as_coda {ArchaeoPhases}

Coerce to Coda

Description

Extracts parallel chains from an MCMC object to create an mcmc.list object for use with coda diagnostic tools.

Usage

as_coda(from, ...)

## S4 method for signature 'MCMC'
as_coda(from, chains = 1)

Arguments

from

from An object to be coerced.

...

Currently not used.

chains

An integer specifying the number of parallel chains (defaults to 1).

Value

An coda::mcmc.list object.

Author(s)

A. Philippe, M.-A. Vibet

See Also

coda::mcmc(), coda::mcmc.list()

Other read methods: as_events(), as_phases(), check, read_bcal(), read_chronomodel, read_oxcal()

Examples

if (requireNamespace("coda", quietly = TRUE)) {
  ## Load coda
  library(coda)

  ## Coerce to MCMC
  eve <- as_events(mcmc_events, calendar = CE(), iteration = 1)

  ## Coerce to coda
  mc <- as_coda(eve[, 1:2], chains = 3)
  plot(mc)

  ## Autocorrelation
  autocorr.plot(mc)

  ## Gelman-Rubin diagnostic
  ## The multivariate criterion can not be evaluated when a phase
  ## contains only one date. This induces colinearity problems.
  gelman.diag(mc)
  gelman.plot(mc)
}