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An RShiny app for modelling environmental DNA data: accounting for false positive and false negative observation error

Diana, A; Matechou, E; Griffin, J; Buxton, A; Griffiths, R; (2021) An RShiny app for modelling environmental DNA data: accounting for false positive and false negative observation error. Ecography , 44 (12) pp. 1838-1844. 10.1111/ecog.05718. Green open access

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Abstract

Environmental DNA (eDNA) surveys have become a popular tool for assessing the distribution of species. However, it is known that false positive and false negative observation error can occur at both stages of eDNA surveys, namely the field sampling stage and laboratory analysis stage. We present an RShiny app that implements the Griffin et al. (2020) statistical method, which accounts for false positive and false negative errors in both stages of eDNA surveys that target single species using quantitative PCR methods. Following Griffin et al. (2020), we employ a Bayesian approach and perform efficient Bayesian variable selection to identify important predictors for the probability of species presence as well as the probabilities of observation error at either stage. We demonstrate the RShiny app using a data set on great crested newts collected by Natural England in 2018, and we identify water quality, pond area, fish presence, macrophyte cover and frequency of drying as important predictors for species presence at a site. The state-of-the-art statistical method that we have implemented is the only one that has specifically been developed for the purposes of modelling false negative and false positive observation error in eDNA data. Our RShiny app is user-friendly, requires no prior knowledge of R and fits the models very efficiently. Therefore, it should be part of the tool-kit of any researcher or practitioner who is collecting or analysing eDNA data.

Type: Article
Title: An RShiny app for modelling environmental DNA data: accounting for false positive and false negative observation error
Open access status: An open access version is available from UCL Discovery
DOI: 10.1111/ecog.05718
Publisher version: https://doi.org/10.1111/ecog.05718
Language: English
Additional information: © 2021 The Authors. Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Keywords: Bayesian variable selection, environmental DNA, multi-level occupancy model, PCR
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Statistical Science
URI: https://discovery.ucl.ac.uk/id/eprint/10134269
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