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

In uyedaj/bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

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(...)

uyedaj/bayou documentation built on Feb. 22, 2025, 8:31 p.m.