Search taxonomic trees

The ALA has its' own internal taxonomy that is derived from authoritative sources. atlas_taxonomy provides a means to query that taxonomy, returning a tibble showing all child nodes and which parent they are derived from.

Usage

atlas_taxonomy(
  request = NULL,
  identify = NULL,
  filter = NULL,
  constrain_ids = NULL
)

Arguments

request

optional data_request object: generated by a call to galah_call().

identify

data.frame: generated by a call to galah_identify().

filter

data.frame: generated by a call to galah_filter(rank == "chosen_rank"). The identity of the clade at which the downwards search should stop.

constrain_ids

string: Optional string to limit which taxon_concept_id's are returned. This is useful for restricting taxonomy to particular authoritative sources. Default is "biodiversity.org.au" for Australia (this can be overridded by setting constrain_ids = NULL) and NULL otherwise. Powered by grepl() meaning it supports regular expressions.

Value

A tibble containing taxon names, ranks and parent/child IDs

Details

The approach used by this function is recursive, meaning that it becomes slow for large queries such as atlas_taxonomy(search_taxa("Plantae"), down_to = galah_down_to(species)). Although the inputs to search_taxa and down_to are case-insensitive, node names are always returned in title case.

See also

search_taxa() to search for an individual taxon; show_all(ranks) for valid ranks used to specify the down_to argument.

Examples

if (FALSE) {
# Get a taxonomic tree of *Chordata* down to the class level
galah_call() |> 
  galah_identify("chordata") |>
  galah_filter(rank == class) |>
  atlas_taxonomy()
}