Quantifying species association with evoregions
calc_spp_association_evoreg.Rd
Quantifying species association with evoregions
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
}