BAMMtools (version 2.1.0)

plotPrior: Plot the prior and posterior distribution of shifts

Description

Generates a barplot of the prior and posterior distributions of the number of shifts.

Usage

plotPrior(mcmc, expectedNumberOfShifts = 1, burnin = 0.15, 
	priorCol = 'light blue', postCol = 'red', legendPos = 'topright', ...)

Arguments

mcmc

a dataframe of the mcmc_out file from a BAMM run, or the filename

expectedNumberOfShifts

Expected number of shifts under the prior

burnin

the fraction of samples to discard as burn-in

priorCol

color for the prior distribution

postCol

color for the posterior distribution

legendPos

placement of the legend, see legend

...

additional parameters that are passed to barplot

Value

• Invisibly returns a matrix with the probability of each shift number under the prior and the posterior.

Examples

data(mcmc.whales)

plotPrior(mcmc.whales, expectedNumberOfShifts = 1, burnin = 0.15)