The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
Advances and applications of occupancy models
Abstract
Summary: 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 possible non‐detection or species misidentification. We discuss some recent occupancy estimation methods and the biological systems that motivated their development. Collectively, these models offer tremendous flexibility, but simultaneously place added demands on the investigator. Unlike many mark–recapture scenarios, investigators utilizing occupancy models have the ability, and responsibility, to define their sample units (i.e. sites), replicate sampling occasions, time period over which species occurrence is assumed to be static and even the criteria that constitute ‘detection’ of a target species. Subsequent biological inference and interpretation of model parameters depend on these definitions and the ability to meet model assumptions. We demonstrate the relevance of these definitions by highlighting applications from a single biological system (an amphibian–pathogen system) and discuss situations where the use of occupancy models has been criticized. Finally, we use these applications to suggest future research and model development.
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Cites
Program MARK: survival estimation from populations of marked animals
White, G. C., & Burnham, K. P. (1999) · Bird Study · doi:10.1080/00063659909477239 · Cited by 7,499
ESTIMATING SITE OCCUPANCY RATES WHEN DETECTION PROBABILITIES ARE LESS THAN ONE
MacKenzie, D. I., Nichols, J. D., Lachman, G. B., Droege, S., Andrew Royle, J., & Langtimm, C. A. (2002) · Ecology · doi:10.1890/0012-9658(2002)083[2248:esorwd]2.0.co;2 · Cited by 4,481
Self-citationunmarked: An R Package for Fitting Hierarchical Models of Wildlife Occurrence and Abundance
Fiske, I., & Chandler, R. (2011) · Journal of Statistical Software · doi:10.18637/jss.v043.i10 · Cited by 2,357
Occupancy Estimation and Modeling. Inferring patterns and dynamics of species occurrence
Yoccoz, N. G. (2006) · Wildlife Biology · doi:10.2981/0909-6396(2006)12[450:oeamip]2.0.co;2 · Cited by 2,300
Berger, L., Speare, R., Daszak, P., Green, D. E., Cunningham, A. A., Goggin, C. L., Slocombe, R., Ragan, M. A., Hyatt, A. D., McDonald, K. R., et al. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.15.9031 · Cited by 2,009
Program MARK : survival estimation from populations of marked animals
Gc, W. (1999) · Bird Study · Cited by 1,973
Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence
MacKenzie, D. I. (2005) · Cited by 1,878
Self-citationThe BUGS project: evolution, critique and future directions
Lunn, D., Spiegelhalter, D., Thomas, A., & Best, N. (2009) · Statistics in Medicine · doi:10.1002/sim.3680 · Cited by 1,876
ESTIMATING SITE OCCUPANCY, COLONIZATION, AND LOCAL EXTINCTION WHEN A SPECIES IS DETECTED IMPERFECTLY
MacKenzie, D. I., Nichols, J. D., Hines, J. E., Knutson, M. G., & Franklin, A. B. (2003) · Ecology · doi:10.1890/02-3090 · Cited by 1,741
Self-citationDesigning occupancy studies: general advice and allocating survey effort
MACKENZIE, D. I., & ROYLE, J. A. (2005) · Journal of Applied Ecology · doi:10.1111/j.1365-2664.2005.01098.x · Cited by 1,405
Self-citation
Cited by
Burton, A. C., Neilson, E., Moreira, D., Ladle, A., Steenweg, R., Fisher, J. T., Bayne, E., & Boutin, S. (2015) · Journal of Applied Ecology · doi:10.1111/1365-2664.12432 · Cited by 1,258
Is my species distribution model fit for purpose? Matching data and models to applications
Guillera‐Arroita, G., Lahoz‐Monfort, J. J., Elith, J., Gordon, A., Kujala, H., Lentini, P. E., McCarthy, M. A., Tingley, R., & Wintle, B. A. (2015) · Global Ecology and Biogeography · doi:10.1111/geb.12268 · Cited by 961
Guillera‐Arroita, G. (2017) · Ecography · doi:10.1111/ecog.02445 · Cited by 426
Species Distribution Modeling for Machine Learning Practitioners: A Review
Beery, S., Cole, E., Parker, J., Perona, P., & Winner, K. (2021) · ACM SIGCAS Conference on Computing and Sustainable Societies · doi:10.1145/3460112.3471966 · Cited by 100
Bouchet, P. J., & Meeuwig, J. J. (2015) · Ecosphere · doi:10.1890/es14-00380.1 · Cited by 59
Metadata
- Authors
- Bailey, L. L., MacKenzie, D. I., & Nichols, J. D.
- Venue
- Methods in Ecology and Evolution
- Publisher
- Wiley
- Published
- 2013-09-04
- Volume
- 5
- Issue
- 12
- Pages
- 1269-1279
- ISSN
- 2041-210X (ISSN-L)
- OpenAlex
- W2034112342
- Cited by
- 260
- References
- 64
- FWCI
- 12.09
- Type
- journal article
- Language
- en
- Open access
- closed
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
