}
-    choice is not available in S-PLUS.}
+  \item{version}{The version of OpenBUGS to use.  \ocde{version} is ignored
+    with linux execution or if \code{OpenBUGS.pgm} is specified.}
   \item{working.directory}{sets working directory during execution of
-    this function; \pkg{WinBUGS}' in- and output will be stored in this
+    this function; \pkg{OpenBUGS}' in- and output will be stored in this
     directory; if \code{NULL}, a temporary working directory via
     \code{\link{tempdir}} is used.}
   \item{clearWD}{logical; indicating whether the files \file{data.txt},
@@ -92,23 +89,21 @@
     and \file{coda[1:nchains].txt} should be removed after \pkg{WinBUGS} has
     finished.  If set to \code{TRUE}, this argument is only respected if
     \code{codaPkg=FALSE}.}
-
   \item{useWINE}{logical; attempt to use the Wine emulator to run
-    \pkg{WinBUGS}, defaults to \code{FALSE} on Windows, and \code{TRUE}
-    otherwise. Not available in S-PLUS.}
-  \item{WINE}{character, path to \file{wine} binary file, it is
+    \pkg{OpenBUGS}. Default is \code{FALSE}.}
+  \item{WINE}{Character, path to \file{wine} binary file, it is
     tried hard (by a guess and the utilities \code{which} and \code{locate}) 
     to get the information automatically if not given.}
   \item{newWINE}{Use new versions of Wine that have \file{winepath}
     utility}
-  \item{WINEPATH}{character, path to \file{winepath} binary file, it is
+  \item{WINEPATH}{Character, path to \file{winepath} binary file, it is
     tried hard (by a guess and the utilities \code{which} and \code{locate}) 
     to get the information automatically if not given.}
-  \item{bugs.seed}{random seed for \pkg{WinBUGS} (default is no seed)}
+  \item{bugs.seed}{Random seed for \pkg{OpenBUGS}}.
   \item{summary.only}{If \code{TRUE}, only a parameter summary for very quick analyses is given, 
     temporary created files are not removed in that case.}
   \item{save.history}{If \code{TRUE} (the default), trace plots are generated at the end.}
-  \item{over.relax}{If \code{TRUE}, over-relaxed form of MCMC is used if available from WinBUGS.}
+  \item{over.relax}{If \code{TRUE}, over-relaxed form of MCMC is used if available from OpenBUGS.}
 }
 
 \details{
@@ -119,36 +114,34 @@
     \item Go into \R / S-PLUS.
     \item Prepare the inputs for the \code{bugs} function and run it (see
       Example section).
-    \item A \pkg{WinBUGS} window will pop up and \R / S-PLUS will freeze
-    up. The model will now run in \pkg{WinBUGS}. It might take awhile. You
-    will see things happening in the Log window within \pkg{WinBUGS}. When
-    \pkg{WinBUGS} is done, its window will close and \R / S-PLUS will work
+    \item An \pkg{OpenBUGS} window will pop up and \R / S-PLUS will freeze
+    up. The model will now run in \pkg{OpenBUGS}. It might take awhile. You
+    will see things happening in the Log window within \pkg{OpenBUGS}. When
+    \pkg{OpenBUGS} is done, its window will close and \R / S-PLUS will work
     again.
     \item If an error message appears, re-run with \code{debug=TRUE}.
   }
 
   BUGS version support:
   \itemize{
-    \item{\pkg{WinBUGS} 1.4.*}{default}
-    \item{\pkg{OpenBUGS} 2.*}{via argument \code{program="OpenBUGS"}}
+    \item{\pkg{OpenBUGS} >3.1}{}
   }
 
   Operation system support:
   \itemize{
     \item{\pkg{MS Windows}}{no problem}
-    \item{\pkg{Linux}, \pkg{Mac OS X} and \pkg{Unix} in
-      general}{possible with Wine emulation via \code{useWINE=TRUE}, but
-      only for \pkg{WinBUGS} 1.4.*}
+    \item{\pkg{Linux, intel processors}}{GUI display and graphics not available.}
+    \item{\pkg{Mac OS X} and \pkg{Unix} in
+      general}{possible with Wine emulation via \code{useWINE=TRUE}}
   }
 
   If \code{useWINE=TRUE} is used, all paths (such as
   \code{working.directory} and \code{model.file}, must be given in
   native (Unix) style, but \code{bugs.directory} can be given in
-  Windows path style (e.g. \dQuote{c:/Program Files/WinBUGS14/}) or
+  Windows path style (e.g. \dQuote{c:/Program Files/OpenBUGS/}) or
   native (Unix) style
   (e.g. \dQuote{/path/to/wine/folder/dosdevices/c:/Program
-  Files/WinBUGS14}).  This is done to achieve greatest portability with
-  default argument value for \code{bugs.directory}.
+  Files/OpenBUGS}).  }.
 
 }
 
@@ -193,7 +186,7 @@
   \item{indexes.short}{indexes of \code{root.short}}
   \item{last.values}{list of simulations from the most recent
     iteration; they can be used as starting points if you wish to run
-    \pkg{WinBUGS} for further iterations}
+    \pkg{OpenBUGS} for further iterations}
   \item{pD}{an estimate of the effective number of parameters, for
     calculations see the section \dQuote{Arguments}.}
   \item{DIC}{\code{mean(deviance) + pD}}
@@ -211,14 +204,14 @@
 \author{Andrew Gelman, \email{ge...@st...},
   \url{http:/www.stat.columbia.edu/~gelman/bugsR/}; modifications and
   packaged by Sibylle Sturtz, \email{st...@st...},
-  and Uwe Ligges.}
+  Uwe Ligges. and Neal Thomas}
 
 \seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, as well as
   \pkg{coda} and \pkg{BRugs} packages}
 
 \examples{
 # An example model file is given in:
-model.file <- system.file(package="R2WinBUGS", "model", "schools.txt")
+model.file <- system.file(package="R2OpenBUGS", "model", "schools.txt")
 # Let's take a look:
 file.show(model.file)
 
@@ -249,8 +242,7 @@
 ## You may need to edit "bugs.directory",
 ## also you need write access in the working directory:
 schools.sim <- bugs(data, inits, parameters, model.file,
-    n.chains=3, n.iter=5000,
-    bugs.directory="c:/Program Files/WinBUGS14/")
+    n.chains=3, n.iter=5000)
 print(schools.sim)
 plot(schools.sim)
 }

Modified: trunk/R2OpenBUGS/man/bugs.run.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.run.Rd	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/man/bugs.run.Rd	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,20 +1,19 @@
 \name{bugs.run}
 \alias{bugs.run}
-\title{Calling WinBUGS}
+\title{Calling OpenBUGS}
 
-\description{Updates the lengths of the adaptive phases in the
-  \pkg{WinBUGS} registry (using \code{\link{bugs.update.settings}}),
-  calls \pkg{WinBUGS} and runs it with \file{script.txt} - intended for
+\description{
+  Calls \pkg{OpenBUGS} and runs it with \file{script.txt} - intended for
   internal use}
 
 \usage{
-bugs.run(n.burnin, bugs.directory,
-         useWINE=.Platform$OS.type != "windows", WINE=NULL,
+bugs.run(n.burnin, OpenBUGS.pgm, 
+         useWINE=FALSE, WINE=NULL,
          newWINE=TRUE, WINEPATH=NULL)
 }
 \arguments{
   \item{n.burnin}{length of burn in}
-  \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable}
+  \item{OpenBUGS.pgm}{Full path to the \pkg{OpenBUGS} executable or shell script}
   \item{useWINE}{as in \code{\link{bugs}} meta function}
   \item{WINE}{as in \code{\link{bugs}} meta function}
   \item{newWINE}{as in \code{\link{bugs}} meta function}
@@ -22,7 +21,7 @@
 }
 
 \value{Nothing, but has side effects as documented in
-  \code{\link{bugs.update.settings}} and calls \pkg{WinBUGS}.}
+  \code{\link{bugs.update.settings}} and calls \pkg{OpenBUGS}.}
 
 \seealso{The main function to be called by the user is \code{\link{bugs}}.}
 \keyword{internal}

Modified: trunk/R2OpenBUGS/man/bugs.script.Rd
===================================================================
--- trunk/R2OpenBUGS/man/bugs.script.Rd	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/man/bugs.script.Rd	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,42 +1,46 @@
 \name{bugs.script}
 \alias{bugs.script}
 
-\title{Writes script for running WinBUGS}
+\title{Writes script for running OpenBUGS}
 
-\description{Write file \file{script.txt} for \pkg{WinBUGS} to read -
+\description{Write file \file{script.txt} for \pkg{OpenBUGS} to read -
   intended for internal use}
 
 \usage{
-bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
-    model.file, debug=FALSE, is.inits, bin, DIC=FALSE,
-    useWINE=.Platform$OS.type != "windows", newWINE=TRUE, WINEPATH=NULL, 
-    bugs.seed=NULL, summary.only=FALSE, save.history=TRUE, 
-    bugs.data.file, bugs.inits.files, over.relax = FALSE)
+bugs.script(parameters.to.save, n.chains, n.iter, n.burnin,
+           n.thin, model.file, debug=FALSE, is.inits, 
+           DIC=FALSE, useWINE=FALSE,
+           newWINE=TRUE, WINEPATH=NULL, bugs.seed=NULL, summary.only=FALSE,
+           save.history=(.Platform$OS.type = "windows" | useWINE=TRUE),
+           bugs.data.file, bugs.inits.files,
+           over.relax = FALSE) 
 }
 \arguments{
   \item{parameters.to.save}{parameters that should be monitored}
   \item{n.chains}{number of Markov chains}
   \item{n.iter}{number of total iterations (including burn in)}
   \item{n.burnin}{length of burn in}
-  \item{n.thin}{size of thinning parameter}
-  \item{model.file}{file containing the model written in \pkg{WinBUGS} code}
-  \item{debug}{if \code{FALSE}, \pkg{WinBUGS} is closed automatically,
-    otherwise \pkg{WinBUGS} remains open for further investigation}
+  \item{n.thin}{thinning parameter}
+  \item{model.file}{file containing the model written in \pkg{OpenBUGS} code}
+  \item{debug}{if \code{FALSE}, \pkg{OpenBUGS} is closed automatically,
+    otherwise \pkg{OpenBUGS} remains open for further investigation. With 
+    \code{debug} = \code{TRUE}, no modelQuit() command is added to the
+      end of the script, which can cause an infinite loop with linux
+      execution.}
   \item{is.inits}{logical; whether initial values are given by the user
-    (\code{TRUE}) or have to be generated by \pkg{WinBUGS}}
-  \item{bin}{number of iterations between saving of results}
+    (\code{TRUE}) or have to be generated by \pkg{OpenBUGS}}
   \item{DIC}{logical; if \code{TRUE}, compute deviance, pD, and DIC
-    automatically in \pkg{WinBUGS}}
+    automatically in \pkg{OpenBUGS}}
   \item{useWINE}{as in \code{\link{bugs}} meta function}
   \item{newWINE}{as in \code{\link{bugs}} meta function}
   \item{WINEPATH}{as in \code{\link{bugs}} meta function}
-  \item{bugs.seed}{random seed for \pkg{WinBUGS} (default is no seed)}
+  \item{bugs.seed}{random seed for \pkg{OpenBUGS} (default is no seed specified)}
   \item{summary.only}{If \code{TRUE}, only a parameter summary for very quick analyses is given, 
     temporary created files are not removed in that case.}
   \item{save.history}{If \code{TRUE} (the default), trace plots are generated at the end.}
   \item{bugs.data.file}{character name of the data file}
   \item{bugs.inits.files}{character vector of names of the inits files}  
-  \item{over.relax}{If \code{TRUE}, over-relaxed form of MCMC is used if available from WinBUGS.}
+  \item{over.relax}{If \code{TRUE}, over-relaxed form of MCMC is used if available from OpenBUGS.}
 }
 
 \value{Nothing, but as a side effect, the script file \file{script.txt}

Deleted: trunk/R2OpenBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2OpenBUGS/man/openbugs.Rd	2010-07-25 02:45:16 UTC (rev 160)
+++ trunk/R2OpenBUGS/man/openbugs.Rd	2010-08-06 14:07:38 UTC (rev 161)
@@ -1,118 +0,0 @@
-\name{openbugs}
-\alias{openbugs}
-\title{Wrapper to run OpenBUGS}
-\description{The \code{openbugs} function takes data and starting values
-  as input.  It automatically calls the package \pkg{BRugs} and runs
-  something similar to \code{\link[BRugs]{BRugsFit}}.  Not available in
-  S-PLUS.}
-
-\usage{
-openbugs(data, inits, parameters.to.save,
-    model.file = "model.txt", n.chains = 3, n.iter = 2000,
-    n.burnin = floor(n.iter/2),
-    n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)),
-    n.sims = 1000,  DIC = TRUE, 
-    bugs.directory = "c:/Program Files/OpenBUGS/",
-    working.directory = NULL, digits = 5, over.relax = FALSE, seed=NULL)
-}
-
-\arguments{
-  \item{data}{either a named list (names corresponding to variable names
-    in the \code{model.file}) of the data for the \pkg{OpenBUGS} model,
-    \emph{or} a vector or list of the names of the data objects used by
-    the model.  If \code{data} is a one element character vector (such as \code{"data.txt"}), 
-    it is assumed that data have already been written to the working directory into that file, 
-    e.g. by the function \code{\link{bugs.data}}.}
-  \item{inits}{a list with \code{n.chains} elements; each element of the
-    list is itself a list of starting values for the \pkg{OpenBUGS} model,
-    \emph{or} a function creating (possibly random) initial values.
-    Alternatively, if \code{inits} are missing or \code{inits = NULL},
-    initial values are generated by \pkg{OpenBUGS}.}
-  \item{parameters.to.save}{character vector of the names of the
-    parameters to save which should be monitored}
-  \item{model.file}{file containing the model written in \pkg{OpenBUGS} code.
-    The extension can be either \file{.bug} or \file{.txt}.  If
-    \file{.bug}, a copy of the file with extension \file{.txt} will be
-    created in the \code{bugs()} call and removed afterwards.  Note that
-    similarly named \file{.txt} files will be overwritten.}
-  \item{n.chains}{number of Markov chains (default: 3)}
-  \item{n.iter}{number of total iterations per chain (including burn in;
-    default: 2000)}
-  \item{n.burnin}{length of burn in, i.e. number of iterations to
-    discard at the beginning.  Default is \code{n.iter/2}, that is,
-    discarding the first half of the simulations.}
-  \item{n.thin}{thinning rate.  Must be a positive integer.  Set
-    \code{n.thin} > 1 to save memory and computation time if
-    \code{n.iter} is large.  Default is \code{max(1, floor(n.chains *
-    (n.iter-n.burnin) / 1000))} which will only thin if there are at
-    least 2000 simulations.}
-  \item{n.sims}{The approximate number of simulations to keep after thinning.}
-  \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD, and
-    DIC.  This is done in \pkg{BRugs} directly.}
-  \item{digits}{number of significant digits used for \pkg{OpenBUGS} input,
-    see \code{\link{formatC}}}
-  \item{bugs.directory}{directory that contains the \pkg{OpenBUGS} executable
-    - currently unused}
-  \item{working.directory}{sets working directory during execution of
-    this function; \pkg{WinBUGS} in- and output will be stored in this
-    directory; if \code{NULL}, a temporary working directory via
-    \code{\link{tempdir}} is used.}
-  \item{over.relax}{If \code{TRUE}, over-relaxed form of MCMC is used if available from OpenBUGS.}
-  \item{seed}{random seed (default is no seed)}
-}
-
-\value{A \code{\link{bugs}} object.}
-
-\author{Andrew Gelman, \email{ge...@st...},
-  \url{http:/www.stat.columbia.edu/~gelman/bugsR/}; modifications and
-  packaged by Sibylle Sturtz, \email{st...@st...},
-  and Uwe Ligges.
-}
-
-\note{By default, BRugs (and hence \code{openbugs()}) is quite verbose. 
-    This can be controlled for the whole BRugs package by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
-    which is set to \code{TRUE} by default.
-}
-
-\seealso{\code{\link{bugs}} and the \pkg{BRugs} package}
-
-\examples{
-# An example model file is given in:
-model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
-# Let's take a look:
-file.show(model.file)
-
-# Some example data (see ?schools for details):
-data(schools)
-schools
-
-J <- nrow(schools)
-y <- schools$estimate
-sigma.y <- schools$sd
-data <- list ("J", "y", "sigma.y")
-inits <- function(){
-    list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
-         sigma.theta = runif(1, 0, 100))
-}
-## or alternatively something like:
-# inits <- list(
-#   list(theta = rnorm(J, 0, 90), mu.theta = rnorm(1, 0, 90),
-#        sigma.theta = runif(1, 0, 90)),
-#   list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
-#        sigma.theta = runif(1, 0, 100))
-#   list(theta = rnorm(J, 0, 110), mu.theta = rnorm(1, 0, 110),
-#        sigma.theta = runif(1, 0, 110)))
-
-parameters <- c("theta", "mu.theta", "sigma.theta")
-
-\dontrun{
-## both write access in the working directory and package BRugs required:
-schools.sim <- bugs(data, inits, parameters, model.file,
-    n.chains = 3, n.iter = 5000,
-    program = "openbugs", working.directory = NULL)
-print(schools.sim)
-plot(schools.sim)
-}
-}
-\keyword{interface}
-\keyword{models}


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Thread: [Bugs-r-devel] SF.net SVN: bugs-r:[161] trunk/R2OpenBUGS

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