Smoothing population size estimates for time-stratified mark-recapture experiments using Bayesian P-splines

Biometrics

Volumn 67, Issue 4, 2011, Pages 1498-1507

  Bonner, Simon J ^a   Schwarz, Carl J ^b  

^a UNIVERSITY OF KENTUCKY   (United States)

^b SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Atlantic salmon; Bayesian inference; Hierarchical model; Mark recapture; OpenBUGS; Penalized spline; Stratified Petersen

Indexed keywords

BAYESIAN NETWORKS; HIERARCHICAL SYSTEMS; INFERENCE ENGINES; POPULATION STATISTICS; UNCERTAINTY ANALYSIS;

ATLANTIC SALMON; BAYESIAN; BAYESIAN INFERENCE; HIERARCHICAL MODEL; MARK-RECAPTURE; OPENBUGS; PENALIZED SPLINES; PETERSEN; POPULATION SIZES; STRATIFIED PETERSEN;

FISH;

ACCURACY ASSESSMENT; BAYESIAN ANALYSIS; DATA SET; ESTIMATION METHOD; EXPERIMENTAL STUDY; MARK-RECAPTURE METHOD; MIGRATION; NUMERICAL MODEL; POPULATION SIZE; POPULATION STRUCTURE; SALMONID; UNCERTAINTY ANALYSIS;

CANADA; NEWFOUNDLAND; NEWFOUNDLAND AND LABRADOR;

EID: 83655180971     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2011.01599.x     Document Type: Article

References (28)

1. Banneheka, S. G., Routledge, R. D., and Schwarz, C. J. (1997). Stratfied two-sample tag-recovery census of closed populations. Biometrics 53, 1212-1224.
2. Bjorkstedt, E. P. (2000). DARR (Darroch analysis with rank-reduction): A method for analysis of stratified mark-recapture data from small populations, with application to estimating abundance of smolts from outmigrant trap data. Technical Report, National Marine Fisheries Service, Southwest Fisheries Science Center Santa Cruz, California.
3. Bonner, S. J. (2008). Heterogeneity in capture-recapture: Bayesian methods to balance realism and model complexity. Ph.D. Thesis, Simon Fraser University, Burnaby, BC, Canada.
4. Bonner, S. J., Thomson, D., and Schwarz, C. J. (2009). Time-varying covariates and semiparametric regression in capture-recapture: An adaptive spline approach. In Modeling Demographic Processes in Marked Populations, Environmental and Ecological Statistics 3, D. L. Thomson, E. G. Cooch, and M. J. Conroy (eds), 657-676. New York: Springer.
5. Brooks, S. P., Catchpole, E. A., and Morgan, B. J. T. (2000). Bayesian animal survival estimation. Statistical Science 15, 357-376.
6. Brooks, S. P. and Gelman, A. (1998). General methods for monitoring convergence of iterative simulations. Journal of Computational and Graphical Statistics 7, 434-455.
7. Chapman, D. G. and Junge, Jr., C. O. (1956). The estimation of the size of a stratified animal population. The Annals of Mathematical Statistics 27, 375-389.
8. Darroch, J. N. (1961). The two-sample capture-recapture census when tagging and sampling are stratified. Biometrika 48, 241-260.
9. Dobson, A. J. (2002). An Introduction to Generalized Linear Models, 2nd edition. Boca Raton, Florida: Chapman and Hall/CRC Press.
10. Gelman, A. and Meng, X.-L. (1996). Model checking and model improvement. In Markov Chain Monte Carlo in Practice, W. Gilks, S. Richardson, and D. Spiegelhalter (eds), 189-201. London: Chapman and Hall.
11. Gelman, A., Carlin, J. B., Stern, H. S., and Rubin, D. B. (2003). Bayesian Data Analysis, 2nd edition. New York: Chapman and Hall.
12. Gimenez, O. and Barbraud, C. (2009). The efficient semiparametric regression modeling of capture-recapture data: Assessing the impact of climate on survival of two Antarctic seabird species. In Modeling Demographic Processes in Marked Populations, Environmental and Ecological Statistics 3, D. L. Thomson, E. G. Cooch, and M. J. Conroy (eds), 43-58. New York: Springer.
13. Gimenez, O., Crainiceanu, C., Barbraud, C., Jenouvrier, S., and Morgan, B. J. T. (2006). Semiparametric regression in capture-recapture modelling. Biometrics 62, 691-698.
14. Gimenez, O., Grégoire, A., and Lenormand, T. (2009). Estimating and visualizing fitness surfaces using mark-recapture data. Evolution 63, 3097-3105.
15. Green, P. J. (1995). Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82, 711-732.
16. Lang, S. and Brezger, A. (2004). Bayesian P-splines. Journal of Computational and Graphical Statistics 13, 183-212.
17. Macdonald, P. D. and Smith, H. D. (1980). Mark-recapture estimation of salmon smolt runs. Biometrics 36, 401-417.
18. Mantyniemi, S. and Romakkaniemi, A. (2002). Bayesian mark-recapture estimation with an application to a salmonid smolt population. Canadian Journal of Fisheries and Aquatic Science 59, 1748-1758.
19. Plante, N., Rivest, L.-P., and Tremblay, G. (1998). Stratified capture-recapture estimation of the size of a closed population. Biometrics 54, 47-60.
20. Poole, D. and Raftery, A. E. (2000). Inference for deterministic simulation models: The Bayesian melding approach. Journal of the American Statistical Association 95, 1244-1255.
21. Ruppert, D., Wand, M. P., and Carroll, R. J. (2003). Semiparametric Regression. Cambridge, U.K.: Cambridge University Press.
22. Schwarz, C. J. and Dempson, J. B. (1994). Mark-recapture estimation of a salmon smolt population. Biometrics 50, 98-108.
23. Schwarz, C. J. and Taylor, C. G. (1998). Use of the stratified-Petersen estimator in fisheries management: Estimating the number of pink salmon (Oncorhyncus gorbuscha) spawners in the Fraser River. Canadian Journal of Fisheries and Aquatic Science 55, 281-296.
24. Schwarz, C. J., Pickard, D., Marine, K., and Bonner, S. J. (2009). Juvenile Salmonid Outmigrant Monitoring Evaluation. Technical Report, Prepared for the Trinity River Restoration Program, Weaverville, California.
25. Seber, G. A. F. (2002). The Estimation of Animal Abundance and Related Parameters, 2nd edition. Caldwell, New Jersey: The Blackburn Press.
26. Spiegelhalter, D. J., Best, N. G., Carlin, B. P., and van der Linde, A. (2002). Bayesian measures of model complexity and fit (with discussion). Journal of the Royal Statistical Society, Series B 64, 583-640.
27. Steinhorst, K., Wu, Y., Dennis, B., and Kline, P. (2004). Confidence intervals for fish out-migration estimates using stratified trap efficiency methods. Journal of Agricultural, Biological and Environmental Statistics 9, 284-299.
28. Thomas, A., O'Hara, B., Ligges, U., and Stutz, S. (2006). Making BUGS open. R News 6, 12-17.