taxize-package: Taxonomic Information from Around the Web
In taxize: Taxonomic Information from Around the Web

taxize-package

R Documentation

Taxonomic Information from Around the Web

Description

This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.

About

Allows users to search over many websites for species names (scientific and common) and download up- and downstream taxonomic hierarchical information - and many other things.

The functions in the package that hit a specific API have a prefix and suffix separated by an underscore. They follow the format of service_whatitdoes. For example, gnr_resolve uses the Global Names Resolver API to resolve species names.

General functions in the package that don't hit a specific API don't have two words separated by an underscore, e.g., classification

You need API keys for some data sources. See taxize-authentication for more information.

Currently supported APIs

API	prefix	SOAP?
Encyclopedia of Life (EOL)	eol	FALSE
Integrated Taxonomic Information Service (ITIS)	itis	FALSE
Global Names Resolver (from EOL/GBIF)	gnr	FALSE
Global Names Index (from EOL/GBIF)	gni	FALSE
IUCN Red List	iucn	FALSE
Tropicos (from Missouri Botanical Garden)	tp	FALSE
Theplantlist.org	tpl	FALSE
National Center for Biotechnology Information	ncbi	FALSE
CANADENSYS Vascan name search API	vascan	FALSE
International Plant Names Index (IPNI)	ipni	FALSE
World Register of Marine Species (WoRMS)	worms	TRUE
Barcode of Life Data Systems (BOLD)	bold	FALSE
Pan-European Species directories Infrastructure (PESI)	pesi	TRUE
Mycobank	myco	TRUE
National Biodiversity Network (UK)	nbn	FALSE
Index Fungorum	fg	FALSE
EU BON	eubon	FALSE
Index of Names (ION)	ion	FALSE
Open Tree of Life (TOL)	tol	FALSE
World Register of Marine Species (WoRMS)	worms	FALSE
NatureServe	natserv	FALSE

If the source above has a TRUE in the ⁠SOAP?⁠ column, it is not available in this package. They are available from a different package called taxizesoap. See the GitHub repo for how to install https://github.com/ropensci/taxizesoap

Catalogue of Life (COL)

COL introduced rate limiting recently in 2019 - which has made the API essentially unusable - CoL+ is coming soon and we'll incorporate it here when it's stable. See https://github.com/ropensci/colpluz for the R implementation for CoL+