validate_taxonomy_no_cycles: Detect circular dependencies in taxonomy table

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

Detect circular dependencies in taxonomy table

Description

Validates full taxonomy consistency by checking for cyclical relationships between every pair of adjacent ranks (coarsest to finest), not just the canonical domain/phylum/class/order chain. For example:

• domain <-> phylum, phylum <-> class, class <-> order,

• order <-> family, family <-> genus, genus <-> species

A circular dependency means a value appears as both a high-rank and a low-rank member forming a loop (e.g. Row 1: d__A;p__B, Row 2: d__B;p__A).

Usage

validate_taxonomy_no_cycles(taxa_df, filepath = "<taxonomy>")

Arguments

taxa_df	data.frame with taxonomy columns (domain, phylum, class, etc.).
filepath	Character. Source file for error messages.

Value

Invisibly returns TRUE if no cycles. Aborts on detection (class Rclade_validate_error).

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