Uncovering ecological state dynamics with hidden Markov models

BT McClintock, R Langrock, O Gimenez, E Cam… - Ecology …, 2020 - Wiley Online Library
Ecological systems can often be characterised by changes among a finite set of underlying
states pertaining to individuals, populations, communities or entire ecosystems through time …

Advances and applications of occupancy models

LL Bailey, DI MacKenzie… - Methods in Ecology and …, 2014 - Wiley Online Library
The past decade has seen an explosion in the development and application of models
aimed at estimating species occurrence and occupancy dynamics while accounting for …

Improving occupancy estimation when two types of observational error occur: Non‐detection and species misidentification

DA Miller, JD Nichols, BT McClintock, EHC Grant… - Ecology, 2011 - Wiley Online Library
Efforts to draw inferences about species occurrence frequently account for false negatives,
the common situation when individuals of a species are not detected even when a site is …

Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen

BR Schmidt, M Kéry, S Ursenbacher… - Methods in Ecology …, 2013 - Wiley Online Library
The use of environmental DNA (eDNA) to detect species in aquatic environments such as
ponds and streams is a powerful new technique with many benefits. However, species …

Statistical approaches to account for false‐positive errors in environmental DNA samples

JJ Lahoz‐Monfort, G Guillera‐Arroita… - Molecular Ecology …, 2016 - Wiley Online Library
Environmental DNA (eDNA) sampling is prone to both false‐positive and false‐negative
errors. We review statistical methods to account for such errors in the analysis of eDNA data …

Occupancy models for citizen‐science data

R Altwegg, JD Nichols - Methods in Ecology and Evolution, 2019 - Wiley Online Library
Large‐scale citizen‐science projects, such as atlases of species distribution, are an
important source of data for macroecological research, for understanding the effects of …

Dealing with false‐positive and false‐negative errors about species occurrence at multiple levels

G Guillera‐Arroita, JJ Lahoz‐Monfort… - Methods in Ecology …, 2017 - Wiley Online Library
Accurate knowledge of species occurrence is fundamental to a wide variety of ecological,
evolutionary and conservation applications. Assessing the presence or absence of species …

Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model

H Doi, K Fukaya, S Oka, K Sato, M Kondoh, M Miya - Scientific Reports, 2019 - nature.com
Environmental DNA (eDNA) metabarcoding is a recently developed method to assess
biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in …

Outbreak of peste des petits ruminants among critically endangered Mongolian saiga and other wild ungulates, Mongolia, 2016–2017

M Pruvot, AE Fine, C Hollinger… - Emerging infectious …, 2020 - pmc.ncbi.nlm.nih.gov
The 2016–2017 introduction of peste des petits ruminants virus (PPRV) into livestock in
Mongolia was followed by mass mortality of the critically endangered Mongolian saiga …

Modeling false positive detections in species occurrence data under different study designs

T Chambert, DAW Miller, JD Nichols - Ecology, 2015 - Wiley Online Library
The occurrence of false positive detections in presence–absence data, even when they
occur infrequently, can lead to severe bias when estimating species occupancy patterns …