taxonstand: An r package for species names standardisation in vegetation databases

• Published in: Methods in ecology and evolution Vol. 3; no. 6; pp. 1078 - 1083
• Main Authors: Cayuela, Luis, Granzow‐de la Cerda, Íñigo, Albuquerque, Fabio S., Golicher, Duncan J.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.12.2012; John Wiley & Sons, Inc
• Subjects: data cleaning; nomenclature; Taxonomy; The Plant List; Vegetation
• ISSN: 2041-210X; 2041-210X
• DOI: 10.1111/j.2041-210X.2012.00232.x

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.