bayou.lik: Function for calculating likelihood of an OU model in bayou...
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

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

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

`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".

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).

bayou documentation built on May 2, 2019, 2:46 a.m.