R: Taxonomic Information from Around the Web

taxize-package {taxize} | 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 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
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

### Author(s)

Scott Chamberlain myrmecocystus@gmail.com

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

[Package taxize version 0.9.0 Index]