tfr.pardensity.plot {bayesTFR}R Documentation

Plotting MCMC Parameter Density


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


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, ...)



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


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.


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


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


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.


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


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


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.


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.


Hana Sevcikova

See Also



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

## End(Not run)

[Package bayesTFR version 7.4-2 Index]