tfr.pardensity.plot {bayesTFR} | R Documentation |
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 |
sim.dir |
Directory with the MCMC simulation results. It is only used if |
chain.ids |
List of MCMC identifiers to be plotted. If it is |
par.names |
Names of parameters for which density should be plotted. By default all (possibly transformed) country-independent parameters are plotted if used within |
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 |
low.memory |
Logical indicating if the processing should run in a low-memory mode. If it is |
... |
Further arguments passed to the |
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
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)