build_taxonomy_lookup: Build taxonomy lookup from file

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

Build taxonomy lookup from file

Description

Creates a lookup table from a taxonomy file that can be used to supplement or override label-based taxonomy parsing.

Usage

build_taxonomy_lookup(file, sep = "auto", header = FALSE, table_sep = ";")

Arguments

file	Character. Path to the taxonomy table file.
sep	Character. Column separator. Default: "auto".
header	Logical. Whether the file has a header row. Default: FALSE.
table_sep	Character. Separator between taxonomy ranks in the second column. Default: ";".

Value

A named list where names are tip labels and values are data.frame rows with taxonomy information.

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