Analysis of size trajectory data using an energetic-based growth model

Ecology

Volumn 86, Issue 6, 2005, Pages 1441-1451

  Fujiwara, Masami ^a   Kendall, Bruce E ^a   Nisbet, Roger M ^a   Bennett, William A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA DAVIS   (United States)

Author keywords

Bioenergetics; Dynamic energy budget; Energy reserves; Fluctuating food; Hypomesus transpacificus; Individual growth model; Nonlinear state space analysis; Numerical maximum likelihood; Parameter estimation; Size trajetory data

Indexed keywords

BIOENERGETICS; GROWTH MODELING; GROWTH RATE; INDIVIDUAL-BASED MODEL; PARAMETERIZATION;

ANIMALIA; HYPOMESUS TRANSPACIFICUS;

EID: 20444371368     PISSN: 00129658     EISSN: None     Source Type: Journal    
DOI: 10.1890/04-1351     Document Type: Article

References (45)

1. Bennett, W. A., and P. B. Moyle. 1996. Where have all the fishes gone? Factors producing fish declines in the San Francisco Bay estuary. Pages 519-541 in J. T. Hollibaugh, editor. San Francisco Bay: the ecosystem. Pacific Division, American Association for the Advancement of Science, San Francisco, California, USA.
2. Bennett, W. A., D. J. Ostrach, and D. E. Hinton. 1995. Condition of larval striped bass in a drought-stricken estuary: evaluating pelagic food web limitation. Ecological Applications 5:680-692.
3. Burnham, K. P., and D. R. Anderson. 1997. Model selection and inference: a practical information-theoretic approach. Springer-Verlag, New York, New York, USA.
4. Campana, S. E., and J. D. Neilson. 1985. Microstructure of fish otoliths. Canadian Journal of Fisheries and Aquatic Sciences 42:1014-1032.
5. Caswell, H. 2001. Matrix population models: construction, analysis and interpretation. Second edition. Sinauer Associates, Sunderland, Massachusetts, USA.
6. Catchpole, E., and B. Morgan. 1997. Detecting parameter redundancy. Biometrika 84:187-196.
7. Cox, D. K., and C. C. Coutant. 1981. Growth dynamics of juvenile striped bass as functions of temperature and ration. Transactions of the American Fisheries Society 110:226-238.
8. DeAngelis, D. L., and M. A. Huston. 1987. Effects of growth rates in models of size distribution formation in plants and animals. Ecological Modelling 36:119-137.
9. DeAngelis, D. L., L. B. Rose, E. A. Crowder, E. A. Marshall, and D. Lika. 1993. Fish cohort dynamics: application of complementary modeling approaches. American Naturalist 142:604-622.
10. de Valpine, P. 2004. Monte Carlo state-space likelihoods by weighted posterior kernel density estimation. Journal of the American Statistical Association 99:523-536.
11. de Valpine, P., and A. Hastings. 2001. Fitting population models incorporating process noise and observation error. Ecological Monographs 72:57-76.
12. Diggle, P. J., P. Heagerty, K. Y. Liang, and S. L. Zeger. 2002. Analysis of longitudinal data. Second edition. Oxford Statistical Science Series 25. Oxford University Press, Oxford, UK.
13. Doucet, A., N. de Freitas, and N. J. Gordon. 2001. Sequential Monte Carlo methods in practice. Springer-Verlag, New York, New York, USA.
14. Fujiwara, M., and H. Caswell. 2001. A general approach to temporary emigration in mark-recapture analysis. Ecology 83:3266-3275.
15. Fujiwara, M., B. E. Kendall, and R. M. Nisbet. 2004. Growth autocorrelation and animal size variation. Ecology Letters 7:106-113.
16. Gordon, N. J., D. J. Salmond, and A. F. M. Smith. 1993. Novel-approach to nonlinear non-Gaussian Bayesian state estimation. IEE (Institute of Electrical Engineers) Proceedings, F Radar and Signal Processing 140:107-113.
17. Gurney, W. S. C., W. Jones, A. R. Veitch, and R. M. Nisbet. 2003. Resource allocation, hyperphagia, and compensator growth in juveniles. Ecology 84:2777-2787.
18. Gurney, W. S. C., E. McCauley, R. M. Nisbet, and W. W. Murdoch. 1990. The physiological ecology of daphnia: a dynamic-model of growth and reproduction. Ecology 71: 716-732.
19. Higham, D. J. 2001. An algorithmic introduction to numerical simulation of stochastic differential equations. Society for Industrial and Applied Mathematics SIAM Review 43:525-546.
20. Hobbs, J. A., W. A. Bennett, J. E. Burton, and B. Baskerville-Bridges. 2004. Age and growth validation of delta smelt (Hypomesus transpacificus) in the San Francisco Estuary. Dissertation. University of California, Davis, California, USA.
21. Kooijman, S. A. L. M. 1986. Population dynamics on the basis of budgets. In J. A. J. Metz and O. Diekmann, editors. The dynamics of physiologically structured populations. Springer Lecture Notes in Biomathematics. Springer-Verlag, Berlin, Germany.
22. Kooijman, S. A. L. M. 2000. Dynamic energy and mass budgets in biological systems. Second edition. Cambridge University Press, Cambridge, UK.
23. Kooijman, S. A. L. M., and J. J. M. Bedaux. 1996. The analysis of aquatic toxicity data. VU (Vrije Universiteit) University Press, Amsterdam, The Netherlands.
24. MathWorks. 2001. MATLAB. Version 6.1, release 12. MathWorks, Natick, Massachusetts, USA.
25. McCullagh, P., and J. A. Neider. 1989. Generalized linear models. Monographs on statistics and applied probability 37. Second edition. CRC Press, Boca Raton, Florida, USA.
26. MediaCybernetics. 1998. Image-Pro Plus: Version 4. Media Cybernetics, Silver Spring, Maryland, USA.
27. Moyle, P. B., B. Herbold, D. E. Stevens, and L. W. Miller. 1992. Life history and status of delta smelt in the Sacramento-San Joaquin estuary, California. Transactions of the American Fisheries Society 121:67-77.
28. Muller, E. B., and R. M. Nisbet. 2000. Survival and production in variable resource environments. Bulletin of Mathematical Biology 62:1163-1189.
29. Nisbet, R. M., and W. S. C. Gurney. 2004. Modeling flauctuating populations. Blackburn Press, Caldwell, New Jersey, USA.
30. Nisbet, R. M., E. McCauley, W. S. C. Gurney, W. W. Murdoch, and S. N. Wood. 2004. Formulating and testing a dynamic energy budget model. Ecology 85:3132-3139.
31. Nisbet, R. M., E. B. Muller, K. Lika, and S. A. L. M. Kooijman. 2000. From molecules to ecosystems through dynamic energy budget models. Journal of Animal Ecology 69:913-926.
32. Nobriga, M. 2002. Larval delta smelt diet composition and feeding incidence: environmental and ontogenetic influences. California Fish and Game 88(4):149-164.
33. Noonburg, E. G., R. M. Nisbet, E. McCauley, W. S. C. Gurney, W. W. Murdoch, and A. M. De Roos. 1998. Experimental testing of dynamic energy budget models. Functional Ecology 12:211-222.
34. Pfister, C. A., and S. D. Peacor. 2003. Variable performance of individuals: the role of population density and endogenously formed landscape heterogeneity. Journal of Animal Ecology 72:725-735.
35. Pfister, C. A., and F. R. Stevens. 2002. Genesis of size variability in plants and animals. Ecology 83:59-72.
36. Quinn, T. J.,II, and R. B. Deriso. 1999. Quantitative fish dynamics. Oxford University Press, Oxford, UK.
37. Rice, J. A., T. J. Miller, K. A. Rose, L. B. Crowder, E. A. Marschall, A. S. Trebitz, and D. L. DeAngelis. 1993. Growth-rate variation and larval survival - inferences from an individual-based size-dependent predation model. Canadian Journal of Fisheries and Aquatic Sciences 50:133-142.
38. Ricker, W. E. 1958. Handbook of computations for biological statistics of fish populations. The Fisheries Research Board of Canada, Ottawa, Canada.
39. Rogers, B. A., and D. T. Westin. 1981. Laboratory studies on effects of temperature and delayed initial feeding on development of striped bass larvae. Transactions of the American Fisheries Society 110:100-110.
40. Rose, K. A., and J. H. Cowan. 1993. Individual-based model of young-of-the-year striped bass population dynamics. I. Model description and baseline simulations. Transactions of the American Fisheries Society 122:415-438.
41. Sweetnam, D. A. 1999. Status of delta smelt in the Sacramento-San Joaquin Estuary. California Fish and Game 85: 22-27.
42. U.S. Department of Interior. 1994. Endangered and threatened wildlife and plants: critical habitat determination for delta smelt. U.S. Fish and Wildlife Service, Washington, D.C., USA. Federal Register Document 94-31063.
43. van Haren, R. J. F., and S. A. L. M. Kooijman. 1993. Application of a dynamic energy budget model to Mytilus edulis (L.). Netherlands Journal of Sea Research 31(2): 119-133.
44. von Bertalanffy, L. 1938. A quantitative theory of organic growth (inquiries on growth laws II). Human Biology 10(2):181-213.
45. Wikelski, M., V. Carrillo, and F. Trillmich. 1997. Energy limits to body size in a grazing reptile, the Galapagos marine iguana. Ecology 78:2204-2217.