taxize (version 0.7.9)

taxize-package: 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 Encyclopedia of Life (EOL), and Tropicos.

Currently supported APIs

API	prefix
SOAP?	Encyclopedia of Life (EOL)
eol	FALSE
Taxonomic Name Resolution Service	tnrs
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	Catalogue of Life
col	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	API

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