Extract tip states from a phylod object

Extract tip states from a phylod object

Usage

get_sse_tip_states(phylod, sse_model = "musse")

Arguments

phylod

A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.

sse_model

either "musse" (default) or "geosse". MuSSE expects state values 1, 2, 3, which here we encode as "not_present", "endemic", "nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and "endemic", respectively.

Value

an integer vector of tip states, as expected by SSE models