inst/examples/marginalPlotHelp.R

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

## Generate a test likelihood function. 
ll <- generateTestDensityMultiNormal(sigma = "no correlation")

## Create a BayesianSetup
bayesianSetup <- createBayesianSetup(likelihood = ll, lower = rep(-10, 3), upper = rep(10, 3))

## Finally we can run the sampler and have a look
settings = list(iterations = 1000, adapt = FALSE)
out <- runMCMC(bayesianSetup = bayesianSetup, sampler = "Metropolis", settings = settings)

marginalPlot(out, prior = TRUE)

## We can plot the marginals in several ways:
## violin plots
marginalPlot(out, type = 'v', singlePanel = TRUE) 
marginalPlot(out, type = 'v', singlePanel = FALSE)
marginalPlot(out, type = 'v', singlePanel = TRUE, prior = TRUE)

## density plot
marginalPlot(out, type = 'd', singlePanel = TRUE) 
marginalPlot(out, type = 'd', singlePanel = FALSE)
marginalPlot(out, type = 'd', singlePanel = TRUE, prior = TRUE)

## if you have a very wide prior you can use the xrange option to plot only
## a certain parameter range
marginalPlot(out, type = 'v', singlePanel = TRUE, xrange = matrix(rep(c(-5, 5), 3), ncol = 3))

##Further options
# We can pass arguments to getSample (check ?getSample) and to the density and violin plots
marginalPlot(out, type = 'v', singlePanel = TRUE, 
             settings = list(col = c('#FC006299','#00BBAA88')), prior = TRUE)
marginalPlot(out, type = 'v', singlePanel = TRUE, numSamples = 500)