letsRept: An R package to access the Global Reptile Database and facilitate taxonomic harmonization

Abstract

Taxonomy is a highly dynamic science upon which most biodiversity studies rely. Constant revisions of species delimitation hypotheses, using ever-growing amounts of data and tools cause species numbers and identities to continuously and rapidly change. Reptiles are the most species rich terrestrial vertebrate group and are amongst the most threatened and least known vertebrate taxa, representing nearly half of all data deficient terrestrial vertebrate species. Every year hundreds of new species are described and dozens are revised, resulting in synonymizations, splittings, generic reassignments, or elevation from synonymy or from subspecies into species status. The nomenclature of this group is therefore highly dynamic and consequently, to integrate available reptile datasets generally requires extensive nomenclature review, especially for broad scale analyses. letsRept is a new R package that integrates the Reptile Database – the best curated and reliable global taxonomic reference for reptiles – into the R programming environment. Its main functions allow users to retrieve the most up-to-date taxonomic information in real time, to compare lists of species names to current nomenclature, and to detect names that have been changed by either lumping or splitting, all through web scraping techniques. Additional functions allow to produce quick taxonomic summaries, access species accounts, retrieve full reference lists and more. By permitting to embed the Reptile Database directly into R workflows, the letsRept package improves the integration of datasets from different sources, with authoritative taxonomy, reducing data loss due to nomenclature mismatch and improving the consistency in biodiversity analyses.