Species occurrence in each evoregion
get_region_occ.RdAuxiliary 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
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
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)
#> A B C D E F G H I
#> A_aerosus 1 1 0 0 0 0 0 0 0
#> A_affinis 0 1 0 0 0 0 0 0 0
#> A_albiventer 1 1 0 0 0 0 0 0 0
#> A_azarae 0 0 1 0 0 1 0 0 1
#> A_boliviensis 1 0 0 0 0 0 0 0 0
#> A_budini 1 0 0 0 0 0 0 0 0
#> A_cursor 0 0 0 0 0 0 0 1 0
#> A_dayi 1 0 0 1 0 0 0 0 0
#> A_dolores 0 0 1 1 0 0 0 0 0
#> A_fumeus 1 0 0 0 0 0 0 0 0
#> A_iniscatus 0 0 0 1 1 0 0 0 0
#> A_juninensis 1 0 0 0 0 0 0 0 1
#> A_kofordi 1 0 0 0 0 0 0 0 0
#> A_lindberghi 1 0 0 0 0 0 0 1 0
#> A_lutescens 1 0 0 0 0 0 0 0 0
#> A_mimus 1 0 0 0 0 0 0 0 0
#> A_mollis 0 1 0 0 0 0 0 0 0
#> A_montensis 0 0 0 0 0 0 0 1 0
#> A_mystax 0 0 0 0 0 0 0 1 0
#> A_orophilus 0 1 0 0 0 0 0 0 0
#> A_paranaensis 0 0 0 0 0 1 0 1 0
#> A_reigi 0 0 0 0 0 1 0 0 0
#> A_siberiae 1 0 0 0 0 0 0 0 0
#> A_simulator 1 0 0 0 0 0 0 0 0
#> A_spegazzinii 1 0 1 0 0 0 0 0 0
#> A_subfuscus 1 0 0 0 0 0 0 0 0
#> A_sylvanus 1 0 0 0 0 0 0 0 0
#> A_toba 0 0 1 0 0 0 1 0 0
#> A_torques 1 0 0 0 0 0 0 0 0
#> A_varius 1 0 0 0 1 0 0 0 0