taxize (version 0.6.2)

taxize-package: Taxnomic search and phylogeny retrieval.

Description

Taxnomic search and phylogeny retrieval.

About

We are developing taxize as a package to allow 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), the Universal Biological Indexer and Organizer (uBio), Tropicos, and Plantminer.

Currently supported APIs

llc{ API prefix SOAP? Encyclopedia of Life (EOL) eol FALSE Taxonomic Name Resolution Service tnrs FALSE Integrated Taxonomic Information Service (ITIS) itis FALSE Phylomatic phylomatic FALSE uBio ubio 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 Plantminer plantminer FALSE Theplantlist.org tpl FALSE Catalogue of Life col FALSE Global Invasive Species Database gisd 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 }

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