extract_species_asr: Extracts the colonisation, diversification, and endemicty...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

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
)

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
)

DAISIEprep documentation built on April 3, 2025, 9:26 p.m.