Node contrasts of a phylogeny

Codes each node of a tree as a contrast between its two descendant clades, as in Leibold et al. (2010). One clade starts at -1 and the other at 1, and the value is halved at each node on the way to the tips. Species outside the node get zero.

Usage

node_contrasts(tree, cherries = TRUE, branch_lengths = FALSE)

Arguments

tree

A phylo object with dichotomous nodes.

cherries

Keep nodes that join two tips? The article tests them (its Figure 3), but the function CreateNodeContrasts of the authors leaves them out.

branch_lengths

Use the branch lengths of tree?

Value

Matrix with one row per tip and one column per node, named by the node numbers of tree.

Details

With branch_lengths = TRUE, values follow section III of the supplement of Leibold et al. (2010): each branch between a species and the node counts its length divided by the number of species below it, and the sum is divided by the total length of that side of the node. Species that share history get less weight, and each side still sums to 1. The supplement proposes this coding for trees in which all species are equally distant from the root.

Note

Adapted from the MATLAB function CreateNodeContrasts in the supplement of Leibold et al. (2010).

References

Leibold, M. A., Economo, E. P., & Peres-Neto, P. (2010). Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography. Ecology Letters, 13, 1290–1299. doi:10.1111/j.1461-0248.2010.01523.x

Examples

node_contrasts(ape::read.tree(text = "((a,b),(c,(d,e)));"))
#>       6  7    8  9
#> a -0.50 -1  0.0  0
#> b -0.50  1  0.0  0
#> c  0.50  0 -1.0  0
#> d  0.25  0  0.5 -1
#> e  0.25  0  0.5  1

# Figure S2 of the supplement
tree <- ape::read.tree(text = "((((A:0.2,B:0.2):0.65,C:0.85):0.15,D:1):0.4,(E:0.5,F:0.5):0.9);")
round(node_contrasts(tree, branch_lengths = TRUE), 3)
#>        7      8    9 10 11
#> A -0.196 -0.280 -0.5 -1  0
#> B -0.196 -0.280 -0.5  1  0
#> C -0.290 -0.439  1.0  0  0
#> D -0.319  1.000  0.0  0  0
#> E  0.500  0.000  0.0  0 -1
#> F  0.500  0.000  0.0  0  1