Taxnomic search and phylogeny retrieval.
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 are:
| API | prefix |
| Encyclopedia of Life (EOL) | eol_ |
| Integrated Taxonomic Information Service (ITIS) | itis_ |
| Phylomatic | phylomatic_ |
| uBio | ubio_ |
| Global Names Resolver (from EOL/GBIF) | gnr_ |
| Global Names Index (from EOL/GBIF) | gni_ |
| IUCN Red List | iucn_ |
| Tropicos (from Missouri Botanical Garden) | tp_ |
| Plantminer | plantminer_ |
| Theplantlist.org | tpl_ |
| Catalogue of Life | col_ |
| Global Invasive Species Database | gisd_ |
| Freshwaterecology.info | fresh_ |
Scott Chamberlain myrmecocystus@gmail.com
Eduard Szoecs szoe8822@uni-landau.de
Carl Boettiger cboettig@gmail.com
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