DAISIEprep (version 1.0.1)

extract_species_asr: Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object using the "asr" algorithm that extract island species given their ancestral states of either island presence or absence.

Description

Extracts the colonisation, diversification, and endemicty data from phylogenetic and endemicity data and stores it in an Island_tbl object using the "asr" algorithm that extract island species given their ancestral states of either island presence or absence.

Usage

extract_species_asr(
  phylod,
  species_label,
  species_endemicity,
  island_tbl,
  include_not_present
)

Value

An object of island_tbl class

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.

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.

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(0.8, 0.1, 0.1))
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
phylod <- add_asr_node_states(
  phylod = phylod,
  asr_method = "parsimony"
)
island_tbl <- island_tbl()
extract_species_asr(
  phylod = phylod,
  species_label = "bird_i",
  species_endemicity = "endemic",
  island_tbl = island_tbl,
  include_not_present = FALSE
)