ConvertPhangornReconstructions {corHMM}

Convert phangorn reconstruction to a vector

Description

Converts a character reconstruction from phangorn into a vector of tip and node states. Nodes where there are equal weights among states, ties are broken at random.

Usage

ConvertPhangornReconstructions(x, site = 1, best = TRUE)

Arguments

x

The phyDat object that contains a character reconstruction from phangorn

site

The character number to convert into a vector

best

A logical indicating whether the state that maximizes some function (likelihood, parsimony, etc.) is to be returned.

Details

Creates a vector that contains the best tips and node state from a phangorn reconstruction.