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

Description

Functions for accessing traces of the MCMC parameters, either country-independent or country-specific. Functions get.tfr.parameter.traces and get.tfr.parameter.traces.cs access Phase II MCMCs; Functions get.tfr3.parameter.traces and get.tfr3.parameter.traces.cs access Phase III MCMCs.

Usage

get.tfr.parameter.traces(mcmc.list, par.names = tfr.parameter.names(), 
    burnin = 0, thinning.index = NULL, thin = NULL)
    
get.tfr.parameter.traces.cs(mcmc.list, country.obj, 
    par.names=tfr.parameter.names.cs(), 
    burnin=0, thinning.index=NULL, thin=NULL)
    
get.tfr3.parameter.traces(mcmc.list, par.names = tfr3.parameter.names(), ...)
    
get.tfr3.parameter.traces.cs(mcmc.list, country.obj, 
    par.names=tfr3.parameter.names.cs(), ...)

Value

All 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.tfr.parameter.traces and get.tfr3.parameter.traces return country-independent parameters, get.tfr.parameter.traces.cs and get.tfr3.parameter.traces.cs return country-specific parameters.

Arguments

mcmc.list: List of bayesTFR.mcmc objects.
country.obj: Country object list (see get.country.object).
par.names: Names of country-independent parameters (in case of get.tfr.parameter.traces) or country-specific parameters (in case of get.tfr.parameter.traces.cs) to be included.
burnin: Burnin 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. 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. In the above example it would be thin=4.
...: Arguments passed to underlying functions (i.e. to get.tfr.parameter.traces or get.tfr.parameter.traces.cs).

Author

Hana Sevcikova

Examples

Run this code

sim.dir <- file.path(find.package("bayesTFR"), "ex-data", "bayesTFR.output")
m <- get.tfr.mcmc(sim.dir)
tfr.values <- get.tfr.parameter.traces(m$mcmc.list, burnin=10, par.names="sigma0")
if (FALSE) {
hist(tfr.values, main=colnames(tfr.values))
}
tfr.values.cs <- get.tfr.parameter.traces.cs(m$mcmc.list, 
                    get.country.object("Canada", meta=m$meta),
                    burnin=10, par.names="Triangle_c4")
if (FALSE) {
hist(tfr.values.cs, main=colnames(tfr.values.cs))
}