build_full_taxa_df: Build a full-rank taxonomy data.frame in a single pass (M-D4...

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

Build a full-rank taxonomy data.frame in a single pass (M-D4 helper)

Description

Used by clade-specific collapsing to avoid re-parsing every rank (and re-reading any taxonomy file) once per search rank. Produces one label-based full parse (format-specific parsers already compute all ranks at once) supplemented/overridden by a single taxonomy-file read when taxonomy_file is supplied.

Usage

build_full_taxa_df(
  labels,
  format = "auto",
  custom_patterns = NULL,
  taxonomy_file = NULL,
  file_sep = "auto",
  file_header = FALSE,
  file_priority = TRUE,
  table_sep = ";",
  delimiter_mode = "reverse",
  taxonomy_levels = NULL
)

Arguments

labels	Character vector of tip labels.
format	Format: "auto", "GTDB", "Silva", "NCBI", "custom_rank", "custom_regex", "embedded".
custom_patterns	Custom regex patterns (for "custom_regex" format).
taxonomy_file	Character. Path to external taxonomy file. Default: NULL.
file_sep	Character. Column separator for taxonomy file. Default: "auto".
file_header	Logical. Whether taxonomy file has header row. Default: FALSE.
file_priority	Logical. If TRUE, file taxonomy takes priority over label-based parsing. Default: TRUE.
table_sep	Character. Separator between taxonomy ranks. Default: ";".
delimiter_mode	Character. Embedded parsing strategy.
taxonomy_levels	Custom taxonomy level configuration. Default: NULL.

Value

data.frame with a label column plus one column per rank.

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