coda.mcmc.list: Convertion to coda's Objects
In PPgp/bayesTFR: Bayesian Fertility Projection

coda.list.mcmc

R Documentation

Convertion to coda's Objects

Description

The functions convert MCMC traces (simulated using run.tfr.mcmc and run.tfr3.mcmc) into objects that can be used with the coda package.

Usage

coda.list.mcmc(mcmc = NULL, country = NULL, chain.ids = NULL, 
    sim.dir = file.path(getwd(), "bayesTFR.output"), 
    par.names = tfr.parameter.names(), 
    par.names.cs = tfr.parameter.names.cs(), 
    rm.const.pars = FALSE, burnin = 0, 
    low.memory = FALSE, ...)
    
coda.list.mcmc3(mcmc = NULL, country = NULL, chain.ids = NULL, 
    sim.dir = file.path(getwd(), "bayesTFR.output"), 
    par.names = tfr3.parameter.names(), 
    par.names.cs = tfr3.parameter.names.cs(), 
    burnin = 0, low.memory = FALSE, ...)
	
## S3 method for class 'bayesTFR.mcmc'
coda.mcmc(mcmc, country = NULL, 
    par.names = NULL, par.names.cs = NULL, 
    burnin = 0, thin = 1, ...)

Arguments

`mcmc`	In `coda.mcmc`, it is an object of class `bayesTFR.mcmc`. In `coda.list.mcmc` and `coda.list.mcmc3`, it is either a list of `bayesTFR.mcmc` objects, or an object of class `bayesTFR.mcmc.set` or in case of `coda.list.mcmc` it can be `bayesTFR.prediction`. If it is `NULL`, the MCMCs are loaded from `sim.dir`. Either `mcmc` or `sim.dir` must be given.
`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. In `coda.mcmc` the default names are `tfr.parameter.names()` if the `mcmc` object is an MCMC of phase II or `tfr3.parameter.names()` if the MCMC is of phase III.
`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. In `coda.mcmc` the default names are `tfr.parameter.names.cs()` if the `mcmc` object is an MCMC of phase II or `tfr3.parameter.names.cs()` if the MCMC is of phase III.
`rm.const.pars`	Logical indicating if parameters with constant values should be removed.
`burnin`	Burnin indicating how many iterations should be removed from the beginning of each chain.
`low.memory`	Logical indicating if the function should run in a memory-efficient mode.
`thin`	Thinning interval.
`...`	Additional arguments passed to the coda's `mcmc` function.

Details

Function coda.list.mcmc is for accessing all chains of phase II MCMCs; Function coda.list.mcmc3 is for accessing all chains of phase III MCMCs.

Value

The function coda.list.mcmc and coda.list.mcmc3 return an object of class “mcmc.list”. The function coda.mcmc returns an object of class “mcmc”, both defined in the coda package.