resolve_taxonomy_source_priority: Resolve taxonomy source priority (embedded vs table)

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

Resolve taxonomy source priority (embedded vs table)

Description

Unifies the no_taxonomy_file_priority flag (CLI) and the explicit taxonomy_source_priority value (CLI / Shiny) into a single canonical "embedded" / "table" string. Replaces the inline if previously duplicated in cli.R and plot_timetree().

Usage

resolve_taxonomy_source_priority(
  no_taxonomy_file_priority = FALSE,
  taxonomy_source_priority = "table"
)

Arguments

no_taxonomy_file_priority	Logical. When TRUE, file taxonomy is only used as a fallback (embedded takes priority).
taxonomy_source_priority	Character "embedded" or "table". Ignored when no_taxonomy_file_priority is TRUE.

Value

Character: "embedded" or "table".

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