calc_spp_association_evoreg: Quantifying species association with evoregions

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

Quantifying species association with evoregions

Description

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

Author(s)

Leandro Duarte, Renan Maestri and Gabriel Nakamura [e-mail]

References

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

Examples

## Not run: 
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

## End(Not run)

GabrielNakamura/Rrodotus documentation built on Aug. 31, 2023, 2:13 p.m.