atlas_taxonomy: Search taxonomic trees

Description

The ALA has its' own internal taxonomy that is derived from authoritative sources. atlas_taxonomy provides a means to query that taxonomy, returning a tree (class Node) showing which lower clades are contained within the specified taxon.

Usage

atlas_taxonomy(request = NULL, identify = NULL, down_to = NULL)

Value

A tree consisting of objects of class Node, containing the requested taxonomy. Each node contains the following attributes:

name: The scientific name of the taxon in question
rank: The taxonomic rank to which that taxon belongs
guid: A unique identifier used by the ALA
authority: The source of the taxonomic name & identifier

Arguments

request: optional data_request object: generated by a call to galah_call().
identify: data.frame: generated by a call to galah_identify().
down_to: The identity of the clade at which the downwards search should stop. Should be specified using an object of class character and galah_down_to, as returned from galah_down_to(). Also accepts a string.

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.

Examples

Run this code

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