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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.

Source: R/extract_species_asr.R
extract_species_asr.Rd

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
)

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.

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(0.8, 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
)
#> Class:  Island_tbl 
#>   clade_name  status missing_species   col_time col_max_age branching_times
#> 1     bird_i endemic               0 0.04960523       FALSE              NA
#>   min_age species clade_type
#> 1      NA  bird_i          1