ComputeVCV: Compute the variance-covariance matrix

In BMhyb: Comparative Methods for Phylogenetic Networks

Description

Creates a variance-covariance matrix for a network and parameters.

Usage

ComputeVCV(phy.graph, sigma.sq = 1, mu = 0, bt = 1, vh = 0,
  SE = 0, measurement.error = 0, gamma = 0.5)

Arguments

phy.graph	An ape::evonet object (a phylogeny stored in phylo format that also includes a reticulation matrix)
sigma.sq	Value for sigma squared
mu	Value for state at the root
bt	Value for beta parameter
vh	Value for Vh, the variance that comes from a hybridization event
SE	Standard error
measurement.error	How much uncertainty there is in tip values; a single number is applied to all taxa, a vector is applied to the corresponding taxa
gamma	In a hybridization event, what proportion of the trait comes from the donating parent. 0.5 means half comes from each parent

Value

Returns the variance-covariance matrix

BMhyb documentation built on Aug. 3, 2019, 1:02 a.m.