plotDiagnostic: Diagnostic Plot

In BayesianTools: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

Diagnostic Plot

Description

This function plots the DIC, WAIC, mPSRF, PSRF(with upper C.I.) and traces of the parameters in dependence of iterations. DIC, WAIC are plotted separately for the chains and the trace plots also for the internal chains.

Usage

plotDiagnostic(
  out,
  start = 50,
  numSamples = 100,
  window = 0.2,
  plotWAIC = F,
  plotPSRF = T,
  plotDIC = T,
  plotTrace = T,
  graphicParameters = NULL,
  ...
)

Arguments

out	object of class "bayesianOutput"
start	start value for calculating DIC, WAIC, mPSRF and PSRF, default = 50
numSamples	for calculating WAIC, default = 10 because of high computational costs
window	plot range to show, vector of percents or only one value as start value for the window
plotWAIC	whether to calculate WAIC or not, default = T
plotPSRF	calculate and plot mPSRF/PSRF or not, default = T
plotDIC	calculate and plot DICor not, default = T
plotTrace	show trace plots or not, default = T
graphicParameters	graphic parameters as list for plot function
...	parameters to give to getSample

Author(s)

Maximilian Pichler

Examples

## Not run: 
  
  # Create bayesian setup with  
  bayesianSetup <- createBayesianSetup(likelihood = testDensityNormal, 
                                       prior = createUniformPrior(lower = -10,
                                                                  upper = 10))
  # running MCMC
  out = runMCMC(bayesianSetup = bayesianSetup)
  
  # diagnostic plots
  plotDiagnostic(out)

## End(Not run)

BayesianTools documentation built on Feb. 16, 2023, 8:44 p.m.