Partition island species richness into in-situ, import, and export components

For each island, counts in-situ speciation, import, and export events. In-situ speciation events are identified as cases in which an ancestral node is assigned to the same region as its descendant. Import events are cases where a descendant node is assigned to a different region than its ancestor. Export events are the reverse: the ancestral node is assigned to the focal island while its descendant is assigned to a different region. Both ancestor and descendant must be assigned to a region for any event to be detected.

Usage

decompose_diversity(phy, events, PAM)

Arguments

phy: The matched phylogenetic tree.
events: The data frame returned by map_insitu_events, with columns node, island, in_situ, export, and import.
PAM: The presence-absence matrix with islands as rows and species as columns, with a locale column for island names.

Value

A data frame with one row per island and columns:

island: Island name.
n_species: Total extant species on the island.
n_insitu: Species derived from in-situ speciation.
n_import: Import events into this island.
n_export: Export events out of this island.
prop_insitu: Proportion of species from in-situ speciation.