Journal ArticleDOI
Multi-scale occupancy estimation and modelling using multiple detection methods
James D. Nichols,Larissa L. Bailey,Allan F. O'Connell,Neil W. Talancy,Evan H. Campbell Grant,Andrew T. Gilbert,Elizabeth M. Annand,Thomas P. Husband,James E. Hines +8 more
TLDR
Occupancy estimation and modelling based on detection‐nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty.Abstract:
Summary 1. Occupancy estimation and modelling based on detection‐nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use of multiple detection methods. When multiple methods or devices are used at the same sample sites, animals can be detected by more than one method. 2. We develop occupancy models for multiple detection methods that permit simultaneous use of data from all methods for inference about method-specific detection probabilities. Moreover, the approach permits estimation of occupancy at two spatial scales: the larger scale corresponds to species’ use of a sample unit, whereas the smaller scale corresponds to presence of the species at the local sample station or site. 3. We apply the models to data collected on two different vertebrate species: striped skunks Mephitis mephitis and red salamanders Pseudotriton ruber . For striped skunks, large-scale occupancy estimates were consistent between two sampling seasons. Small-scale occupancy probabilities were slightly lower in the late winter/spring when skunks tend to conserve energy, and movements are limited to males in search of females for breeding. There was strong evidence of method-specific detection probabilities for skunks. As anticipated, large- and small-scale occupancy areas completely overlapped for red salamanders. The analyses provided weak evidence of method-specific detection probabilities for this species. 4. Synthesis and applications. Increasingly, many studies are utilizing multiple detection methods at sampling locations. The modelling approach presented here makes efficient use of detections from multiple methods to estimate occupancy probabilities at two spatial scales and to compare detection probabilities associated with different detection methods. The models can be viewed as another variation of Pollock’s robust design and may be applicable to a wide variety of scenarios where species occur in an area but are not always near the sampled locations. The estimation approach is likely to be especially useful in multispecies conservation programmes by providing efficient estimates using multiple detection devices and by providing device-specific detection probability estimates for use in survey design.read more
Citations
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Journal ArticleDOI
Detecting range shifts from historical species occurrences: new perspectives on old data
TL;DR: It is suggested that keepers of historical data have crucial roles in curating and aiding accessibility to data, and it is recommended that collectors of contemporary specimen data organize their sampling efforts to include repeated surveys to estimate detection probabilities.
Journal ArticleDOI
Improving occupancy estimation when two types of observational error occur: non‐detection and species misidentification
David A. W. Miller,James D. Nichols,Brett T. McClintock,Evan H. Campbell Grant,Larissa L. Bailey,Linda A. Weir +5 more
TL;DR: It is shown that models that account for possible misidentification have greater support and can yield substantially different occupancy estimates than those that do not and can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur.
Journal ArticleDOI
Modelling of species distributions, range dynamics and communities under imperfect detection: advances, challenges and opportunities
TL;DR: Modelling advances in imperfect detection of species distributions are summarized, evidence about effects of imperfect detection and the difficulties of working with it are discussed, and the current outlook for future research and application of these methods are concluded.
Journal ArticleDOI
Tigers on trails: occupancy modeling for cluster sampling.
James E. Hines,James D. Nichols,J. A. Royle,Darryl I. MacKenzie,Arjun M. Gopalaswamy,N. Samba Kumar,K.U. Karanth +6 more
TL;DR: This work develops two new occupancy models for data collected under an increasingly popular sampling design based on spatial replicates that are not selected randomly and that are expected to exhibit Markovian dependence, and fits these models to data from a large-scale tiger occupancy survey recently conducted in Karnataka State, southwestern India.
Journal ArticleDOI
Occupancy estimation and the closure assumption
TL;DR: It is shown that habitats may frequently be open to changes in site occupancy at time-scales typical of many occupancy investigations, with 71% and 100% of species investigated in Montana and New Hampshire respectively, showing violation of closure across time periods of 3 weeks and 8 days respectively.
References
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Book
Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach
TL;DR: The second edition of this book is unique in that it focuses on methods for making formal statistical inference from all the models in an a priori set (Multi-Model Inference).
Journal ArticleDOI
Program MARK: survival estimation from populations of marked animals
Gary C. White,Kenneth P. Burnham +1 more
TL;DR: Mark as discussed by the authors provides parameter estimates from marked animals when they are re-encountered at a later time as dead recoveries, or live recaptures or re-sightings.
Journal ArticleDOI
Terrestrial Ecoregions of the World: A New Map of Life on Earth
Journal ArticleDOI
Estimating site occupancy rates when detection probabilities are less than one
Darryl I. MacKenzie,James D. Nichols,Gideon B. Lachman,Sam Droege,J. Andrew Royle,Catherine A. Langtimm +5 more
TL;DR: In this paper, a model and likelihood-based method for estimating site occupancy rates when detection probabilities are 0.3 was proposed for American toads (Bufo americanus) and spring peepers (Pseudacris crucifer).
Book
Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence
TL;DR: This chapter discusses single-species, Single-season Occupancy Models with Heterogeneous Detection Probabilities, and interspecific Relationships Between Species.