R: Options settings for the codamenu driver

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 `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)
    .Coda.Options
    .Coda.Options.Default

### 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`

[Package coda version 0.19-1 Index]