Taxonomy database class

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

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_id(), taxon_name(), taxon_rank(), taxonomy(), taxon()

Examples

# create a database entry
(x <- taxon_database(
  "ncbi",
  "http://www.ncbi.nlm.nih.gov/taxonomy",
  "NCBI Taxonomy Database",
  "*"
))
#> <database> ncbi
#>   url: http://www.ncbi.nlm.nih.gov/taxonomy
#>   description: NCBI Taxonomy Database
#>   id regex: *
x$name
#> [1] "ncbi"
x$url
#> [1] "http://www.ncbi.nlm.nih.gov/taxonomy"

# use pre-created database objects
database_list
#> $ncbi
#> <database> ncbi
#>   url: http://www.ncbi.nlm.nih.gov/taxonomy
#>   description: NCBI Taxonomy Database
#>   id regex: .*
#> 
#> $gbif
#> <database> gbif
#>   url: http://www.gbif.org/developer/species
#>   description: GBIF Taxonomic Backbone
#>   id regex: .*
#> 
#> $bold
#> <database> bold
#>   url: http://www.boldsystems.org
#>   description: Barcode of Life
#>   id regex: .*
#> 
#> $col
#> <database> col
#>   url: http://www.catalogueoflife.org
#>   description: Catalogue of Life
#>   id regex: .*
#> 
#> $eol
#> <database> eol
#>   url: http://eol.org
#>   description: Encyclopedia of Life
#>   id regex: .*
#> 
#> $nbn
#> <database> nbn
#>   url: https://nbn.org.uk
#>   description: UK National Biodiversity Network
#>   id regex: .*
#> 
#> $tps
#> <database> tps
#>   url: http://www.tropicos.org/
#>   description: Tropicos
#>   id regex: .*
#> 
#> $itis
#> <database> itis
#>   url: http://www.itis.gov
#>   description: Integrated Taxonomic Information System
#>   id regex: .*
#> 
database_list$ncbi
#> <database> ncbi
#>   url: http://www.ncbi.nlm.nih.gov/taxonomy
#>   description: NCBI Taxonomy Database
#>   id regex: .*