pars2simmap: Convert a bayou parameter list into a simmap formatted...

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

Convert a bayou parameter list into a simmap formatted phylogeny

Description

This function converts a bayou formatted parameter list specifying regime locations into a simmap formatted tree that can be plotted using plotSimmap from phytools or the plotRegimes function from bayou.

Usage

pars2simmap(pars, tree)

Arguments

pars	A list that contains sb (a vector of branches with shifts), loc (a vector of shift locations), t2 (a vector of theta indices indicating which theta is present after the shift).
tree	A tree of class 'phylo'

Details

pars2simmap takes a list of parameters and converts it to simmap format

Value

A list with elements: tree A simmap formatted tree, pars bayou formatted parameter list, and cols A named vector of colors.

Examples

tree <- reorder(sim.bdtree(n=100), "postorder")

pars <- list(k=5, sb=c(195, 196, 184, 138, 153), loc=rep(0, 5), t2=2:6)
tr <- pars2simmap(pars, tree)
plotRegimes(tr$tree, col=tr$col)

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