phyl.vcv: Compute evolutionary VCV matrix for a tree & dataset
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

phyl.vcv

R Documentation

Compute evolutionary VCV matrix for a tree & dataset

Description

Internal function for phyl.pca.

Usage

phyl.vcv(X, C, lambda)

Arguments

`lambda`	value for `\lambda` transformation.
`X`	data matrix.
`C`	matrix containing the height above the root of each pair of species in the tree. Typically this will have been produced by calling `vcv.phylo`.

Details

Primarily designed as an internal function for phyl.pca; phyl.vcv can be used to compute the phylogenetic trait variance-covariance matrix given a phylogenetic VCV, \lambda, and a data matrix.

This function should not be confused with vcv.phylo in the ape package (although one of the objects returned is the output of vcv.phylo).

Value

A list containing three elements, as follows: C, the matrix vcv.phylo transformed by lambda; R, the among trait variance-covariance matrix for the data in X; and alpha, a vector of ancestral states at the root node of the tree.