resolve_target_domains: Resolve the target/expected taxonomy domains for a special...

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

Resolve the target/expected taxonomy domains for a special ancestral identifier.

Description

Single source of truth for which taxonomy domains a special identifier maps to. Shared by resolve_special_identifier() (to find the tips belonging to the identifier) and check_special_monophyly() (to decide which domains are "inside" the clade), so the two call sites cannot drift apart.

Usage

resolve_target_domains(identifier, all_domains)

Arguments

identifier	Character, one of "ROOT", "LUCA", "LACA", "LBCA".
all_domains	Character vector of domain names present in the relevant tip set (full tree for resolution, MRCA clade for monophyly checking).

Value

Character vector of target domains.

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