Embed accepted taxon info at build time (synonym self-join)

Used by the taxifydb build pipeline and by taxify's own test fixtures. For every synonym row, resolves the accepted taxon and embeds its name, family, genus, and (when authorship_col is supplied) authorship directly. Handles synonym chains by iterating until stable (max 10 hops).

Usage

embed_accepted(
  df,
  id_col,
  acc_id_col,
  name_col,
  family_col,
  genus_col,
  status_col,
  synonym_pattern = "SYNONYM",
  authorship_col = NULL
)

Arguments

df: The full backbone data.frame.
id_col: Name of the taxon ID column.
acc_id_col: Name of the accepted name usage ID column.
name_col: Name of the canonical name column.
family_col: Name of the family column.
genus_col: Name of the genus column.
status_col: Name of the taxonomic status column.
synonym_pattern: Regex pattern to detect synonyms in status column.
authorship_col: Optional name of the authorship column. When supplied, the resolved accepted name's authorship is embedded as accepted_authorship (so a synonym row carries the accepted taxon's author, not its own). When NULL, accepted_authorship is filled with NA.

Value

The data.frame with added columns: accepted_name, accepted_family, accepted_genus, accepted_taxon_id, accepted_authorship, is_synonym.