plotPrior: Plot the prior and posterior distribution of shifts

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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.

Author(s)

Pascal Title

Examples

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

BAMMtools documentation built on Sept. 13, 2024, 1:10 a.m.