Phylogenetic eigenvectors

Principal coordinates of the patristic distances among species, the first step of the phylogenetic community composition of Peres-Neto & Kembel (2015).

Usage

phylo_eigenvectors(tree, squared = FALSE)

Arguments

tree

A phylo object.

squared

Use -PD^2 / 2, as in a classic principal coordinate analysis, instead of -PD / 2, the form printed by Peres-Neto & Kembel (2015)?

Value

Matrix with one row per tip and one column per positive eigenvalue.

References

Peres-Neto, P. R., & Kembel, S. W. (2015). Phylogenetic gradient analysis: environmental drivers of phylogenetic variation across ecological communities. Plant Ecology, 216, 709–724. doi:10.1007/s11258-014-0405-0

Examples

set.seed(1)
dim(phylo_eigenvectors(treeshapesim::sim_tree_shape(10)))
#> [1] 10  9