List all descendants of a taxon down to a target rank

Returns every accepted taxon at downto rank that sits beneath taxon – for example every species in an order or family. The parent's rank is detected from the backbone, then descendants are read from the denormalized classification the backbone stores. children() is the same query for a genus or family parent.

Usage

downstream(
  taxon,
  backbone = NULL,
  downto = "species",
  kingdom = NULL,
  verbose = TRUE
)

Arguments

taxon

A single higher-taxon name (a genus, family, order, class, phylum, or kingdom).

backbone

A single backbone name or a taxify_backend object. NULL (default) uses the highest-priority installed backbone; name one that stores the higher ranks (e.g. "col") to reach above genus.

downto

Target rank of the descendants to return ("species" by default), or "any" (or NULL) for every accepted taxon beneath taxon regardless of rank. The parent itself is never returned.

kingdom

Optional kingdom (or kingdoms) the parent belongs to, as in taxify() ("plantae", "animals", ...). A name can be used in more than one kingdom (Morus is both mulberries and gannets); kingdom picks one, and also decides the parent's rank when the homonyms sit at different ranks. Without it such a result mixes the kingdoms, with a warning.

verbose

Logical. Default TRUE.

Value

A data.frame of accepted descendants, columns: name, authorship, rank, kingdom_group (the coarse kingdom, as in taxify() output), family, genus, taxon_id, parent, parent_rank, backbone. Empty when taxon is not found, its rank is one the backbone does not store as a column (e.g. subfamily, tribe), or it has no descendants at downto.

See also

children() for a genus or family parent, upstream() for the ancestors, taxify(), synonyms().

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

# Every species the backbone places in the genus
downstream("Quercus", backbone = "col")

options(old)