taxon_database {metacoder}

Taxonomy database class

Description

Used to store information about taxonomy databases. This is typically used to store where taxon information came from in [taxon()] objects.

Usage

taxon_database(name = NULL, url = NULL, description = NULL, id_regex = NULL)

Arguments

name

(character) name of the database

url

(character) url for the database

description

(character) description of the database

id_regex

(character) id regex

Value

An 'R6Class' object of class 'TaxonDatabase'

See Also

[database_list]

Other classes: hierarchies(), hierarchy(), taxa(), taxmap(), taxon(), taxon_id(), taxon_name(), taxon_rank(), taxonomy()

Examples

# create a database entry
(x <- taxon_database(
  "ncbi",
  "http://www.ncbi.nlm.nih.gov/taxonomy",
  "NCBI Taxonomy Database",
  "*"
))
x$name
x$url

# use pre-created database objects
database_list
database_list$ncbi