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taxize (version 0.9.100.1)

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.

Arguments

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

APIprefixSOAP?
Encyclopedia of Life (EOL)eolFALSE
Integrated Taxonomic Information Service (ITIS)itisFALSE
Global Names Resolver (from EOL/GBIF)gnrFALSE
Global Names Index (from EOL/GBIF)gniFALSE
IUCN Red ListiucnFALSE
Tropicos (from Missouri Botanical Garden)tpFALSE
Theplantlist.orgtplFALSE
National Center for Biotechnology InformationncbiFALSE
CANADENSYS Vascan name search APIvascanFALSE
International Plant Names Index (IPNI)ipniFALSE
World Register of Marine Species (WoRMS)wormsTRUE
Barcode of Life Data Systems (BOLD)boldFALSE
Pan-European Species directories Infrastructure (PESI)pesiTRUE
MycobankmycoTRUE
National Biodiversity Network (UK)nbnFALSE
Index FungorumfgFALSE
EU BONeubonFALSE
Index of Names (ION)ionFALSE
Open Tree of Life (TOL)tolFALSE
World Register of Marine Species (WoRMS)wormsFALSE
NatureServenatservFALSE

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+

Author

Scott Chamberlain

Eduard Szoecs eduardszoecs@gmail.com

Zachary Foster zacharyfoster1989@gmail.com

Carl Boettiger cboettig@gmail.com

Karthik Ram karthik@ropensci.org

Ignasi Bartomeus nacho.bartomeus@gmail.com

John Baumgartner johnbb@student.unimelb.edu.au

James O'Donnell jodonnellbio@gmail.com