as_coda: Coerce to Coda

In ArchaeoPhases: Post-Processing of Markov Chain Monte Carlo Simulations for Chronological Modelling

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)
}

ArchaeoPhases documentation built on June 22, 2024, 9:24 a.m.