resolve_group: Resolve group name or special identifier to MRCA node

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

Resolve group name or special identifier to MRCA node

Description

Unified function that handles both regular group names and special identifiers (LUCA, LACA, LBCA).

Usage

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

Arguments

tree	A phylo object.
group	Character. Group name or special identifier.
rank	Character. Taxonomic rank (ignored for special identifiers).
format	Character. Taxonomy label format. Default: "auto".
quiet	Logical. If TRUE, suppress messages. Default: FALSE.
delimiter_mode	Character. Embedded parsing strategy: "reverse", "greedy", or "segment". Default: "reverse".
custom_patterns	Named list of regex patterns for custom format. Required when format = "custom_regex".
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 or identifier.

is_special

Logical. Whether this is a special identifier.

node

Integer or NULL. The MRCA node number.

n_tips

Integer. Number of tips in the group.

outsiders

Character vector. Tips in MRCA not belonging to group.

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