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taxonstand: An r package for species names standardisation in vegetation databases
Article first published online: 5 JUL 2012
DOI: 10.1111/j.2041-210X.2012.00232.x
© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society
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How to Cite
Cayuela, L., Granzow-de la Cerda, Í., Albuquerque, F. S. and Golicher, D. J. (2012), taxonstand: An r package for species names standardisation in vegetation databases. Methods in Ecology and Evolution, 3: 1078–1083. doi: 10.1111/j.2041-210X.2012.00232.x
Publication History
- Issue published online: 11 DEC 2012
- Article first published online: 5 JUL 2012
- Received: 30 March 2012; accepted 2 June 2012 Handling Editor: Robert Freckleton
- Abstract
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Keywords:
- data cleaning;
- nomenclature;
- taxonomy;
- The Plant List
Summary
1. Compilation of vegetation databases has contributed significantly to the advancement of vegetation science all over the world. Yet, methodological problems result from the use of plant names, particularly in data that originate from numerous and heterogeneous sources. One of the main problems is the inordinate number of synonyms that can be found in vegetation lists.
2. We present Taxonstand, an r package to automatically standardise plant names using The Plant List (http://www.theplantlist.org). The scripts included in this package allow connection to the online search engine of the Plant List and retrieve information from each species about its current taxonomic status. In those cases where the species name is a synonym, it is replaced by the current accepted name. In addition, this package can help correcting orthographic errors in specific epithets.
3. This tool greatly facilitates the preparation of large vegetation databases prior to their analyses, particularly when they cover broad geographical areas (supranational or even continental scale) or contain data from regions with rich floras where taxonomic problems have not been resolved for many of their taxa. Automated workflows such as the one provided by the taxonstand package can ease considerably this task using a widely accessible working nomenclatural authority list for plant species names such as The Plant List.