pcd {phyr}

pairwise site phylogenetic community dissimilarity (PCD) within a community

Description

Calculate pairwise site PCD, users can specify expected values from pcd_pred().

Usage

pcd(comm, tree, expectation = NULL, cpp = TRUE, verbose = TRUE, ...)

Arguments

comm

A site by species data frame or matrix, sites as rows.

tree

A phylogeny for species.

expectation

nsp_pool, psv_bar, psv_pool, and nsr calculated from pcd_pred().

cpp

Whether to use loops written with c++, default is TRUE.

verbose

Do you want to see the progress?

...

Other arguments.

Value

A list of a variety of pairwise dissimilarities.

References

Ives, A. R., & Helmus, M. R. 2010. Phylogenetic metrics of community similarity. The American Naturalist, 176(5), E128-E142.

Examples

x1 = pcd_pred(comm_1 = comm_a, comm_2 = comm_b, tree = phylotree, reps = 100)
pcd(comm = comm_a, tree = phylotree, expectation = x1)