is_multi_tip_species: Checks if a species is represented in the tree has multiple...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Checks if a species is represented in the tree has multiple tips and those tips form a monophyletic group (i.e. one species with multiple samples) all labeled as with the same endemicity status

Description

Checks if a species is represented in the tree has multiple tips and those tips form a monophyletic group (i.e. one species with multiple samples) all labeled as with the same endemicity status

Usage

is_multi_tip_species(phylod, species_label)

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.

Details

is_multi_tip_species() only returns TRUE if all tips for each sample of the species (i.e. conspecific tips) are labelled the same. It is possible that a phylogeny has multiple tips for the same species but only the island samples are labelled as "endemic" or "nonendemic" as the other tips are from samples from the mainland, and are labelled "not_present", see vignette("Multi_tip_extraction", package = "DAISIEprep").

Value

Boolean

DAISIEprep documentation built on April 3, 2025, 9:26 p.m.