rm_duplicate_island_species: Remove any duplicated species from the 'island_tbl' after...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Remove any duplicated species from the island_tbl after "asr" extraction

Description

Removes any duplicates species from the island_tbl by choosing to either have duplicated species be in smaller, more recently colonised clade(s) and removing them from the larger, older clade(s) (nested_asr_species = "split"), or removing the smaller, more recently colonised clade(s) in favour of leaving them in the larger, older clade(s) (nested_asr_species = "group").

Usage

rm_duplicate_island_species(
  island_tbl,
  phylod,
  nested_asr_species,
  include_not_present
)

Arguments

island_tbl	An instance of the Island_tbl class.
phylod	A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.
nested_asr_species	A character string which determines whether nested island colonists are split into separate colonists ("split"), or grouped into a single clade ("group"). Nested species are those whose tip state is on the island, and they have ancestral nodes on the island, but there are nodes in between these island state nodes that have the state not_present (i.e. not on the island). Therefore, the colonisation time can be extracted as the most recent node state on the island (this can be the branching time before the tip if the ancestor node of the tip is not on the island), or the older node state of the larger clade, for "split" or "group" respectively. Note This argument only applies when extraction_method = "asr".
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_tbl class

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