create_endemicity_status: Creates a data frame with the endemicity status (either...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Creates a data frame with the endemicity status (either 'endemic', 'nonendemic', 'not_present') of every species in the phylogeny using a phylogeny and a data frame of the island species and their endemicity (either 'endemic' or 'nonendemic') provided.

Description

Creates a data frame with the endemicity status (either 'endemic', 'nonendemic', 'not_present') of every species in the phylogeny using a phylogeny and a data frame of the island species and their endemicity (either 'endemic' or 'nonendemic') provided.

Usage

create_endemicity_status(phylo, island_species)

Arguments

phylo	A phylogeny either as a phylo (from the ape package) or phylo4 (from the phylobase package) object.
island_species	Data frame with two columns. The first is a character string of the tip_labels with the tip names of the species on the island. The second column a character string of the endemicity status of the species, either endemic or nonendemic.

Details

Species included in the island_species data frame but not included in the phylo will not be included in the output and warning will print all of the species that are in the island_species that are not found in the phylo.

Value

Data frame with single column of character strings and row names

Examples

set.seed(
  1,
  kind = "Mersenne-Twister",
  normal.kind = "Inversion",
  sample.kind = "Rejection"
)
phylo <- ape::rcoal(4)
phylo$tip.label <- c("species_a", "species_b", "species_c", "species_d")
phylo <- methods::as(phylo, "phylo4")
island_species <- data.frame(
  tip_labels = c("species_a", "species_b", "species_c", "species_d"),
  tip_endemicity_status = c("endemic", "endemic", "endemic", "nonendemic")
)
endemicity_status <- create_endemicity_status(
  phylo = phylo,
  island_species = island_species
)

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