Species Occupancy Modeling for Detection Data Collected Along a Transect
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The proportion of sampling sites occupied by a species is a concept of interest in ecology and biodiversity conservation. Occupancy surveys based on collecting detection data along transects have become increasingly popular to monitor some species. To date, the analysis of such data has been carried out by discretizing the data, dividing the transects into discrete segments. Here we propose alternative occupancy models which describe the detection process as a continuous point process. These models provide a more natural description of the data and eliminate the need to divide transects into segments, which can be arbitrary and may lead to increased bias in the estimator of occupancy or increased chances of obtaining estimates on the boundary of the parameter space. We present a model that assumes independence between detections and an alternative model that describes the detection process as a Markov modulated Poisson process to account for potential clustering in the detections. The utility of these models is illustrated with the analysis of data from a recent survey of the Sumatran tiger Panthera tigris sumatrae. The models can also be applied to surveys that collect continuous data in time, such as those based on the use of camera-trap devices. Supplementary materials for this article are available online.
- Corless, R. M., Gonnet, G. H., Hare, D. E. G., Jeffrey, D. J., and Knuth, D. E. (2005), “On the Lambert W Function,” Advances in Computational Mathematics, 5, 329–359. CrossRef
- Cox, D. R., and Isham, V. (1980), Point Processes, London: Chapman and Hall.
- Cox, D. R., and Oakes, D. (1984), Analysis of Survival Data, London: Chapman & Hall.
- Fischer, W., and Meier-Hellstern, K. (1992), “The Markov-Modulated Poisson Process (MMPP) Cookbook,” Performance Evaluation, 18, 149–171. CrossRef
- Guillera-Arroita, G., Ridout, M. S., and Morgan, B. J. T. (2010), “Design of Occupancy Studies with Imperfect Detection,” Methods in Ecology and Evolution, 1, 131–139. CrossRef
- Hedley, S. L., and Buckland, S. T. (2004), “Spatial Models for Line Transect Sampling,” Journal of Agricultural, Biological, and Environmental Statistics, 9, 181–199. CrossRef
- Hines, J. E., Nichols, J. D., Royle, J. A., MacKenzie, D. I., Gopalaswamy, A. M., Samba Kumar, N., and Karanth, K. U. (2010), “Tigers on Trails: Occupancy Modeling for Cluster Sampling,” Ecological Applications, 20, 1456–1466. CrossRef
- Kaplan, E. L., and Meier, P. (1958), “Nonparametric Estimation from Incomplete Observations,” Journal of the American Statistical Association, 53, 457–481. CrossRef
- Karanth, K. U., and Nichols, J. D. (2002), Monitoring Tigers and Their Prey: A Manual for Researchers, Managers and Conservationists in Tropical Asia, Bangalore: Centre for Wildlife Studies.
- Linkie, M., Dinata, Y., Nugroho, A., and Haidir, I. A. (2007), “Estimating Occupancy of a Data Deficient Mammalian Species Living in Tropical Rainforests: Sun Bears in the Kerinci Seblat Region, Sumatra,” Biological Conservation, 137, 20–27. CrossRef
- MacKenzie, D. I., and Royle, J. A. (2005), “Designing Occupancy Studies: General Advice and Allocating Survey Effort,” Journal of Applied Ecology, 42, 1105–1114. CrossRef
- MacKenzie, D. I., Bailey, L. L., and Nichols, J. D. (2004), “Investigating Species Co-occurrence Patterns When Species are Detected Imperfectly,” Journal of Animal Ecology, 73, 546–555. CrossRef
- MacKenzie, D. I., Nichols, J. D., Lachman, G. B., Droege, S., Royle, J. A., and Langtimm, C. A. (2002), “Estimating Site Occupancy Rates When Detection Probabilities Are Less Than One,” Ecology, 83, 2248–2255. CrossRef
- MacKenzie, D. I., Nichols, J. D., Hines, J. E., Knutson, M. G., and Franklin, A. B. (2003), “Estimating Site Occupancy, Colonization, and Local Extinction When a Species is Detected Imperfectly,” Ecology, 84, 2200–2207. CrossRef
- MacKenzie, D. I., Nichols, J. D., Royle, J. A., Pollock, K. H., Bailey, L. L., and Hines, J. E. (2006), Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, New York: Academic Press.
- Morgan, B. J. T., Revell, D. J., and Freeman, S. N. (2007), “A Note on Simplifying Likelihoods for Site Occupancy Models,” Biometrics, 63, 618–621. CrossRef
- Royle, A. J. (2006), “Site Occupancy Models With Heterogeneous Detection Probabilities,” Biometrics, 62, 97–102. CrossRef
- Rydén, T. (1994), “Parameter Estimation for Markov Modulated Poisson Processes,” Communications in Statistics—Stochastic Models, 10, 795–829. CrossRef
- Skaug, H. J. (2006), “Markov Modulated Poisson Processes for Clustered Line Transect Data,” Environmental and Ecological Statistics, 13, 199–211. CrossRef
- Species Occupancy Modeling for Detection Data Collected Along a Transect
Journal of Agricultural, Biological, and Environmental Statistics
Volume 16, Issue 3 , pp 301-317
- Cover Date
- Print ISSN
- Online ISSN
- Additional Links
- Clustered data
- Markov modulated Poisson process
- Wildlife monitoring
- Zero-inflated Poisson process
- Author Affiliations
- 1. School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, CT2 7NZ, UK
- 2. Fauna & Flora International (FFI) in Aceh, Jln Tgk. Chik Dipasi No. 50, Desa Limpok, Darussalam, Aceh Besar, Nanggroe Aceh Darussalam, 23373, Indonesia
- 3. Durrell Institute of Conservation and Ecology, University of Kent, Canterbury, CT2 7NR, UK