inst/examples/ex-coda.R

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

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)
}