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eDNAoccupancy: An R package for multi-scale occupancy modeling of environmental DNA data

Molecular Ecology Resources

By:
ORCID iD and ORCID iD
https://doi.org/10.1111/1755-0998.12735

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Abstract

In this article we describe eDNAoccupancy, an R package for fitting Bayesian, multi-scale occupancy models. These models are appropriate for occupancy surveys that include three, nested levels of sampling: primary sample units within a study area, secondary sample units collected from each primary unit, and replicates of each secondary sample unit. This design is commonly used in occupancy surveys of environmental DNA (eDNA). eDNAoccupancy allows users to specify and fit multi-scale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria. We illustrate these features by analyzing two published data sets: eDNA surveys of a fungal pathogen of amphibians and eDNA surveys of an endangered fish species.

Additional publication details

Publication type:
Article
Publication Subtype:
Journal Article
Title:
eDNAoccupancy: An R package for multi-scale occupancy modeling of environmental DNA data
Series title:
Molecular Ecology Resources
DOI:
10.1111/1755-0998.12735
Edition:
Online First
Year Published:
2017
Language:
English
Publisher:
Wiley
Contributing office(s):
Wetland and Aquatic Research Center