resolve_special_identifier: Resolve special ancestral node identifiers

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

Resolve special ancestral node identifiers

Description

Handles special identifiers for key ancestral nodes in the tree of life:

• LUCA: Last Universal Common Ancestor - MRCA of all Bacteria and Archaea

• LACA: Last Archaeal Common Ancestor - MRCA of all Archaea

• LBCA: Last Bacterial Common Ancestor - MRCA of all Bacteria

Usage

resolve_special_identifier(
  tree,
  identifier,
  format = "auto",
  quiet = FALSE,
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

tree	A phylo object.
identifier	Character. One of "ROOT", "LUCA", "LACA", "LBCA". ROOT Root of the tree LUCA Last Universal Common Ancestor (MRCA of all Bacteria and Archaea) LACA Last Archaeal Common Ancestor (MRCA of all Archaea) LBCA Last Bacterial Common Ancestor (MRCA of all Bacteria)
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:

node

Integer. The node number of the MRCA, or NULL if not found.

identifier

Character. The identifier name.

description

Character. Human-readable description.

n_tips

Integer. Number of descendant tips.

tip_labels

Character vector. Labels of descendant tips.

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