phyloDesign {phytools}

Compute design matrix for least squares analyses

Description

Primarily an internal function for optim.phylo.ls, this function creates a design matrix for least squares phylogenetic analysis.

Usage

phyloDesign(tree)

Arguments

tree

phylogenetic tree.

Details

This function returns a matrix containing the edges in the tree (in columns) and pairs of tip node numbers (in rows). Values in the matrix are either 1 if the edge is on the shortest path between the two tips; and 0 otherwise. Probably do not use unless you know what you're doing.

Value

A matrix.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.