mig.coda.list.mcmc: Conversion to coda-formatted objects

Description

The functions convert MCMC traces (simulated using run.mig.mcmc) into objects that can be used with the coda package.

Usage

mig.coda.list.mcmc(
  mcmc.list = NULL,
  country = NULL,
  chain.ids = NULL,
  sim.dir = NULL,
  par.names = NULL,
  par.names.cs = NULL,
  low.memory = FALSE,
  ...
)

Value

Returns an object of class mcmc.list defined in the coda package.

Arguments

mcmc.list: A list of objects of class bayesMig.mcmc, or an object of class bayesMig.mcmc.set or bayesMig.prediction. If NULL, the MCMCs are loaded from sim.dir. Either mcmc or sim.dir must be given.
country: Location name or code. Used in connection with the par.names.cs argument (see below).
chain.ids: Vector of chain identifiers. By default, all chains available in the mcmc.list object are included.
sim.dir: Directory with the MCMC simulation results. Only used if mcmc.list is NULL.
par.names: Names of country-independent parameters to be included. Default names are those returned by the mig.parameter.names function, which includes all country-independent parameters in the BHM.
par.names.cs: Names of country-specific parameters to be included. The argument country is used to filter out traces that correspond to a specific location. If country is not given, traces of each parameter are given for all countries. Default names are those returned by mig.parameter.names.cs(), which includes all country-specific parameters in the BHM.
low.memory: Logical indicating if the function should run in a memory-efficient mode.
...: Additional arguments passed to the coda's mcmc function, such as burnin and thin.