parse_taxonomy: Unified taxonomy parsing entry point

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

Unified taxonomy parsing entry point

Description

Parses taxonomic information from tip labels using the specified format and returns a data.frame of group assignments. Intended for use as a stable library API by external workflows (e.g., Snakemake/Nextflow).

Usage

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

Arguments

labels	Character vector of tip labels
rank	Taxonomic rank (abbreviation or full name)
format	Format: "auto", "embedded", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex"
custom_patterns	Custom regex patterns (required when format = "custom_regex")
taxonomy_levels	Custom taxonomy level configuration (list with codes and names)
delimiter_mode	Character. Embedded parsing strategy: "reverse", "greedy", "segment".

Value

data.frame with columns: label, Group

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