pars2simmap: Convert a bayou parameter list into a simmap formatted...
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description Usage Arguments Details Value Examples

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.

1	pars2simmap(pars, tree)

`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'

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

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

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)

Loading required package: ape
Loading required package: geiger
Loading required package: phytools
Loading required package: maps
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Loading required package: coda