plotRECON: Plot ancestral state reconstructions

In corHMM: Hidden Markov Models of Character Evolution

Plot ancestral state reconstructions

Description

Plots maximum likelihood ancestral state estimates on tree

Usage

plotRECON(phy, likelihoods, piecolors=NULL, cex=0.5, pie.cex=0.25, file=NULL, 
height=11, width=8.5, show.tip.label=TRUE, title=NULL, ...)

Arguments

phy	a phylogenetic tree, in ape “phylo” format.
likelihoods	likelihoods for ancestral states (see Details).
piecolors	a vector of colors for states.
cex	specifies the size of the font for labels (if used).
pie.cex	specifies the size of the symbols to plot on tree.
file	filename to which a pdf is saved.
height	height of plot.
width	width of plot.
show.tip.label	a logical indicating whether to draw tip labels to tree. The default is TRUE.
title	an optional title for the plot.
...	Additional arguments to be passed to the plot device

Details

Plots ancestral state estimates on provided tree. The likelihoods can be the states of an object of class rayDISC or class corDISC, or the lik.anc of an object of class ace (from the ape package).

Value

A plot indicating the maximum likelihood ancestral states at each internal node.

Author(s)

Jeffrey C. Oliver

See Also

corDISC, rayDISC

Examples

data(rayDISC.example)
## Perform ancestral state estimation, using a single rate of evolution and marginal 
## reconstruction of ancestral states
recon <- rayDISC(rayDISC.example$tree,rayDISC.example$trait,model="ER",
node.states="marginal")
## Plot reconstructions on tree
plotRECON(rayDISC.example$tree,recon$states,title="rayDISC Example")

corHMM documentation built on June 14, 2022, 1:05 a.m.