check_monophyly: Check if a taxonomic group is monophyletic

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

Check if a taxonomic group is monophyletic

Description

Tests whether all tips belonging to a specified taxonomic group form a monophyletic clade in the tree.

Usage

check_monophyly(
  tree,
  group,
  rank,
  format = "auto",
  custom_patterns = NULL,
  quiet = FALSE,
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

tree	A phylo object.
group	Character. The name of the taxonomic group to check (e.g., "P1", "Mammalia").
rank	Character. Taxonomic rank of the group. One of "domain", "phylum", "class", "order", "family", "genus", "species", or abbreviations "d", "p", "c", "o", "f", "g", "s".
format	Character. Taxonomy label format. One of "auto", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex". Default: "auto".
custom_patterns	Named list of regex patterns for custom format. Required when format = "custom_regex".
quiet	Logical. If TRUE, suppress informational messages. Default: FALSE.
delimiter_mode	Character. Embedded (Format A) parsing strategy: "reverse" (right-to-left, default), "greedy" (left-to-right), or "segment" (delimiter-to-delimiter extraction).
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.

group

Character. The group name.

n_tips

Integer. Number of tips belonging to the group.

mrca_node

Integer or NULL. The MRCA node number, or NULL if the group has fewer than 2 tips.

outsiders

Character vector. Tips in the MRCA clade that do not belong to the group (empty if monophyletic).

Case sensitivity (L-A2)

Group matching is case-insensitive. The query group and every parsed Group label are lower-cased with tolower() at comparison time (not during parsing) before matching, so "Proteobacteria" and "proteobacteria" match the same clade. parse_taxonomy itself preserves the original case of parsed labels; the lower-casing applied here is local to this comparison and keeps the two modules consistent about what a group name refers to.

Examples

data(example_tree)

# Check if phylum P1 is monophyletic
result <- check_monophyly(example_tree, "P1",
                          rank = "phylum", format = "GTDB")
if (result$is_monophyletic) {
  message("P1 is monophyletic!")
} else {
  message("P1 is NOT monophyletic.")
}

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