Applies decision rules to reconstructed nodes to classify each speciation event as in-situ, colonization, or ambiguous

Usage

map_insitu_events(recons, phy, PAM, threshold = 0.5)

Arguments

recons: A list of ancestral state reconstructions returned by run_geo_asr. We do not recommend inputting a custom list for this function, but if you need to, make sure that the list is composed of ape::ace objects, each named after a locality. Refer to run_geo_asr for more information about how the original function estimates ancestral states.
phy: The phylogenetic tree associated with your data
PAM: A presence-absence matrix reflecting where each species of interest is located. The match_island_phylo function will create this PAM, but if the user would prefer to input a custom PAM, make sure that it has a column titled "locale" with the name of an island in each row, and each subsequent column is titled with a species name. Each species column should include either a 0 (absence) or a 1 (presence), signifying whether that species occurs on the island in a given row.
threshold: The threshold of probability at which it is reasonable to infer that a given ancestral node occurred on the same island as a given set of tips. Default: 0.5

Value

A dataframe including node numbers, islands associated with those nodes, and whether an in situ speciation event was likely at that node/island combination.