[Bugs-r-devel] SF.net SVN: bugs-r: [26] trunk/R2WinBUGS

[<gg...@us...>]

Revision: 26
          http://svn.sourceforge.net/bugs-r/?rev=26&view=rev
Author:   ggorjan
Date:     2007-06-12 02:58:15 -0700 (Tue, 12 Jun 2007)

Log Message:
-----------
bugs.Rd
 - fixed useWINE documentation
 - some formatting

bugs.R
 - fixed use of is.null(DIC)
 - some formatting

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/man/bugs.Rd

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2007-06-12 09:57:21 UTC (rev 25)
+++ trunk/R2WinBUGS/R/bugs.R	2007-06-12 09:58:15 UTC (rev 26)
@@ -1,81 +1,83 @@
 "bugs" <-
-function(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) / 1000)),
-    bin = (n.iter - n.burnin) / n.thin,
-    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$OS.type != "windows", WINE = Sys.getenv("WINE"),
-    newWINE = FALSE, WINEPATH = NULL){
-    
+function(data, inits, parameters.to.save, model.file="model.bug",
+    n.chains=3, n.iter=2000, n.burnin=floor(n.iter / 2),
+    n.thin=max(1, floor(n.chains * (n.iter - n.burnin) / 1000)),
+    bin=(n.iter - n.burnin) / n.thin,
+    debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
+    bugs.directory="c:/Program Files/WinBUGS14/",
+    program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+    working.directory=NULL,
+    clearWD=FALSE, useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
+    newWINE=FALSE, WINEPATH=NULL)
+{
   program <- match.arg(program)
-  if (program %in% c("openbugs", "OpenBugs"))
-    if (is.R()){
-        ## If OpenBUGS, we only call openbugs() and exit...
-        return(openbugs(data, inits, parameters.to.save, model.file,
-          n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
-          working.directory, digits))
+  if(program %in% c("openbugs", "OpenBugs")) {
+    if(is.R()) {
+      ## If OpenBUGS, we only call openbugs() and exit...
+      return(openbugs(data, inits, parameters.to.save, model.file,
+                      n.chains, n.iter, n.burnin, n.thin, DIC, bugs.directory,
+                      working.directory, digits))
     } else {
-        stop ("OpenBUGS is not yet available in S-PLUS")
+      stop ("OpenBUGS is not yet available in S-PLUS")
     }
+  }
   ## Checking number of inits, which is NOT save here:
   if(!missing(inits) && !is.function(inits) && !is.null(inits) && (length(inits) != n.chains))
     stop("Number of initialized chains (length(inits)) != n.chains")
-  if(useWINE) {     
-    if (!is.R())
-        stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
+  if(useWINE) {
+    if(!is.R())
+      stop ("Non-Windows platforms not yet supported in R2WinBUGS for S-PLUS")
     ## attempt to find wine and winepath
-    if (!nchar(WINE)) {
-        WINE <- system("locate wine | grep bin/wine$", intern = TRUE)
-        WINE <- WINE[length(WINE)]
+    if(!nchar(WINE)) {
+      WINE <- system("locate wine | grep bin/wine$", intern=TRUE)
+      WINE <- WINE[length(WINE)]
     }
-    if (!length(WINE)) stop("couldn't locate WINE binary")
-    if (!nchar(WINEPATH)) {
-        WINEPATH <- system("locate winepath | grep bin/winepath$", intern = TRUE)
-        WINEPATH <- WINEPATH[length(WINEPATH)]
+    if(!length(WINE)) stop("couldn't locate WINE binary")
+    if(!nchar(WINEPATH)) {
+      WINEPATH <- system("locate winepath | grep bin/winepath$", intern=TRUE)
+      WINEPATH <- WINEPATH[length(WINEPATH)]
     }
-    if (!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
-    }
-  if(!is.null(working.directory)){
-      savedWD <- getwd()
-      setwd(working.directory)
-      on.exit(setwd(savedWD))
+    if(!length(WINEPATH)) stop("couldn't locate WINEPATH binary")
   }
-  if(!file.exists(model.file)) stop(paste(model.file, "does not exist."))
-  if(file.info(model.file)$isdir) stop(paste(model.file, "is a directory, but a file is required."))
-  if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")){
-    bugs.data(data, dir = getwd(), digits)
+  if(!is.null(working.directory)) {
+    savedWD <- getwd()
+    setwd(working.directory)
+    on.exit(setwd(savedWD))
+  }
+  if(!file.exists(model.file))
+    stop(paste(model.file, "does not exist."))
+  if(file.info(model.file)$isdir)
+    stop(paste(model.file, "is a directory, but a file is required."))
+  if(!(length(data) == 1 && is.vector(data) && is.character(data) && data == "data.txt")) {
+    bugs.data(data, dir=getwd(), digits)
   } else if(!file.exists(data))
     stop("File data.txt does not exist.")
   bugs.inits(inits, n.chains, digits)
   if(DIC) parameters.to.save <- c(parameters.to.save, "deviance")
   ## Model files with extension ".bug" need to be renamed to ".txt"
-  if(length(grep("[.]bug$", model.file))){
+  if(length(grep("[.]bug$", model.file))) {
     new.model.file <- sub("[.]bug$", ".txt", model.file)
-    file.copy(model.file, new.model.file, overwrite = TRUE)
-    on.exit(try(file.remove(new.model.file)), add = TRUE)
-  } else new.model.file <- model.file
+    file.copy(model.file, new.model.file, overwrite=TRUE)
+    on.exit(try(file.remove(new.model.file)), add=TRUE)
+  } else {
+    new.model.file <- model.file
+  }
   bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
-    new.model.file, debug=debug, is.inits=!is.null(inits),
-    bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
-  bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, WINEPATH = WINEPATH)
-
+              new.model.file, debug=debug, is.inits=!is.null(inits),
+              bin=bin, DIC=DIC, useWINE=useWINE, newWINE=newWINE,
+              WINEPATH=WINEPATH)
+  bugs.run(n.burnin, bugs.directory, WINE=WINE, useWINE=useWINE,
+           WINEPATH=WINEPATH)
   if(codaPkg)
     return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
-
-  if (is.R()){
-    sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
-        model.file = model.file, is.DIC = !is.null(DIC), program = program)
-  } else {
-    sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin, n.thin, DIC),
-        model.file = model.file, is.DIC = DIC, program = program)
+  sims <- c(bugs.sims(parameters.to.save, n.chains, n.iter, n.burnin,
+                      n.thin, DIC),
+            model.file=model.file, is.DIC=DIC, program=program)
+  if(clearWD) {
+    file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
+                  paste("inits", 1:n.chains, ".txt", sep=""),
+                  paste("coda", 1:n.chains, ".txt", sep="")))
   }
-  if(clearWD)
-    file.remove(c("data.txt", "log.odc", "log.txt", "codaIndex.txt",
-        paste("inits", 1:n.chains, ".txt", sep=""),
-        paste("coda", 1:n.chains, ".txt", sep="")))
   class(sims) <- "bugs"
-  return(sims)
+  sims
 }

Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd	2007-06-12 09:57:21 UTC (rev 25)
+++ trunk/R2WinBUGS/man/bugs.Rd	2007-06-12 09:58:15 UTC (rev 26)
@@ -5,143 +5,172 @@
 It automatically writes a WinBUGS 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)/1000)),
-    bin = (n.iter - n.burnin) / n.thin,
-    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$OS.type != "windows", WINE = Sys.getenv("WINE"),
-    newWINE = FALSE, WINEPATH = NULL)
+bugs(data, inits, parameters.to.save, model.file="model.bug",
+    n.chains=3, n.iter=2000, n.burnin=floor(n.iter/2),
+    n.thin=max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
+    bin=(n.iter - n.burnin) / n.thin,
+    debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE,
+    bugs.directory="c:/Program Files/WinBUGS14/",
+    program=c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
+    working.directory=NULL, clearWD=FALSE,
+    useWINE=.Platform$OS.type != "windows", WINE=Sys.getenv("WINE"),
+    newWINE=FALSE, WINEPATH=NULL)
 }
 \arguments{
-  \item{data}{either a named list (names corresponding to variable names in the \code{model.file}) 
-    of the data for the WinBUGS model, \emph{or}
-    a vector or list of the names of the data objects used by the model.
-    If \code{data = "data.txt"}, it is assumed that data have already been written to the working directory
-    in a file called \file{data.txt}, 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 WinBUGS model, \emph{or}
-    a function creating (possibly random) initial values.
-    Alternatively, if \code{inits = NULL}, initial values are generated by WinBUGS}
-  \item{parameters.to.save}{character vector of the names of the parameters to save which should be monitored}
+  \item{data}{either a named list (names corresponding to variable names
+    in the \code{model.file}) of the data for the WinBUGS model,
+    \emph{or} a vector or list of the names of the data objects used by
+    the model. If \code{data="data.txt"}, it is assumed that data have
+    already been written to the working directory in a file called
+    \file{data.txt}, 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 WinBUGS model,
+    \emph{or} a function creating (possibly random) initial values.
+    Alternatively, if \code{inits=NULL}, initial values are generated
+    by WinBUGS.}
+  \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 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=="winbugs"},
     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.}
+    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{bin}{number of iterations between saving of results 
-    (i.e. the coda files are saved after each \code{bin} iterations); 
+  \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{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), WinBUGS is closed automatically
-  when the script has finished running, otherwise WinBUGS remains open for further investigation}
-  \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD, and DIC.
-    This is done in WinBUGS 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 WinBUGS input, see \code{\link{formatC}}}
-  \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object is returned,
-    if \code{TRUE} file names of WinBUGS output are returned for easy access by the \pkg{coda} package
-    through function \code{\link{read.bugs}}. (not used if \code{program = "openbugs"})}
+    when the script has finished running, otherwise WinBUGS remains open
+    for further investigation}
+  \item{DIC}{logical; if \code{TRUE} (default), compute deviance, pD,
+    and DIC. This is done in WinBUGS 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 WinBUGS input, see
+    \code{\link{formatC}}}
+  \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
+    is returned, if \code{TRUE} file names of WinBUGS output are
+    returned for easy access by the \pkg{coda} package through function
+    \code{\link{read.bugs}} (not used if \code{program="openbugs"}).}
   \item{bugs.directory}{directory that contains the WinBUGS executable}
-  \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{working.directory}{sets working directory during execution of this function;
-    WinBUGS' in- and output will be stored in this directory;
-    if \code{NULL}, the current working directory is chosen.}
-  \item{clearWD}{logical; indicating whether the files \file{data.txt}, 
-    \file{inits[1:n.chains].txt}, \file{log.odc}, \file{codaIndex.txt}, and
-    \file{coda[1:nchains].txt} should be removed after 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 WinBUGS, 
-    defaults to \code{TRUE} on Windows, and \code{FALSE} otherwise.
-    If WINE is used, the arguments \code{bugs.directory} and \code{working.directory} must be given in form of Linux paths
-    rather than Windows paths (if not \code{NULL}).
-    The \code{useWINE = TRUE} option is not available in S-PLUS.}
+  \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{working.directory}{sets working directory during execution of
+    this function; WinBUGS' in- and output will be stored in this
+    directory; if \code{NULL}, the current working directory is chosen.}
+  \item{clearWD}{logical; indicating whether the files \file{data.txt},
+    \file{inits[1:n.chains].txt}, \file{log.odc}, \file{codaIndex.txt},
+    and \file{coda[1:nchains].txt} should be removed after 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
+    WinBUGS, defaults to \code{FALSE} on Windows, and \code{TRUE}
+    otherwise.  If WINE is used, the arguments \code{bugs.directory} and
+    \code{working.directory} must be given in form of Linux paths rather
+    than Windows paths (if not \code{NULL}).  The \code{useWINE=TRUE}
+    option is not available in S-PLUS.}
   \item{WINE}{character; name of WINE binary file}
   \item{newWINE}{Set this one to \code{TRUE} for new versions of WINE.}
-  \item{WINEPATH}{Path the WINE, it is tried hard to get the information automatically if not given.}
+  \item{WINEPATH}{Path to WINE binary file, it is tried hard to get the
+    information automatically if not given.}
 }
 \details{
-To run:
-\enumerate{
-\item Write a WinBUGS model in a ASCII file.
-\item Go into R / S-PLUS.
-\item Prepare the inputs to the \code{bugs} function and run it (see Example).
-\item A WinBUGS window will pop up and R / S-PLUS will freeze up. The model
-    will now run in WinBUGS. It might take awhile. You will see
-    things happening in the Log window within WinBUGS. When WinBugs
-    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}.
-}}
+  To run:
+  \enumerate{
+    \item Write a WinBUGS model in a ASCII file.
+    \item Go into R / S-PLUS.
+    \item Prepare the inputs to the \code{bugs} function and run it (see
+      Example).
+    \item A WinBUGS window will pop up and R / S-PLUS will freeze
+    up. The model will now run in WinBUGS. It might take awhile. You
+    will see things happening in the Log window within WinBUGS. When
+    WinBugs 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}.
+  }
+}
+
 \value{
- If \code{codaPkg = TRUE} the returned values are the names
- of coda output files written by WinBUGS containing
- the Markov Chain Monte Carlo output in the CODA format.
- This is useful for direct access with \code{\link{read.bugs}}.
+  If \code{codaPkg=TRUE} the returned values are the names
+  of coda output files written by WinBUGS containing
+  the Markov Chain Monte Carlo output in the CODA format.
+  This is useful for direct access with \code{\link{read.bugs}}.
 
- If \code{codaPkg = FALSE}, the following values are returned:
+  If \code{codaPkg=FALSE}, the following values are returned:
   \item{n.chains}{see Section \sQuote{Arguments}}
   \item{n.iter}{see Section \sQuote{Arguments}}
   \item{n.burnin}{see Section \sQuote{Arguments}}
   \item{n.thin}{see Section \sQuote{Arguments}}
-  \item{n.keep}{number of iterations kept per chain (equal to \code{(n.iter-n.burnin) / n.thin})}
-  \item{n.sims}{number of posterior simulations (equal to \code{n.chains * n.keep})}
+  \item{n.keep}{number of iterations kept per chain (equal to
+    \code{(n.iter-n.burnin) / n.thin})}
+  \item{n.sims}{number of posterior simulations (equal to
+    \code{n.chains * n.keep})}
   \item{sims.array}{3-way array of simulation output, with dimensions
     n.keep, n.chains, and length of combined parameter vector}
-  \item{sims.list}{list of simulated parameters:\cr
-    for each scalar parameter, a vector of length n.sims\cr
-    for each vector parameter, a 2-way array of simulations,\cr
+  \item{sims.list}{list of simulated parameters:
+    for each scalar parameter, a vector of length n.sims
+    for each vector parameter, a 2-way array of simulations,
     for each matrix parameter, a 3-way array of simulations, etc.
-     (for convenience, the \code{n.keep * n.chains} simulations in
-     sims.matrix and sims.list (but NOT sims.array have been randomly permuted)}
-  \item{sims.matrix}{matrix of simulation output, with \code{n.chains * n.keep} rows and
-    one column for each element of each saved parameter
-    (for convenience, the \code{n.keep * n.chains} simulations in
-     sims.matrix and sims.list (but NOT sims.array have been randomly permuted)}
-  \item{summary}{summary statistics and convergence information for each
-    element of each saved parameter.}
+    (for convenience, the \code{n.keep*n.chains} simulations in
+    sims.matrix and sims.list (but NOT sims.array) have been randomly
+    permuted)}
+  \item{sims.matrix}{matrix of simulation output, with
+    \code{n.chains*n.keep} rows and one column for each element of
+    each saved parameter (for convenience, the \code{n.keep*n.chains}
+    simulations in sims.matrix and sims.list (but NOT sims.array) have
+    been randomly permuted)}
+  \item{summary}{summary statistics and convergence information for
+    each saved parameter.}
   \item{mean}{a list of the estimated parameter means}
   \item{sd}{a list of the estimated parameter standard deviations}
   \item{median}{a list of the estimated parameter medians}
-  \item{root.short}{names of argument \code{parameters.to.save} and \dQuote{deviance}}
+  \item{root.short}{names of argument \code{parameters.to.save} and
+    \dQuote{deviance}}
   \item{long.short}{indexes; programming stuff}
   \item{dimension.short}{dimension of \code{indexes.short}}
   \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 WinBUGS for further iterations}
-  \item{pD}{an estimate of the effective number of parameters, for calculations see the section \dQuote{Arguments}.}
+  \item{last.values}{list of simulations from the most recent
+    iteration; they can be used as starting points if you wish to run
+    WinBUGS 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}}
 }
+
 \references{
     Gelman, A., Carlin, J.B., Stern, H.S., Rubin, D.B. (2003):
     \emph{Bayesian Data Analysis}, 2nd edition, CRC Press.
 
-     Sturtz, S., Ligges, U., Gelman, A. (2005): 
-     R2WinBUGS: A Package for Running WinBUGS from R.  
+     Sturtz, S., Ligges, U., Gelman, A. (2005):
+     R2WinBUGS: A Package for Running WinBUGS from R.
      \emph{Journal of Statistical Software} 12(3), 1-16.
 }
-    
-\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.}
-\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, and the \pkg{coda} package}
+
+\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.}
+
+\seealso{\code{\link{print.bugs}}, \code{\link{plot.bugs}}, and the
+  \pkg{coda} package}
+
 \examples{
 # An example model file is given in:
-model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
+model.file <- system.file(package="R2WinBUGS", "model", "schools.txt")
 # Let's take a look:
 file.show(model.file)
 
@@ -154,17 +183,17 @@
 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))
+    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)))
+#   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")
 
@@ -172,9 +201,9 @@
 ## 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/",
-    working.directory = NULL, clearWD = TRUE)
+    n.chains=3, n.iter=5000,
+    bugs.directory="c:/Program Files/WinBUGS14/",
+    working.directory=NULL, clearWD=TRUE)
 print(schools.sim)
 plot(schools.sim)
 }


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