parse_embedded: Parse Format A: Embedded taxonomy labels

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

Parse Format A: Embedded taxonomy labels

Description

Parses labels like GB_GCA_000252485.1_d_Bacteria_p_Cyanobacteriota_c_... using delimiters _d_, _p_, _c_, _o_, _f_, _g_, _s_.

Usage

parse_embedded(labels, levels = NULL, delimiter_mode = "reverse")

Arguments

labels	Character vector of tip labels
levels	List with codes and names vectors for taxonomy levels.
delimiter_mode	Character. One of "reverse", "greedy", "segment". Default: "reverse".

Details

Supports three delimiter matching strategies:

• "reverse" (default): match ranks from right-to-left to reduce ambiguity when taxonomy names contain underscores.

• "greedy": match ranks left-to-right using a character-class boundary (faster but less robust to underscores in names).

• "segment": extract the segment between each rank delimiter and the next rank delimiter, preserving underscores within values.

All three strategies tolerate double-underscore rank separators (e.g. _p__Nanoarchaeota, common in accession-prefixed embedded labels); leading underscores left over from such schemes are trimmed from parsed values.

Value

data.frame with taxonomy columns

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