extract_island_species {DAISIEprep}

Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object

Description

Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object

Usage

extract_island_species(
  phylod,
  extraction_method,
  island_tbl = NULL,
  include_not_present = FALSE,
  unique_clade_name = TRUE
)

Arguments

phylod

A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.

extraction_method

A character string specifying whether the colonisation time extracted is the minimum time (min) (before the present), or the most probable time under ancestral state reconstruction (asr).

island_tbl

An instance of the Island_tbl class.

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.

unique_clade_name

Boolean determining whether a unique species identifier is used as the clade name in the Island_tbl object or a genus name which may not be unique if that genus has several independent island colonisations

Value

An object of Island_tbl class

Examples

set.seed(
  1,
  kind = "Mersenne-Twister",
  normal.kind = "Inversion",
  sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)
phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e",
                     "bird_f", "bird_g", "bird_h", "bird_i", "bird_j")
phylo <- phylobase::phylo4(phylo)
endemicity_status <- sample(
  c("not_present", "endemic", "nonendemic"),
  size = length(phylobase::tipLabels(phylo)),
  replace = TRUE,
  prob = c(0.6, 0.2, 0.2)
)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
extract_island_species(phylod, extraction_method = "min")