extract_asr_clade {DAISIEprep}

Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species.

Description

Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species.

Usage

extract_asr_clade(phylod, species_label, clade, include_not_present)

Arguments

phylod

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

species_label

The tip label of the species of interest.

clade

A numeric vector which the indices of the species which are in the island clade.

include_not_present

A boolean determining whether species not present on the island should be included in island colonist when embedded within an island clade. Default is FALSE.

Value

An object of Island_colonist class