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\name{read.coda}
\alias{read.coda}
\alias{read.jags}
\title{Read output files in CODA format}
\usage{
read.coda(output.file, index.file, start, end, thin, quiet=FALSE)
read.jags(file = "jags.out", start, end, thin, quiet=FALSE)
}
\arguments{
\item{output.file}{The name of the file containing the monitored
output}
\item{index.file}{The name of the file containing the index, showing
which rows of the output file correspond to which variables}
\item{file}{For JAGS output, the name of the output file. The
extension ".out" may be omitted. There must be a corresponding
".ind" file with the same file stem.}
\item{start}{First iteration of chain}
\item{end}{Last iteration of chain}
\item{thin}{Thinning interval for chain}
\item{quiet}{Logical flag. If true, a progress summary will be printed}
}
\description{
\code{read.coda} reads Markov Chain Monte Carlo output in
the CODA format produced by OpenBUGS and JAGS. By default, all
of the data in the file is read, but the arguments \code{start},
\code{end} and \code{thin} may be used to read a subset of the
data. If the arguments given to \code{start}, \code{end} or
\code{thin} are incompatible with the data, they are ignored.
}
\value{
An object of class \code{mcmc} containing a representation of
the data in the file.
}
\references{
Spiegelhalter DJ, Thomas A, Best NG and Gilks WR (1995).
\emph{BUGS: Bayesian inference Using Gibbs Sampling, Version 0.50.}
MRC Biostatistics Unit, Cambridge.
}
\author{Karen Vines, Martyn Plummer}
\seealso{
\code{\link{mcmc}},
\code{\link{read.coda.interactive}},
\code{\link{read.openbugs}}.
}
\keyword{file}
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