coda.options: Options settings for the codamenu driver

In coda: Output Analysis and Diagnostics for MCMC

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 display.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(...)
display.coda.options(stats = FALSE, plots = FALSE, diags = FALSE)

Arguments

stats	logical flag: show summary statistic options?
plots	logical flag: show plotting options?
diags	logical flag: show plotting options?
...	list of options

See Also

options

coda documentation built on May 29, 2024, 11:23 a.m.