bayou (version 2.1.1)

bayou.lik: Function for calculating likelihood of an OU model in bayou using the threepoint algorithm

Description

Function for calculating likelihood of an OU model in bayou using the threepoint algorithm

Usage

bayou.lik(pars, cache, X, model = "OU")

Arguments

pars

A list of parameters to calculate the likelihood

cache

A bayou cache object generated using .prepare.ou.univariate

X

A named vector giving the tip data

model

Parameterization of the OU model. Either "OU", "QG" or "OUrepar".

Details

This function implements the algorithm of Ho and Ane (2014) implemented in the package phylolm for the OUfixedRoot model. It is faster than the equivalent pruning algorithm in geiger, and can be used on non- ultrametric trees (unlike OU.lik, which is based on the pruning algorithm in geiger).