bayou (version 2.1.1)

phenogram.density: Plot a pheongram with the posterior density for optima values

Description

Plots a phenogram and the posterior density for optima values

Usage

phenogram.density(tree, dat, burnin = 0, chain, colors = NULL,
  pp.cutoff = NULL, K = NULL, ...)

Arguments

tree

A phylogeny of class 'phylo'

dat

A named vector of tip data

burnin

The initial proportion of the MCMC to be discarded

chain

A bayouMCMC object that contains the results of an MCMC chain

colors

An optional named vector of colors to assign to regimes, NULL results in no regimes being plotted.

pp.cutoff

The posterior probability cutoff value. Branches with posterior probabilities of having a shift above this value will have the average location of the regime shift painted onto the branches.

K

A list with the values of K to be plotted. If NULL all values of K are combined and a total posterior produced. This allows separate lines to be plotted for different numbers of shifts so that the location of optima can be compared, for example, between all samples that have 1 vs. 2 shifts in the posterior.

...

Additional parameters passed to phenogram(...)