pt_step2_resolve_taxonomy: Step 2: Resolve taxonomy / collapsing mode

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

Step 2: Resolve taxonomy / collapsing mode

Description

Determines whether we are in clade-specific, custom-groups, or rank-based mode and parses the taxonomy accordingly.

Usage

pt_step2_resolve_taxonomy(
  tree,
  clade,
  strict,
  groups,
  rank,
  taxonomy_format,
  custom_patterns,
  taxonomy_file,
  taxonomy_file_sep,
  taxonomy_file_header,
  taxonomy_file_priority,
  taxonomy_table_sep,
  taxonomy_delimiter_mode,
  taxonomy_levels,
  low_memory
)

Value

A named list with:

group_vec	named vector mapping tip labels to groups
detected_format	resolved taxonomy format string

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