any_outgroup: Checks whether the phylogeny has an outgroup that is not...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Checks whether the phylogeny has an outgroup that is not present on the island. This is critical when extracting data from the phylogeny so the stem age (colonisation time) is correct.

Description

Checks whether the phylogeny has an outgroup that is not present on the island. This is critical when extracting data from the phylogeny so the stem age (colonisation time) is correct.

Usage

any_outgroup(phylod)

Arguments

phylod

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

Value

Boolean

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)
phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))
any_outgroup(phylod)

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