db_ref: Valid taxonomy databases

In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Valid taxonomy databases

Description

This defines the valid taxonomic databases that can be used in taxon_db objects and objects that use taxon_db objects, such as taxon_id and taxon. db_ref$get can be used to see information for the databases. Users can add their own custom databases to the list using db_ref$set. For each database the following information is included:

• The URL for the website associated with the database

• A short description

• The regular expression that defines valid taxon IDs

• The ranks used in the database if specified

Usage

db_ref

Format

An object of class list of length 3.

Attribution

This code is based on the code handling options in the knitr package.

Examples

# List all database definitions
db_ref$get()

# Get a specific database definition
db_ref$get('ncbi')

# Add or overwrite a database definition
db_ref$set(
  name = "my_new_database",
  url = "http://www.my_tax_database.com",
  desc = "I just made this up",
  id_regex = ".*"
)

# Reset definitions to default values
db_ref$reset()

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.