calc_dispersal_from: Proportional contribution of an ancestral area to the species...

In GabrielNakamura/Rrodotus: Tools for Historical Biogeography analysis

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

Description

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

Author(s)

Arthur V Rodrigues [e-mail]

See Also

get_node_range_BioGeoBEARS

Examples

## Not run: 
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

## End(Not run)

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