parmap.W: Calculate the weight matrix of a set of regimes on a...

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Calculate the weight matrix of a set of regimes on a phylogeny

Description

These functions calculate weight matrices from regimes specified by a bayou formatted parameter list parmap.W calculates the weight matrix for a set of regimes from a phylogeny with a stored regime history. .parmap.W calculates the same matrix, but without checks and is generally run internally.

Usage

parmap.W(tree, pars)

Arguments

tree	either a tree of class "phylo" or a cache object produced by bayOU's internal functions. Must include list element 'maps' which is a simmap reconstruction of regime history.
pars	a list of the parameters used to calculate the weight matrix. Only pars$alpha is necessary to calculate the matrix, but others can be present.

Details

.parmap.W is more computationally efficient within a mcmc and is used internally.

Value

A matrix where rows correspond to branches in the phylogenetic tree, and columns correspond to the different evolutionary regimes. Each entry in the matrix represents the weight of a given regime on a given branch.

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