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 display.coda.options()
function, which groups the options into sections.
Available options are
Bandwidth function used when smoothing samples to produce density estimates. Defaults to Silverman's ``Rule of thumb''.
Logical option that determines whether to combine multiple chains when calculating cross-correlations.
Logical option that determines whether to combine multiple chains when plotting.
Logical option that determines whether to combine multiple chains when calculating summary statistics.
For internal use only.
Logical option that determines whether to plot a density plot when plot methods are called for mcmc objects.
Number of significant digits to use when printing.
For Geweke diagnostic, fraction to use from start of chain. Defaults to 0.1
For Geweke diagnostic, fraction to use from end of chain. Default to 0.5.
For Geweke-Brooks plot, number of iterations to use per bin.
For Geweke-Brooks plot, maximum number of bins to
use. This option overrides gr.bin.
For Heidelberger and Welch diagnostic, the target value for the ratio of half width to sample mean.
Logical option that controls whether to plot a smooth line through a trace plot when plotting MCMC output.
For Raftery and Lewis diagnostic, the target quantile to be estimated
For Raftery and Lewis diagnostic, the required precision.
For Raftery and Lewis diagnostic, the probability of obtaining an estimate in the interval (q-r, q+r).
Vector of quantiles to print when calculating summary statistics for MCMC output.
Logical option that determines whether to plot a trace of the sampled output when plotting MCMC output.
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).
coda.options(...)
display.coda.options(stats = FALSE, plots = FALSE, diags = FALSE)
logical flag: show summary statistic options?
logical flag: show plotting options?
logical flag: show plotting options?
list of options