Check if a special identifier corresponds to a monophyletic group

Tests whether the MRCA of the specified domains (identified by LUCA/LACA/LBCA) contains only tips from those domains (i.e., is monophyletic with respect to the target domains).

Usage

check_special_monophyly(
  tree,
  identifier,
  format = "auto",
  quiet = FALSE,
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

tree: A phylo object.
identifier: Character. One of "LUCA", "LACA", "LBCA".
format: Character. Taxonomy label format. Default: "auto".
quiet: Logical. If TRUE, suppress informational messages. Default: FALSE.
delimiter_mode: Character. Embedded parsing strategy: "reverse", "greedy", or "segment". Default: "reverse".
taxonomy_levels: Custom taxonomy level configuration (list with codes and names). Default: NULL.

Value

A list with components:

is_monophyletic: Logical. Whether the group is monophyletic.
identifier: Character. The identifier name.
node: Integer or NULL. The MRCA node number.
n_tips: Integer. Number of tips in the target domains.
n_outsiders: Integer. Number of outsider tips in the MRCA clade.
outsider_domains: Character vector. Domains of outsider tips.

Examples

data(example_tree)
result <- check_special_monophyly(example_tree, "LBCA")
#> LBCA IS monophyletic (50 tips, MRCA node 51).
if (result$is_monophyletic) {
  message("LBCA is monophyletic!")
}
#> LBCA is monophyletic!