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Proportional contribution of an ancestral area to the species in other region

calc_dispersal_from.Rd

For the species present in a site, the function calculates the proportional contribution of ancestral areas to dispersal of lineage in the site's region.

Usage

calc_dispersal_from(W, tree, ancestral.area, biogeo)

Arguments

W

Occurrence matrix, rows are assemblages and columns are species

tree

Phylogenetic tree in newick format

ancestral.area

One column data frame with nodes in rows and one column indicating the occurrence (biome/ecoregion) area of nodes

biogeo

One column data frame with assemblages in rows and their respective biome/ecoregion

Value

A data frame with assemblages in the rows and regions in the columns. The values indicates the percentage of contribution of each region to each assemblage. NA represents no contribution

See also

get_node_range_BioGeoBEARS

Author

Arthur V Rodrigues rodrigues.arthur.v@gmail.com

Examples

if (FALSE) {
data(akodon_sites) # occurrence matrix
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]
data(regions) # biogeographic region
data(resDEC) # output from ancestral area reconstruction
node.area <- get_node_range_BioGeoBEARS(resDEC,
                                        phyllip.file = here::here("inst", 
                                        "extdata", "geo_area_akodon.data")
                                        ,akodon_newick,max.range.size = 4) 
calc_dispersal_from(W=akodon_pa_tree,
                    tree=akodon_newick,
                    ancestral.area=node.area,biogeo=regions) # historical dispersal analysis
}