summarize_taxonomy_quality: Report taxonomy label parsing quality

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

Report taxonomy label parsing quality

Description

Provides a detailed report on how well taxonomic labels can be parsed, including per-rank parse rates and failed labels.

Usage

summarize_taxonomy_quality(
  labels,
  format = "auto",
  custom_patterns = NULL,
  taxonomy_levels = NULL,
  delimiter_mode = "reverse"
)

Arguments

labels	Character vector of tip labels
format	Format: "auto", "embedded", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex"
custom_patterns	Custom regex patterns (for "custom_regex" format)
taxonomy_levels	Custom taxonomy level configuration
delimiter_mode	Character. Embedded parsing strategy: "reverse", "greedy", "segment".

Value

Invisibly returns a list with parsing statistics

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