taxon_database: Taxonomy database class

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

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

metacoder documentation built on April 3, 2025, 8:39 p.m.