add_missing_species {DAISIEprep}

Adds a specified number of missing species to an existing island_tbl at the colonist specified by the species_to_add_to argument given. The species given is located within the island_tbl data and missing species are assigned. This is to be used after extract_island_species() to input missing species.

Description

Adds a specified number of missing species to an existing island_tbl at the colonist specified by the species_to_add_to argument given. The species given is located within the island_tbl data and missing species are assigned. This is to be used after extract_island_species() to input missing species.

Usage

add_missing_species(island_tbl, num_missing_species, species_to_add_to)

Arguments

island_tbl

An instance of the Island_tbl class.

num_missing_species

Numeric for the number of missing species in the clade.

species_to_add_to

Character string with the name of the species to identify which clade to assign missing species to.

Value

Object of Island_tbl class

Examples

set.seed(
  1,
  kind = "Mersenne-Twister",
  normal.kind = "Inversion",
  sample.kind = "Rejection"
)
phylo <- ape::rcoal(5)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- c(
  "not_present", "not_present", "endemic", "not_present", "not_present"
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
island_tbl <- extract_island_species(phylod, extraction_method = "min")
island_tbl <- add_missing_species(
  island_tbl = island_tbl,
  num_missing_species = 1,
  species_to_add_to = "bird_c"
)