get.e0.parameter.traces: Accessing MCMC Parameter Traces

Description

Functions for accessing traces of the MCMC parameters, either country-independent or country-specific.

Usage

get.e0.parameter.traces(mcmc.list, par.names = NULL, 
    burnin = 0, thinning.index = NULL, thin = NULL)
    
get.e0.parameter.traces.cs(mcmc.list, country.obj, 
    par.names = NULL, burnin = 0, thinning.index = NULL, thin = NULL)

Value

Both functions return a matrix with columns being the parameters and rows being the MCMC values, attached to one another in case of multiple chains. get.e0.parameter.traces returns country-independent parameters, get.e0.parameter.traces.cs returns country-specific parameters.

Arguments

mcmc.list: List of bayesLife.mcmc objects.
country.obj: Country object list (see get.country.object).
par.names: Names of country-independent parameters (in case of get.e0.parameter.traces) or country-specific parameters (in case of get.e0.parameter.traces.cs) to be included. By default all parameters are included.
burnin: Burn-in indicating how many iterations should be removed from the beginning of each chain.
thinning.index: Index of the traces for thinning. If it is NULL, thin is used. thinning.index does not include burnin and should be flattened over all chains. For example, if there are two MCMC chains of length 1000, burnin=200 and we want a sample of length 400, then the value should be thinning.index=seq(1,1600, length=400).
thin: Alternative to thinning.index. The above example is equivalent to thin=4.

Author

Hana Sevcikova

Examples

Run this code

sim.dir <- file.path(find.package("bayesLife"), "ex-data", "bayesLife.output")
m <- get.e0.mcmc(sim.dir)
e0.values <- get.e0.parameter.traces(m$mcmc.list, burnin = 10, par.names = "z")
hist(e0.values, main = colnames(e0.values))

e0.values.cs <- get.e0.parameter.traces.cs(m$mcmc.list, 
                    get.country.object("Canada", meta = m$meta),
                    burnin = 10, par.names = "z.c")
hist(e0.values.cs, main = colnames(e0.values.cs))