Compute evolutionary VCV matrix for a tree & dataset
Primarily an internal function for phyl.pca; this can be used to compute the phylogenetic trait variance-covariance matrix given a phylogenetic VCV, λ, 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).
phyl.vcv(X, C, lambda)
lambda |
value for λ 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 |
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.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
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