Accepted names and synonyms
Several functions are provided here to perform simple queries on accepted vs synonymous species names.
1 2 3
genus and species
the database to query, can be squamates, birds, mammals or amphibians.
The workhorse function for matching synonyms to accepted names is
The functions here are more simple, and are intended to be complementary to the main matching function.
The squamate database is a local copy of the Reptile Database (http://reptile-database.reptarium.cz/), which will be updated periodically. The list of accepted names within this R package are those that are listed as such on the website.
The bird database is the BirdLife Taxonomic Checklist v8.0 as downloaded from http://www.birdlife.org/datazone/info/taxonomy.
The mammal database is Wilson and Reeder's Mammal Species of the World, 3rd edition, downloaded from http://www.departments.bucknell.edu/biology/resources/msw3/.
The amphibian database is a local copy of the AmphibiaWeb taxonomy (amphibiaweb.org/taxonomy/index.html), which will be updated periodically.
To see when these datasets were last updated for this R package, run
BirdLife International. 2015. The BirdLife checklist of the birds of the world: Version 8. Downloaded from http://www.birdlife.org/datazone/userfiles/file/Species/Taxonomy/BirdLife_Checklist_Version_80.zip [.xls zipped 1 MB].
Don E. Wilson & DeeAnn M. Reeder (editors). 2005. Mammal Species of the World. A Taxonomic and Geographic Reference (3rd ed), Johns Hopkins University Press, 2,142 pp.
Uetz P., Hosek, J. (ed.). 2016. The Reptile Database, http://www.reptile-database.org (accessed 30 April 2016).
getSynonymsFromAccepted returns a vector of synonyms for the specified accepted species name.
getAcceptedFromSynonym returns the accepted names that have the specified species name as a synonym (as per strict matching).
getAcceptedNames returns the list of accepted species names in the database.
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