check_phylo_data: Checks whether \linkS4class{phylo4d} object conforms to the...

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

Checks whether ⁠\linkS4class{phylo4d}⁠ object conforms to the requirements of the DAISIEprep package. If the function does not return anything the data is ready to be used, if an error is returned the data requires some pre-processing before DAISIEprep can be used

Description

Checks whether ⁠\linkS4class{phylo4d}⁠ object conforms to the requirements of the DAISIEprep package. If the function does not return anything the data is ready to be used, if an error is returned the data requires some pre-processing before DAISIEprep can be used

Usage

check_phylo_data(phylod)

Arguments

phylod

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

Value

Nothing or error message

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))
check_phylo_data(phylod)

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