Internal function for phyl.pca.
phyl.vcv(X, C, lambda)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.
value for \(\lambda\) transformation.
data matrix.
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.
Liam Revell liam.revell@umb.edu
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).
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.