Quantifying species association with evoregions

Usage

calc_spp_association_evoreg(comm, group.comm, spp.association = 0.7)

Arguments

comm: An assemblage/community matrix with communities in rows and species in columns
group.comm: A vector containing the classification of each community in groups
spp.association: A scalar indicating the level of association that will be evaluated to assign species to groups. Default is 0.7

Value

A matrix with species in the rows and one columns indicating the name of the group in which the species is associated given the level of species association used in the argument spp.association. If the species fail to reach the threshold it will be assigned the "fuzzy" status

References

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

Author

Leandro Duarte, Renan Maestri and Gabriel Nakamura gabriel.nakamura.souza@gmail.com

Examples

if (FALSE) {
data(akodon_sites) # occurrence data 
akodon_pa <- akodon_sites %>% dplyr::select(-LONG, -LAT)
data(akodon_newick) # phylogenetic tree
spp_in_tree <- names(akodon_pa) %in% akodon_newick$tip.label
akodon_pa_tree <- akodon_pa[, spp_in_tree]
regions <- calc_evoregions(comm = akodon_pa, phy = akodon_newick) # compute evoregions
groups <- regions$cluster_evoregions
calc_spp_association_evoreg(comm = akodon_pa_tree, 
                       group.comm = groups, 
                       spp.association = 0.7) # calculate species association
}