tfr.pardensity.plot {bayesTFR}

Plotting MCMC Parameter Density

Description

Functions for plotting density of the posterior distribution of the MCMC parameters.

Usage

tfr.pardensity.plot(mcmc.list = NULL, 
    sim.dir = file.path(getwd(), "bayesTFR.output"), 
    chain.ids = NULL, par.names = tfr.parameter.names(trans = TRUE), 
    burnin = NULL, dev.ncol=5, low.memory = TRUE, ...)
    
tfr.pardensity.cs.plot(country, mcmc.list=NULL, 
    sim.dir=file.path(getwd(), "bayesTFR.output"), 
    chain.ids=NULL, par.names=tfr.parameter.names.cs(trans=TRUE), 
    burnin=NULL, dev.ncol=3, low.memory=TRUE, ...)
    
tfr3.pardensity.plot(mcmc.list = NULL, 
    sim.dir = file.path(getwd(), "bayesTFR.output"), 
    chain.ids = NULL, par.names = tfr3.parameter.names(), 
    burnin = NULL, dev.ncol=3, low.memory = TRUE, ...)
    
tfr3.pardensity.cs.plot(country, mcmc.list=NULL, 
    sim.dir=file.path(getwd(), "bayesTFR.output"), 
    chain.ids=NULL, par.names=tfr3.parameter.names.cs(), 
    burnin=NULL, dev.ncol=2, low.memory=TRUE, ...)

Arguments

country

Name or code of a country. The code can be either numeric or ISO-2 or ISO-3 characters.

mcmc.list

List of bayesTFR.mcmc objects, or an object of class bayesTFR.mcmc.set or of class bayesTFR.prediction (allowed only for Phase II MCMCs). If it is NULL, the parameter values are loaded from sim.dir.

sim.dir

Directory with the MCMC simulation results. It is only used if mcmc.list is NULL.

chain.ids

List of MCMC identifiers to be plotted. If it is NULL, all chains found in mcmc.list or sim.dir are plotted.

par.names

Names of parameters for which density should be plotted. By default all (possibly transformed) country-independent parameters are plotted if used within tfr.pardensity.plot and tfr3.pardensity.plot, or country-specific parameters are plotted if used within tfr.pardensity.cs.plot and tfr3.pardensity.cs.plot.

burnin

Number of iterations to be discarded from the beginning of each chain.

dev.ncol

Number of column for the graphics device. If the number of parameters is smaller than dev.ncol, the number of columns is automatically decreased.

low.memory

Logical indicating if the processing should run in a low-memory mode. If it is FALSE, traces of all available parameters are loaded into memory. Otherwise, parameters are loaded as they are needed and are not kept in the memory.

...

Further arguments passed to the density function.

Details

The functions plot the density of the posterior distribution either for country-independent parameters (tfr.pardensity.plot for phase II MCMCs and tfr3.pardensity.plot for phase III MCMCs) or for country-specific parameters (tfr.pardensity.cs.plot for phase II and tfr3.pardensity.cs.plot for phase III), one graph per parameter. One can restrict it to specific chains by setting the chain.ids argument and to specific parameters by setting the par.names argument.

If mcmc.list is an object of class bayesTFR.prediction (which is allowed in tfr.pardensity.plot and tfr.pardensity.cs.plot only) and if this object contains thinned traces, they are used instead of the full chains. In such a case, burnin and chain.ids cannot be modified - their value is set to the one used when the thinned traces were created, namely when running tfr.predict. In a situation with long MCMC chains, this approach can significantly speed-up creation of the density plots.

Author(s)

Hana Sevcikova

See Also

tfr.partraces.plot

Examples

## Not run: 
sim.dir <- file.path(find.package("bayesTFR"), "ex-data", "bayesTFR.output")
tfr.pardensity.plot(sim.dir=sim.dir)
tfr.pardensity.cs.plot(country="Ireland", sim.dir=sim.dir, bw=0.2)

## End(Not run)