Check if a taxonomic group is monophyletic — check

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")
#> Group 'P1' IS monophyletic (10 tips, MRCA node 54).
if (result$is_monophyletic) {
  message("P1 is monophyletic!")
} else {
  message("P1 is NOT monophyletic.")
}
#> P1 is monophyletic!