Tigers on trails: occupancy modeling for cluster sampling

Hines, James E.; Nichols, James D.; Royle, J. Andrew; MacKenzie, Darryl I.; Gopalaswamy, Arjun M.; Kumar, N. Samba; Karanth, Krithi K.

doi:10.1890/09-0321.1

Cited by 227 publications

(426 citation statements)

References 18 publications

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“…For example, an encounter history (h: 10100000) indicates that a bird was detected on the first and third count stop but not in any of the remaining six stops in the segment. BBS routes are unique in that the estimation of parameters is derived from spatial, not temporal replication along route segments or primary sampling units (Hines et al 2010). The sequential placement and sampling of these stops increases the possibility that adjacent stops exhibit greater similarity of habitat than stops further apart.…”

Section: Resultsmentioning

confidence: 99%

“…Failure to account for positive correlation between detection events yields estimates of occupancy that are biased-low. Hines et al (2010) developed spatial dependence models to assess the possibility that the probability of occupancy is influenced by the state, occupied or not, of the previous survey stop or segment, i.e., 1st order spatial Markov process (Williams et al 2002). We tested for this possibility by contrasting support in the data, i.e., lower AIC, for a single season, single species model without spatial dependence (standard occupancy model parameterization) versus two variants of single season, single species models with spatial dependence also available in program PRESENCE.…”

Section: Resultsmentioning

confidence: 99%

“…We used the notation put forth by MacKenzie et al (2002) and Hines et al (2010) to describe the models in the candidate set. Parameters in the models were occupancy (ψ) defined as the probability that a segment is occupied; detection (p) defined as the probability of detection in a segment given that the segment is occupied and the species of interest present on the segment; theta (θ) defined as probability that a stop along the segment is occupied, given the segment is occupied and the previous stop is not occupied; and theta prime (θ`) defined as the probability that a stop along the segment is occupied, given the segment is occupied and the previous stop is occupied.…”

Section: Resultsmentioning

confidence: 99%

“…), p(.)] and the spatial dependence model (Hines et al 2010). We constrained both model structures by all habitat covariates (Doherty et al 2012).…”

Section: Resultsmentioning

confidence: 99%

“…This problem could affect inferences from specieshabitat models because the state, occupied or not, of a sampling site could be misrepresented, and by extension, the strength of or influence of a habitat covariate (MacKenzie et al 2002, MacKenzie 2006. We also incorporated recent advances that account for spatial dependence among count stops along BBS routes as a means to strengthen inferences from models (Hines et al 2010). We discuss the importance of testing expert knowledge-based species-habitat relationships in the context of landscape level conservation and suggest opportunities to strengthen inferences from occupancy models for such tests.…”

Section: Introductionmentioning

confidence: 99%

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Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

Iglecia¹,

Collazo²,

McKerrow³

2012

ACE

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. 2012. Use of occupancy models to evaluate expert knowledge-based species-habitat relationships. Avian Conservation and Ecology 7(2): 5. http://dx.doi. org/10.5751/ACE-00551-070205 ABSTRACT. Expert knowledge-based species-habitat relationships are used extensively to guide conservation planning, particularly when data are scarce. Purported relationships describe the initial state of knowledge, but are rarely tested. We assessed support in the data for suitability rankings of vegetation types based on expert knowledge for three terrestrial avian species in the South Atlantic Coastal Plain of the United States. Experts used published studies, natural history, survey data, and field experience to rank vegetation types as optimal, suitable, and marginal. We used single-season occupancy models, coupled with land cover and Breeding Bird Survey data, to examine the hypothesis that patterns of occupancy conformed to species-habitat suitability rankings purported by experts. Purported habitat suitability was validated for two of three species. Research Papers Use of Occupancy Models to Evaluate ExpertAs predicted for the Eastern Wood-Pewee (Contopus virens) and Brown-headed Nuthatch (Sitta pusilla), occupancy was strongly influenced by vegetation types classified as "optimal habitat" by the species suitability rankings for nuthatches and wood-pewees. Contrary to predictions, Red-headed Woodpecker (Melanerpes erythrocephalus) models that included vegetation types as covariates received similar support by the data as models without vegetation types. For all three species, occupancy was also related to sampling latitude. Our results suggest that covariates representing other habitat requirements might be necessary to model occurrence of generalist species like the woodpecker. The modeling approach described herein provides a means to test expert knowledge-based species-habitat relationships, and hence, help guide conservation planning.RÉSUMÉ. Les relations espèces-habitat établies à partir des connaissances d'experts sont largement utilisées pour orienter la planification de la conservation, surtout lorsque les données sont rares. Ces relations présumées représentent les rudiments de la connaissance, mais sont rarement testées. L'adéquation du classement de milieux établi par des experts a été évaluée pour trois espèces de passereaux de la Plaine côtière de l'Atlantique Sud, aux États-Unis. Les experts ont utilisé des données publiées (recherches, histoire naturelle, relevés) et leur expérience sur le terrain afin de classer les milieux selon trois catégories, soit optimaux, adéquats ou marginaux. Nous avons appliqué des modèles de présence, fondés sur une seule saison, à des données d'occupation du sol et de relevés d'oiseaux nicheurs afin d'examiner l'hypothèse voulant que les profils de présence concordent avec le classement de la qualité des milieux présumé par les experts. La qualité présumée des milieux a été validée pour deux des trois espèces. Comme prédit pour le Pioui de l'Est (Contopus virens) et la Sittelle à t...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…), p(.)] and the spatial dependence model (Hines et al 2010). We constrained both model structures by all habitat covariates (Doherty et al 2012).…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

Iglecia¹,

Collazo²,

McKerrow³

2012

ACE

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Evaluation of camera placement for detection of free‐ranging carnivores; implications for assessing population changes

Geyle

Stevens

Duffy

et al. 2020

Ecol Sol and Evidence

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1. Introduced carnivores are often cryptic, making it difficult to quantify their presence in ecosystems, and assess how this varies in relation to management interventions. Survey design should thus seek to improve detectability and maximize statistical power to ensure sound inference regarding carnivore population trends. Roads may facilitate carnivore movements, possibly leading to high detectability. Therefore, targeting roads may improve inferences about carnivore populations. 2. We assessed our ability to monitor feral cats Felis catus and red foxes Vulpes vulpes on-and off-road, with explicit consideration of the location of monitoring sites on our ability to detect population changes. We also assessed whether there was evidence of spatial or temporal interaction between these species that might influence their roaduse. 3. Surveys were conducted in a conservation reserve in southeastern Australia between 2016 and 2018. At each of 30 sites, we deployed two motion-sensor cameras, one on-road, and the other off-road. Using occupancy models, we estimated cat and fox occupancy and detectability, and conducted a power analysis to assess our ability to detect declines in occupancy under three monitoring regimes (efforts targeted equally on-and off-road, efforts targeted entirely off-road and efforts targeted entirely onroad). 4. On average, on-road detectability was seven times higher for cats and three times higher for foxes. Targeting survey effort on-road yielded the greatest power for detecting declines in both species, but our ability to detect smaller declines decreased with decreasing initial occupancy probability. No level of decline was detectable for cats This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Disassembly of a tadpole community by a multi‐host fungal pathogen with limited evidence of recovery

DiRenzo

Che‐Castaldo

Rugenski

et al. 2017

Ecological Applications

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Emerging infectious diseases can cause host community disassembly, but the mechanisms driving the order of species declines and extirpations following a disease outbreak are unclear. We documented the community disassembly of a Neotropical tadpole community during a chytridiomycosis outbreak, triggered by the generalist fungal pathogen, Batrachochytrium dendrobatidis (Bd). Within the first 11 months of Bd arrival, tadpole density and occupancy rapidly declined. Species rarity, in terms of tadpole occupancy and adult relative abundance, did not predict the odds of tadpole occupancy declines. But species losses were taxonomically selective, with glassfrogs (Family: Centrolenidae) disappearing the fastest and tree frogs (Family: Hylidae) and dart-poison frogs (Family: Dendrobatidae) remaining the longest. We detected biotic homogenization of tadpole communities, with post-decline communities resembling one another more strongly than pre-decline communities. The entire tadpole community was extirpated within 22 months following Bd arrival, and we found limited signs of recovery within 10 years post-outbreak. Because of imperfect species detection inherent to sampling species-rich tropical communities and the difficulty of devising a single study design protocol to sample physically complex tropical habitats, we used simulations to provide recommendations for future surveys to adequately sample diverse Neotropical communities. Our unique data set on tadpole community composition before and after Bd arrival is a valuable baseline for assessing amphibian recovery. Our results are of direct relevance to conservation managers and community ecologists interested in understanding the timing, magnitude, and consequences of disease outbreaks as emerging infectious diseases spread globally.

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Tigers on trails: occupancy modeling for cluster sampling

Cited by 227 publications

References 18 publications

Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

Use of Occupancy Models to Evaluate Expert Knowledge-based Species-Habitat Relationships

Evaluation of camera placement for detection of free‐ranging carnivores; implications for assessing population changes

Disassembly of a tadpole community by a multi‐host fungal pathogen with limited evidence of recovery

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