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Trace-contrast models for capture-recapture without capture histories. (English) Zbl 1442.62211

Summary: Capture-recapture studies increasingly rely upon natural tags that allow animals to be identified by features such as coat markings, DNA profiles, acoustic profiles, or spatial locations. These innovations greatly increase the number of capture samples achievable and enable capture-recapture estimation for many inaccessible and elusive species. However, natural features are invariably imperfect as indicators of identity. Drawing on the recently developed Palm likelihood approach to parameter estimation in clustered point processes, we propose a new estimation framework based on comparing pairs of detections, which we term the trace-contrast framework. Importantly, no reconstruction of capture histories is needed. We show that we can achieve accurate, precise, and computationally fast inference. We illustrate the methods with a camera-trap study of a partially marked population of ship rats (Rattus rattus) in New Zealand.

MSC:

62M30 Inference from spatial processes
62F10 Point estimation
62P10 Applications of statistics to biology and medical sciences; meta analysis

References:

[1] Baddeley, A. and Turner, R. (2005). Spatstat: An R package for analyzing spatial point patterns. J. Stat. Softw.12 1-42.
[2] Barker, R. J., Schofield, M. R., Wright, J. A., Frantz, A. C. and Stevens, C. (2014). Closed-population capture-recapture modeling of samples drawn one at a time. Biometrics70 775-782. · Zbl 1393.62052 · doi:10.1111/biom.12241
[3] Bell, E. A., Bell, B. D. and Merton, D. V. (2016). The legacy of Big South Cape: Rat irruption to rat eradication. NZ J. Ecol.40 205-211.
[4] Borchers, D. L. and Efford, M. G. (2008). Spatially explicit maximum likelihood methods for capture-recapture studies. Biometrics64 377-385, 664. · Zbl 1138.62088 · doi:10.1111/j.1541-0420.2007.00927.x
[5] Borchers, D. L., Distiller, G., Foster, R., Harmsen, B. and Milazzo, L. (2014). Continuous-time spatially explicit capture-recapture models, with an application to a jaguar camera-trap survey. Methods Ecol. Evol.5 656-665.
[6] Carroll, E. L., Patenaude, N. J., Childerhouse, S. J., Kraus, S. D., Fewster, R. M. and Baker, C. S. (2011). Abundance of the New Zealand subantarctic southern right whale population estimated from photo-identification and genotype mark-recapture. Mar. Biol.158 2565-2575.
[7] Charlton, B. D., Ellis, W. A. H., McKinnon, A. J., Brumm, J., Nilsson, K. and Fitch, W. T. (2011). Perception of male caller identity in koalas (Phascolarctos cinereus): Acoustic analysis and playback experiments. PLoS ONE6 e20329.
[8] Cormack, R. (1964). Estimates of survival from the sighting of marked animals. Biometrika51 429-438. · Zbl 0151.25904
[9] Diggle, P. J. (2003). Statistical Analysis of Spatial Point Patterns, 2nd ed. Arnold, London. · Zbl 1021.62076
[10] Fretwell, P. T., Staniland, I. J. and Forcada, J. (2014). Whales from space: Counting southern right whales by satellite. PLoS ONE9 e88655.
[11] Guan, Y. (2006). A composite likelihood approach in fitting spatial point process models. J. Amer. Statist. Assoc.101 1502-1512. · Zbl 1171.62348 · doi:10.1198/016214506000000500
[12] Jolly, G. M. (1965). Explicit estimates from capture-recapture data with both death and immigration-stochastic model. Biometrika52 225-247. · Zbl 0141.36601 · doi:10.1093/biomet/52.1-2.225
[13] Kühl, H. S. and Burghardt, T. (2013). Animal biometrics: Quantifying and detecting phenotypic appearence. Trends Ecol. Evol.28 432-441.
[14] Møller, J. and Waagepetersen, R. P. (2007). Modern statistics for spatial point processes. Scand. J. Stat.34 643-684. · Zbl 1157.62067
[15] Neyman, J. and Scott, E. L. (1958). Statistical approach to problems of cosmology. J. R. Stat. Soc. Ser. B. Stat. Methodol.20 1-43. · Zbl 0085.42906
[16] Palm, C. (1943). Intensitätsschwankungen im Fernsprechverkehr. Ericsson Technics44 1-189. · Zbl 0063.06088
[17] Prokešová, M. and Jensen, E. B. V. (2013). Asymptotic Palm likelihood theory for stationary point processes. Ann. Inst. Statist. Math.65 387-412. · Zbl 1440.62343 · doi:10.1007/s10463-012-0376-7
[18] Robins, J. H., Miller, S. D., Russell, J. C., Harper, G. A. and Fewster, R. M. (2016). Where did the rats of Big South Cape Island come from? NZ J. Ecol.40 229-234.
[19] Seber, G. A. F. (1965). A note on the multiple-recapture census. Biometrika52 249-259. · Zbl 0141.36602 · doi:10.1093/biomet/52.1-2.249
[20] Stevenson, B. C., Borchers, D. L., Altwegg, R., Swift, R. J., Gillespie, D. M. and Measey, G. J. (2015). A general framework for animal density estimation from acoustic detections across a fixed microphone array. Methods Ecol. Evol.6 38-48.
[21] Taberlet, P. and Luikart, G. (1999). Non-invasive genetic sampling and individual identification. Biol. J. Linn. Soc.68 41-55.
[22] Tanaka, U., Ogata, Y. and Stoyan, D. (2008). Parameter estimation and model selection for Neyman-Scott point processes. Biom. J.50 43-57. · Zbl 1442.62645 · doi:10.1002/bimj.200610339
[23] Thomas, M. (1949). A generalization of Poisson’s binomial limit for use in ecology. Biometrika36 18-25. · doi:10.1093/biomet/36.1-2.18
[24] Vale, R. T. R., Fewster, R. M., Carroll, E. L. and Patenaude, N. J. (2014). Maximum likelihood estimation for model \(M_{t,α}\) for capture-recapture data with misidentification. Biometrics70 962-971. · Zbl 1393.62104 · doi:10.1111/biom.12195
[25] Waagepetersen, R. P. (2007). An estimating function approach to inference for inhomogeneous Neyman-Scott processes. Biometrics63 252-258, 315. · Zbl 1122.62073 · doi:10.1111/j.1541-0420.2006.00667.x
[26] Waagepetersen, R. and Schweder, T. (2006). Likelihood-based inference for clustered line transect data. J. Agric. Biol. Environ. Stat.11 264-279.
[27] Wright, J. A., Barker, R. J., Schofield, M. R., Frantz, A. C., Byrom, A. E. and Gleeson, D. M. (2009). Incorporating genotype uncertainty into mark-recapture-type models for estimating abundance using DNA samples. Biometrics65 833-840. · Zbl 1172.62067 · doi:10.1111/j.1541-0420.2008.01165.x
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