63urn:lsid:arphahub.com:pub:0E0032F4-55AE-5263-8B3C-F4DD637C30C2Biodiversity Information Science and StandardsBISS2535-0897Pensoft Publishers10.3897/biss.3.376433764311041Conference AbstractSS31 - Quantification of biodiversity across scalesIntroducing ‘The bdverse’: a family of R packages for biodiversity dataGuetaTomertomer.gu@gmail.comhttps://orcid.org/0000-0003-1557-85961BarveVijayhttps://orcid.org/0000-0002-4852-25672NagarajahThiloshon3GibasPovilashttps://orcid.org/0000-0001-5311-60214CarmelYohay1Department of Civil and Environmental Engineering, The Technion – Israel Institute of Technology, Haifa, IsraelDepartment of Civil and Environmental Engineering, The Technion – Israel Institute of TechnologyHaifaIsraelFlorida Museum of Natural History, Gainesville, United States of AmericaFlorida Museum of Natural HistoryGainesvilleUnited States of AmericaInformatics Institute of Technology, Colombo, Sri LankaInformatics Institute of TechnologyColomboSri LankaVilnius University, Vilnius, LithuaniaVilnius UniversityVilniusLithuania
2019020720193e3764365AB31F0-6E3F-5650-ABB6-68AB00BCD8C1328906624062019Tomer Gueta, Vijay Barve, Thiloshon Nagarajah, Povilas Gibas, Yohay CarmelThis is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
The bdverse is a collection of packages that form a general framework for facilitating biodiversity science in R. We build it to serve as a sustainable and agile infrastructure that enhances the value of biodiversity data by allowing users to conveniently employ R, for data exploration, quality assessment, data cleaning, and standardization. The bdverse supports users with and without programming capabilities. Itincludes six unique packages in a hierarchal structure — representing different functionality levels (Fig. 1). Major features of three core packages will be highlighted and demonstrated: (i) bdDwC provides an interactive Shiny app and a set of functions for standardizing field names in compliance with Darwin Core (DwC) format; (ii) bdchecks is an infrastructure for performing, filtering and managing various biodiversity data checks; (iii) bdclean is a user-friendly data cleaning Shiny app for the inexperienced R user. It provides features to manage complete workflow for biodiversity data cleaning, including data upload; user input - in order to adjust cleaning procedures; data cleaning; and finally, generation of various reports and versions of the data.
We are now working on submitting the bdverse packages to rOpenSci software review, and as soon as the packages meet core requirements, we will officially release the bdverse. The bdverse project won the 2nd prize in the 2018 Ebbe Nielsen Challenge.
biodiversity informaticdata qualityRGoogle100006785http://doi.org/10.13039/1000067852019Biodiversity_NextBiodiversity_Next 2019Leiden, The NetherlandsA joint conference by The Global Biodiversity Information Facility (GBIF), a new pan-European Research Infrastructure initiative (DiSSCo), the national resource for digitized information about vouchered natural history collections (iDigBio), Consortium of European Taxonomic Facilities (CETAF), Biodiversity Information Standards (TDWG) and LifeWatch ERIC, the e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research.Presenting author
Tomer Gueta
Presented at
Biodiversity_Next 2019
Funding program
ISF grant No. 127/16
The Technion, Blumenstein family fund
Google Summer of Code program
Funding program
ISF grant No. 127/16
The Technion, Blumenstein family fund
Google Summer of Code program
A schematic representation of the bdverse, a toolbelt of packages for handling biodiversity data in R. Repositories of all packages can be publicly accessed via GitHub (https://github.com/bd-R).