ConvertPhangornReconstructions: Convert phangorn reconstruction to a vector

In corHMM: Hidden Markov Models of Character Evolution

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.

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