get_region_occ: Species occurrence in each evoregion

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

Species occurrence in each evoregion

Description

Auxiliary function to produce an occurrence data frame of species in each region. This object can be with get_tipranges_to_BioGeoBEARS function to produce a phyllip file needed in BioGeoBEARS ancestral area reconstruction

Usage

get_region_occ(comm, site.region)

Arguments

comm	Occurrence data frame with species in colums and rows corresponding to assemblages
site.region	a character vector indicating the membership of each assemblage to regions

Value

An occurrence data frame with species as rownames and regions as columns

Author(s)

Gabriel Nakamura and Arthur Rodrigues

See Also

get_tipranges_to_BioGeoBEARS

Examples

data(akodon_sites)
data(akodon_newick)
akodon_pa <- akodon_sites %>% dplyr::select(-LONG, -LAT)
spp_in_tree <- names(akodon_pa) %in% akodon_newick$tip.label
akodon_pa_tree <- akodon_pa[, spp_in_tree]
data(regions)
site_evoregion <- regions$Cluster_Evoregions
get_region_occ(comm=akodon_pa_tree,site.region=site_evoregion)

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