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