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

Luis Cayuela, Íñigo Granzow-de la Cerda, Fabio S. Albuquerque, Duncan J. Golicher

Research output: Contribution to journalArticle

87 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1078-1083
Number of pages6
JournalMethods in Ecology and Evolution
Volume3
Issue number6
DOIs
StatePublished - Dec 2012
Externally publishedYes

Keywords

  • Data cleaning
  • Nomenclature
  • Taxonomy
  • The Plant List

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecological Modeling

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