check_special_monophyly: Check if a special identifier corresponds to a monophyletic...

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Check if a special identifier corresponds to a monophyletic group

Description

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")
if (result$is_monophyletic) {
  message("LBCA is monophyletic!")
}

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.