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\name{coda.options}
\alias{coda.options}
\alias{display.coda.options}
\alias{.Coda.Options}
\alias{.Coda.Options.Default}
\title{Options settings for the codamenu driver}
\usage{
coda.options(\dots)
display.coda.options(stats = FALSE, plots = FALSE, diags = FALSE)
.Coda.Options
.Coda.Options.Default
}
\arguments{
\item{stats}{logical flag: show summary statistic options?}
\item{plots}{logical flag: show plotting options?}
\item{diags}{logical flag: show plotting options?}
\item{\dots}{list of options}
}
\description{
\code{coda.options} is a utility function that queries and sets
options for the \code{codamenu()} function. These settings affect
the behaviour of the functions in the coda library only when they
are called via the \code{codamenu()} interface.
The \code{coda.options()} function behaves just like the
\code{options()} function in the base library, with the additional
feature that \code{coda.options(default=TRUE)} will reset all options
to the default values.
Options can be pretty-printed using the \code{display.coda.options()}
function, which groups the options into sections.
Available options are
\describe{
\item{bandwidth}{Bandwidth function used when smoothing samples to
produce density estimates. Defaults to Silverman's ``Rule of thumb''.}
\item{combine.corr}{Logical option that determines whether to
combine multiple chains when calculating cross-correlations.}
\item{combine.plots}{Logical option that determines whether to
combine multiple chains when plotting.}
\item{combine.plots}{Logical option that determines whether to
combine multiple chains when calculating summary statistics.}
\item{data.saved}{For internal use only.}
\item{densplot}{Logical option that determines whether to plot
a density plot when plot methods are called for mcmc objects.}
\item{digits}{Number of significant digits to use when printing.}
\item{frac1}{For Geweke diagnostic, fraction to use from
start of chain. Defaults to 0.1}
\item{frac2}{For Geweke diagnostic, fraction to use from
end of chain. Default to 0.5.}
\item{gr.bin}{For Geweke-Brooks plot, number of iterations to use
per bin.}
\item{gr.max}{For Geweke-Brooks plot, maximum number of bins to
use. This option overrides \code{gr.bin}.}
\item{halfwidth}{For Heidelberger and Welch diagnostic, the target
value for the ratio of half width to sample mean.}
\item{lowess}{Logical option that controls whether to plot a
smooth line through a trace plot when plotting MCMC output.}
\item{q}{For Raftery and Lewis diagnostic, the target quantile to
be estimated}
\item{r}{For Raftery and Lewis diagnostic, the required precision.}
\item{s}{For Raftery and Lewis diagnostic, the probability of
obtaining an estimate in the interval (q-r, q+r).}
\item{quantiles}{Vector of quantiles to print when calculating
summary statistics for MCMC output.}
\item{trace}{Logical option that determines whether to plot a trace
of the sampled output when plotting MCMC output.}
\item{user.layout}{Logical option that determines whether current
value of par("mfrow") should be used for plots (TRUE) or whether
the optimal layout should be calculated (FALSE).}
}
}
\seealso{
\code{\link{options}}
}
\keyword{utilities}
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