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+
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