Full Open Population Capture-Recapture Models With Individual Covariates

Journal of Agricultural, Biological, and Environmental Statistics

Volumn 16, Issue 2, 2011, Pages 253-268

  Schofield, Matthew R ^a,b   Barker, Richard J ^c  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY OF KENTUCKY   (United States)

^c UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Capture recapture; Demographic parameters; Hierarchical modeling; Individual covariates; JAGS BUGS

Indexed keywords

ABUNDANCE; BIRTH RATE; DEMOGRAPHY; NUMERICAL MODEL; POPULATION SIZE; SOFTWARE;

EID: 79958706022     PISSN: 10857117     EISSN: 15372693     Source Type: Journal    
DOI: 10.1007/s13253-010-0052-4     Document Type: Article

References (47)

1. Barker, R. J. (1999), "Joint Analysis of Mark-Recapture, Resighting and Ring-Recovery Data With Age-Dependence and Marking-Effect," Bird Study, 46(suppl), 82-91.
2. Barker, R. J., and Link, W. A. (2010), "Posterior Model Probabilities Computed From Model-Specific Gibbs Output," arXiv: 1012. 0073v1.
3. Bonner, S. J., and Schwarz, C. J. (2006), "An Extension of the Cormack-Jolly-Seber Model for Continuous Covariates With Application to Microtus pennsylvanicus," Biometrics, 62, 142-149.
4. Bonner, S. J., Morgan, B. J. T., and King, R. (2010), "Continuous Covariates in Mark-Recapture-Recovery Analysis: A Comparison of Methods," Biometrics, 66, 1256-1265.
5. Brooks, S. P., and Gelman, A. (1998), "General Methods for Monitoring Convergence of Iterative Simulations," Journal of Computational and Graphical Statistics, 7 (4), 434-455.
6. Brooks, S. P., Catchpole, E. A., and Morgan, B. J. T. (2000), "Bayesian Animal Survival Estimation," Statistical Science, 15 (4), 357-376.
7. Burnham, K. P., Anderson, D. R., White, G. C., Brownie, C., and Pollock, K. H. (1987), "Design and Analysis Methods for Fish Survival Experiments Based on Release-Recapture," American Fisheries Society Monograph, 5, 1-437.
8. Catchpole, E. A., Morgan, B. J. T., and Tavecchia, G. (2008), "A New Method for Analysing Discrete Life History Data With Missing Covariate Values," Journal of the Royal Statistical Society: Series B (Statistical Methodology), 70 (2), 445-460.
9. Conn, P. B., and Cooch, E. G. (2009), "Multistate Capture-Recapture Analysis Under Imperfect State Observation: An Application to Disease Models," Journal of Applied Ecology, 46 (2), 486-492.
10. Dupuis, J. A. (1995), "Bayesian Estimation of Movement and Survival Probabilities From Capture-Recapture Data," Biometrika, 82 (4), 761-772.
11. Dupuis, J. A., and Schwarz, C. J. (2007), "A Bayesian Approach to the Multistate Jolly-Seber Capture-Recapture Model," Biometrics, 63 (4), 1015-1022.
12. Durban, J. W., and Elston, D. A. (2005), "Mark-Recapture With Occasion and Individual Effects: Abundance Estimation Through Bayesian Model Selection in a Fixed Dimensional Parameter Space," Journal of Agricultural, Biological, and Environmental Statistics, 10, 291-305.
13. Gelman, A., Carlin, J. B., Stern, H. S., and Rubin, D. B. (2004), Bayesian Data Analysis (2nd ed.). Boca Raton: Chapman & Hall/CRC.
14. Gimenez, O., Bonner, S. J., King, R., Parker, R. A., Brooks, S. P., Jamieson, L. E., Grosbois, V., Morgan, B. J. T., and Thomas, L. (2009), "WinBUGS for Population Ecologists: Bayesian Modeling Using Markov Chain Monte Carlo Methods," in Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics, Vol. 3, eds. D. L. Thomson, E. G. Cooch, and M. J. Conroy, Berlin: Springer, pp. 885-918.
15. Hastie, T., Tibshirani, R., and Friedman, J. (2009), The Elements of Statistical Learning (2nd ed.), Berlin: Springer.
16. Huggins, R. M. (1989), "On the Statistical Analysis of Capture Experiments," Biometrika, 76 (1), 133-140.
17. King, R., and Brooks, S. P. (2002), "Bayesian Model Discrimination for Multiple Strata Capture-Recapture Data," Biometrika, 89, 785-806.
18. - (2008), "On the Bayesian Estimation of a Closed Population Size in the Presence of Heterogeneity and Model Uncertainty," Biometrics, 64 (3), 816-824.
19. King, R., Brooks, S. P., and Coulson, T. (2008), "Analyzing Complex Capture-Recapture Data in the Presence of Individual and Temporal Covariates and Model Uncertainty," Biometrics, 64 (4), 1187-1195.
20. King, R., Morgan, B. J. T., Gimenez, O., and Brooks, S. P. (2010), Bayesian Analysis for Population Ecology, Boca Raton: Chapman & Hall/CRC.
21. Lebreton, J. D., Burnham, K. P., Clobert, J., and Anderson, D. R. (1992), "Modelling Survival and Testing Biological Hypotheses Using Marked Animals: A Unified Approach with Case Studies," Ecological Monographs, 62 (1), 67-118.
22. Link, W. A., and Barker, R. J. (2005), "Modeling Association Among Demographic Parameters in Analysis of Open Population Capture-Recapture Data," Biometrics, 61, 46-54.
23. - (2006), "Model Weights and the Foundations of Multimodel Inference," Ecology, 87, 2626-2635.
24. - (2010), Bayesian Inference With Ecological Applications, New York: Academic Press.
25. Lunn, D., Thomas, A., Best, N., and Spiegelhalter, D. (2000), "WinBUGS-A Bayesian Modelling Framework: Concepts, Structure, and Extensibility," Statistics and Computing, 10, 325-337.
26. McDonald, T. L., and Amstrup, S. C. (2001), "Estimation of Population Size Using Open Capture-Recapture Models," Journal of Agricultural, Biological, and Environmental Statistics, 206-220.
27. Nichols, J. D., Sauer, J. R., Pollock, K. H., and Hestbeck, J. B. (1992), "Estimating Transition Probabilities for Stage-Based Population Projection Matrices Using Capture-Recapture Data," Ecology, 73 (1), 306-312.
28. Nichols, J. D., Kendall, W. L., Hines, J. E., and Spendelow, J. A. (2004), "Estimation of Sex-Specific Survival from Capture-Recapture Data When Sex in Not Always Known," Ecology, 85, 3192-3201.
29. Plummer, M. (2003), "JAGS: A Program for Analysis of Bayesian Graphical Models Using Gibbs Sampling," in Proceedings of the 3rd International Workshop on Distributed Statistical Computing, March, pp. 20-22.
30. Pollock, K. H. (1982), "A Capture-Recapture Design Robust to Unequal Probability of Capture," Journal of Wildlife Management, 46 (3), 752-757.
31. Pollock, K. H., Hines, J. E., and Nichols, J. D. (1985), "Goodness-of-Fit Tests for Open Capture-Recapture Models," Biometrics, 41, 399-410.
32. Pradel, R. (1996), "Utilization of Capture-Mark-Recapture for the Study of Recruitment and Population Growth Rate," Biometrics, 52 (2), 703-709.
33. Pradel, R., Wintrebert, C., and Gimenez, O. (2003), "A Proposal for a Goodness-of-Fit Test to the Arnason-Schwarz Multisite Capture-Recapture Model," Biometrics, 59, 43-53.
34. Royle, J. A. (2009), "Analysis of Capture-Recapture Models With Individual Covariates Using Data Augmentation," Biometrics, 65 (1), 267-274.
35. Royle, J. A., and Dorazio, R. M. (2008), Hierarchical Modeling and Inference in Ecology: The Analysis of Data from Populations, Metapopulations and Communities, New York: Academic Press.
36. Royle, J. A., Dorazio, R. M., and Link, W. A. (2007), "Analysis of Multinomial Models with Unknown Index Using Data Augmentation," Journal of Computational and Graphical Statistics, 16, 67-85.
37. Rubin, D. B. (1976), "Inference and Missing Data," Biometrika, 63 (3), 581-592.
38. Schofield, M. R. (2007), "Hierarchical Capture-Recapture Models," Ph. D. thesis, University of Otago.
39. Schofield, M. R., and Barker, R. J. (2008), "A Unified Capture-Recapture Framework," Journal of Agricultural, Biological and Environmental Statistics, 13, 458-477.
40. - (2009), "A Further Step Toward the Mother-of-All-Models: Flexibility and Functionality in the Modeling of Capture-Recapture Data," in Modeling Demographic Processes in Marked Populations. Environmental and Ecological Statistics, Vol. 3, eds. D. L. Thomson, E. G. Cooch, and M. J. Conroy, Berlin: Springer, pp. 677-689.
41. Schofield, M. R., Barker, R. J., and MacKenzie, D. I. (2009), "Flexible Hierarchical Mark-Recapture Modeling for Open Populations Using WinBUGS," Environmental and Ecological Statistics, 16, 369-387.
42. Schwarz, C. J., and Arnason, A. N. (1996), "A General Methodology for the Analysis of Capture-Recapture Experiments in Open Populations," Biometrics, 52 (3), 860-873.
43. Schwarz, C. J., Schweigert, J. F., and Arnason, A. N. (1993), "Estimating Migration Rates Using Tag-Recovery Data," Biometrics, 49, 177-193.
44. Su, Y.-S., and Yajima, M. (2009), R2jags: A Package for Running JAGS From R. R package version 0. 01-26.
45. Tanner, M. A., and Wong, W. H. (1987), "The Calculation of Posterior Distributions by Data Augmentation" (with discussion), Journal of the American Statistical Association, 82, 529-550.
46. Williams, B. K., Nichols, J. D., and Conroy, M. J. (2002), Analysis and Management of Animal Populations, New York: Academic Press.
47. 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," Biometrics, 65(9999), 833-840. doi: 10. 1111/j. 1541-0420. 2008. 01165. x.