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2023 | OriginalPaper | Chapter

4. Occupancy, Abundance, and Related Topics

Authors : George A. F. Seber, Matthew R. Schofield

Published in: Estimating Presence and Abundance of Closed Populations

Publisher: Springer International Publishing

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Abstract

Models for occupancy, where it is important to determine whether a particular species is present or not, have a long history. The literature is very extensive, as referred to in some reviews mentioned, and both frequentist and Bayesian methods have been developed for all kinds of population, including those of animal signs. The methods are particularly important in dealing with the incomplete detection of rare species or species with a low detection rate and with detecting the presence of an invasive species.
In addition to the basic models used in the past based on single surveys, there have been several extensions to include multiple surveys, multiple seasons, multiple species, and multistate models. The use of so-called robust models with primary and secondary surveys is discussed. The aim is to either overcome or allow for violations of traditional model assumptions such as nonclosure, non-independent replicates, heterogeneous detection, and false positives. Key assumptions are listed, and appropriate tests for them are described in two places using goodness-of-fit tests and residual plots for covariate regressions, as well as tests for occupancy differences.
As well as estimating detection probabilities, abundance estimates can be made with some models. Design questions are considered in several places, such as determining the number of visits to a site and dealing with possible dependent visits. Covariates have also been used more frequently, and these help to reduce the number of unknown parameters.
A general collection of various models is presented including an introduction to spatial models with spatial autocorrelation, time-to-detection removal models, and staggered arrival and departure times. For example, adaptive-type methods using a two-phase design or a conditional design are given for rare species. Multi-scale models are considered as species distributions depend critically on the scales at which data is used for model building.
Types of observation errors are discussed as well as combining types of detection using multiple detection devices. DNA and eDNA (environmental DNA) as genetic tags are being used increasingly. Sometimes, there is incomplete data information such as having presence-only data, but extra environmental information can often be incorporated. In addition to using specialist observers, it can be cost-effective to use “opportunistic” data such as data from volunteers, called “citizen” science.
Occupancy models are extended to allow for the possibility that individuals are being detected in one of the several states (multistate models), including disease modeling. Undetected states are considered along with the use of dynamic state models. It is shown how multiple data sources can be combined. The chapter ends with a brief discussion on fisheries and marine environments.

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Metadata
Title
Occupancy, Abundance, and Related Topics
Authors
George A. F. Seber
Matthew R. Schofield
Copyright Year
2023
DOI
https://doi.org/10.1007/978-3-031-39834-6_4

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