Test phylogenetic community composition against the environment

Implements the phylogenetic community composition (PCC) framework of Peres-Neto & Kembel (2015). Phylogenetic eigenvectors are standardised with species weights and averaged within sites, and each resulting variable is regressed on the predictors with site weights. The test statistic is the variance of the adjusted R2 across eigenvectors. It is tested by permuting sites, which breaks the link between composition and environment, and by permuting species across the tips, which breaks the link between composition and phylogeny. The association requires both, so the p-value to report is the larger of the two.

Usage

pcc_test(
  comm,
  tree,
  env,
  n_perm = 999,
  squared = FALSE,
  site_permutations = NULL
)

Arguments

comm

Matrix with one row per site and one column per species. Species are matched to the tips of tree by name, in any order, and those in only one of the two are dropped with a warning. Every site needs at least one individual.

tree

A phylo object.

env

Predictor, or matrix or data frame of predictors, with one row per site.

n_perm

Number of permutations of sites and of species.

squared

Passed to phylo_eigenvectors().

site_permutations

Optional matrix of site indices with one permutation per row, for example from torus_permutations(), to use instead of free permutations of sites.

Value

List of class mc_pcc with r2, the mean of the positive adjusted R2 values, which is the value the authors recommend reporting; statistic, the variance of the adjusted R2 across eigenvectors; p_site, p_taxa and p_max; r2_adjusted, with one value per eigenvector; and permutations.

Details

The authors used presences and absences. Abundances are accepted, with species and site totals as weights. Species without individuals leave the analysis.

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)
tree <- treeshapesim::sim_tree_shape(20)
traits <- species_traits(tree, lambda = 1, optima_range = c(-1, 101),
                         rmax_range = c(0, 30))
env <- runif(50, 0, 100)
comm <- simulate_static(traits, env, incidence = TRUE)$abundance
keep <- rowSums(comm) > 0
pcc_test(comm[keep, ], tree, env[keep], n_perm = 99)
#> <mc_pcc> phylogenetic community composition
#> mean positive adjusted R2: 0.0965 
#> permutations: 99 free of sites, 99 of species; smallest possible p: 0.01 
#> p (sites): 0.01  p (species): 0.01  p (max): 0.01