regime.plot: Adds visualization of regimes to a plot

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

Adds visualization of regimes to a plot

Description

Adds visualization of regimes to a plot

Usage

regime.plot(pars, tree, cols, type = "rect", transparency = 100)

Arguments

pars	A bayou formatted parameter list
tree	A tree of class 'phylo'
cols	A vector of colors to give to regimes, in the same order as pars$sb
type	Either "rect", "density" or "lines". "rect" plots a rectangle for the 95% CI for the stationary distribution of a regime. "density" varies the transparency of the rectangles according to the probability density from the stationary distribution. "lines" plots lines for the mean and 95% CI's without filling them.
transparency	The alpha transparency value for the maximum density, max value is 255.

uyedaj/bayou documentation built on Jan. 28, 2024, 5:09 a.m.