gamma_pruning: Internally used function

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Internally used function

Description

Internally used function to compute the likelihood under a \Gamma model.

Usage

gamma_pruning(par, nrates=4, tree, x, model=NULL, median=TRUE,
  expm.method="Higham08.b", ...)

Arguments

par	function parameters.
nrates	number of discrete rate categories.
tree	object of class "phylo".
x	data in the form of a binary matrix.
model	design matrix of fitted model.
median	use the median of each rate category.
expm.method	method used for matrix exponentiation.
...	optional arguments.

Value

A value of the log-likelihood.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

phytools documentation built on April 3, 2025, 10:43 p.m.