e0.coda.list.mcmc: Convertion to coda's Objects

Description

The functions convert MCMC traces (simulated using run.e0.mcmc) into objects that can be used with the coda package.

Usage

e0.coda.list.mcmc(mcmc.list = NULL, country = NULL, chain.ids = NULL, 
    sim.dir = file.path(getwd(), "bayesLife.output"), 
    par.names = NULL, par.names.cs = NULL, low.memory = FALSE, ...)
    
# S3 method for bayesLife.mcmc
coda.mcmc(mcmc, country = NULL, par.names = NULL, par.names.cs = NULL, ...)

Value

The function e0.coda.list.mcmc returns an object of class “mcmc.list”. The function coda.mcmc returns an object of class “mcmc”, both defined in the coda package.

Arguments

mcmc.list: List of bayesLife.mcmc objects, or an object of class bayesLife.mcmc.set or bayesLife.prediction. If it is NULL, the MCMCs are loaded from sim.dir. Either mcmc.list or sim.dir must be given.
mcmc: Object of class bayesLife.mcmc.
country: Country name or code. It is 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.
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 country. If country is not given, for each parameter, traces for all countries are included.
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.

Author

Hana Sevcikova

Examples

Run this code

sim.dir <- file.path(find.package("bayesLife"), "ex-data", "bayesLife.output")
coda.list <- e0.coda.list.mcmc(sim.dir = sim.dir, country = "France", burnin = 30)
summary(coda.list)