Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object using the "min" algorithm that extract island species as the shortest time to the present.

Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object using the "min" algorithm that extract island species as the shortest time to the present.

Usage

extract_species_min(
  phylod,
  species_label,
  species_endemicity,
  island_tbl,
  unique_clade_name
)

Arguments

phylod: A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.
species_label: The tip label of the species of interest.
species_endemicity: A character string with the endemicity, either "endemic" or "nonendemic" of an island species, or "not_present" if not on the island.
island_tbl: An instance of the Island_tbl class.
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))
island_tbl <- island_tbl()
extract_species_min(
  phylod = phylod,
  species_label = "bird_g",
  species_endemicity = "nonendemic",
  island_tbl = island_tbl,
  unique_clade_name = TRUE
)
#> Class:  Island_tbl 
#>   clade_name     status missing_species  col_time col_max_age branching_times
#> 1     bird_g nonendemic               0 0.3800341       FALSE              NA
#>   min_age species clade_type
#> 1      NA  bird_g          1