Allow forcing non-endemic to be singletons and new vignette on use and limits #45
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This PR addresses #36 by adding new functionality to
extract_island_species(), with the new argumentforce_nonendemic_singleton. This allows non-endemic species that would have previously been grouped as an endemic clade if the ancestral state reconstruction inferred their ancestral node to be on the island, to be force to be separate island colonists.This new functionality comes with complexity and nuance so we have drafted a new package vignette outlining the problem the new functionality aims to solve as well as the known limitations of this approach.
All of this work was done collaboratively with @luislvalente during the Naturalis Hackathon 2024.