Affiliation of assemblages based on phylogenetic turnover

Affiliation of assemblages based on phylogenetic turnover

Usage

calc_affiliation_evoreg(phylo.comp.dist, groups)

Arguments

phylo.comp.dist

A distance matrix indicating the phylogenetic (or taxonomic/functional) distance composition among assemblages

groups

A character vector indicating the group of each assemblage. This object can be obtained with calc_evoregions

Value

A list with two matrix, one containing affiliation values and the group in which each cell is classified and the other containing cell coordinates

Details

The function calculates the degree of affiliation of each community to the region (or evoregion), in which that community was classified. If used coupled with a analysis of Principal Coordinates of Phylogenetic Structure (PCPS) to represent the phylogenetic distances the analysis output of the analysis will represent the degree of membership of assemblages to each evoregion, as described in Maestri and Duarte 2020.

References

Maestri, R and Duarte L.d.S. (2020). Evoregions: Mapping shifts in phylogenetic turnover across biogeographic regions. Methods in Ecology and Evolution, 11, 1652-1662.

Examples

if (FALSE) {
# First run the classification
#' data(akodon_newick) # phylogenetic tree
data(akodon_sites) # occurrence data 
akodon_pa <- akodon_sites %>% 
    dplyr::select(-LONG, -LAT)
spp_in_tree <- names(akodon_pa) %in% akodon_newick$tip.label
akodon_pa_tree <- akodon_pa[, spp_in_tree]
regions <- calc_evoregions(comm = akodon_pa, phy = akodon_newick)
site_region <- regions$Cluster_Evoregions # classification of each community in regions

axis_sel <- which(regions$PCPS$prop_explainded >= 
    regions$PCPS$tresh_dist) # significant PCPS axis
PCPS_thresh <- regions$PCPS$vectors[, axis_sel] # only significant axis
dist_phylo_PCPS <- vegan::vegdist(PCPS_thresh, method = "euclidean") # distance matrix 
calc_affiliation_evoreg(phylo.comp.dist = dist_phylo_PCPS,
    groups = regions$Cluster_Evoregions) # affiliation
}