occumb: An R package for site occupancy modeling of eDNA metabarcoding data

Abstract

Environmental DNA (eDNA) metabarcoding has become an increasingly popular method for the rapid assessment of species distribution and diversity. However, the detection of DNA sequences of species in eDNA metabarcoding is not flawless; thus, accounting for potential false negatives (nondetection of DNA sequences of existing species) is crucial for the effective implementation of eDNA-based monitoring and research. This study introduces the occumb R package, which was developed to facilitate the easy and flexible application of community site occupancy modeling for eDNA metabarcoding that accounts for the imperfect detection of DNA sequences of species. The package provides functions for specifying models using the formula syntax, Bayesian model fitting using Markov chain Monte Carlo (MCMC), posterior inferences, and model assessments and exploring optimal study settings based on the fitted model. A case study of eDNA metabarcoding on riverine aquatic insects is illustrated using the occumb package, emphasizing the importance of ensuring biological replicates in achieving reliable species detection in eDNA metabarcoding. By making complex community site occupancy models easily accessible to users, we hope that the development of the occumb package will promote eDNA metabarcoding applications for the accurate assessment of species distribution and diversity.