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.

Value

Data frame with single column of character strings and row names

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.

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
)