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

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).

Value

A list containing:

loglik

The log-likelihood value of the fitted OU model.

theta

A vector of estimated optima for each evolutionary regime.

resid

The residuals, i.e., the differences between observed and expected values.

comp

A list of computed values from the three-point algorithm, including necessary likelihood calculations.

transf.phy

The transformed phylogenetic tree with modified branch lengths based on the model parameters.

bayou documentation built on June 10, 2025, 5:13 p.m.