Phylogenetic beta diversity between communities

Mean phylogenetic distance between the species of each pair of communities (COMDIST), the metric used by Peres-Neto & Kembel (2015). Values in comm are the weights of the species, so incidence data give the unweighted mean and abundances give the abundance-weighted mean.

Usage

phylo_beta(comm, tree)

Arguments

comm

Matrix with one row per site and one column per species, named as the tips of tree. Every site needs at least one individual.

tree

A phylo object with the same species as comm.

Value

A dist object.

Details

Two communities with the same species have a distance equal to their mean pairwise distance, not zero, whereas the distance of a community to itself is set to zero. Peres-Neto & Kembel (2015) describe the matrix as fully Euclidean, but this does not always hold. If sites a and b both have species x and y, site c has only x and site d has only y, then a and b lie halfway between c and d and should coincide, yet their distance is not zero. The pseudo-F of phylo_beta_test() does not require a Euclidean matrix (McArdle & Anderson 2001).

References

McArdle, B. H., & Anderson, M. J. (2001). Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology, 82, 290–297. doi:10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2

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)
tree <- treeshapesim::sim_tree_shape(5)
comm <- matrix(rbinom(20, 1, 0.7) + diag(1, 4, 5), 4,
               dimnames = list(NULL, tree$tip.label))
phylo_beta(comm > 0, tree)
#>          1        2        3
#> 2 1.168432                  
#> 3 1.097033 1.108714         
#> 4 1.251324 1.261214 1.251324