Dynamic Energy Budget theory meets individual-based modelling: A generic and accessible implementation

Methods in Ecology and Evolution

Volumn 3, Issue 2, 2012, Pages 445-449

  Martin, Benjamin T ^a   Zimmer, Elke I ^b   Grimm, Volker ^a   Jager, Tjalling ^b  

^a HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Bioenergetics model; Dynamic Energy Budget; Individual based model; Population dynamics

Indexed keywords

EID: 84867373809     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2011.00168.x     Document Type: Article

References (31)

1. Alunno-Bruscia, M., van der Veer, H.W. & Kooijman, S.A.L.M. (2009) The AquaDEB project (phase I): analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using Dynamic Energy Budgets. Journal of Sea Research, 62, 43-48.
2. Alver, M., Alfredsen, J. & Olsen, Y. (2006) An individual-based population model for rotifer (Brachionus plicatilis) cultures. Hydrobiologia, 560, 93-108.
3. Bacher, C. & Gangnery, A. (2006) Use of dynamic energy budget and individual based models to simulate the dynamics of cultivated oyster populations. Journal of Sea Research, 56, 140-155.
4. Berger, U., Hildenbrandt, H. & Grimm, V. (2002) Towards a standard for the individual-based modeling of plant populations: self-thinning and the field-of-neighborhood approach. Natural Resource Modelling, 15, 39-54.
5. Billoir, E., Péry, A.R.R. & Charles, S. (2007) Integrating the lethal and sublethal effects of toxic compounds into the population dynamics of Daphnia magna: a combination of the DEBtox and matrix population models. Ecological Modelling, 203, 204-214.
6. De Roos, A.M., Diekmann, O. & Metz, J.A.J. (1992) Studying the dynamics of structured population models: a versatile technique and its application to daphnia. The American Naturalist, 139, 123-147.
7. DeAngelis, D.L. & Mooij, W.M. (2005) Individual-based modelling of ecological and evolutionary processes. Annual Review Ecology, Evolution, and Systematics, 36, 147-168.
8. Denney, N.H., Jennings, S. & Reynolds, J.D. (2002) Life-history correlates of maximum population growth rates in marine fishes. Proceedings of the Royal Society B, 269, 2229-2237.
9. Grimm, V. (1999) Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future?. Ecological Modelling, 155, 129-148.
10. Grimm, V. & Railsback, S.F. (2005) Individual-based Modeling and Ecology. Princeton University Press, Princeton, NJ.
11. Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., Goss-Custard, J., Grand, T., Heinz, S., Huse, G., Huth, A., Jepsen, J.U., Jørgensen, C., Mooij, W.M., Müller, B., Pe'er, G., Piou, C., Railsback, S.F., Robbins, A.M., Robbins, M.M., Rossmanith, E., Rüger, N., Strand, E., Souissi, S., Stillman, R.A., Vabø, R., Visser, U. & DeAngelis, D.L. (2006) A standard protocol for describing individual-based and agent-based models. Ecological Modelling, 198, 115-126.
12. Grimm, V., Berger, U., DeAngelis, D.L., Polhill, G., Giske, J. & Railsback, S.F. (2010) The ODD protocol: a review and first update. Ecological Modelling, 221, 2760-2768.
13. Jager, T., Heugens, E.H.W. & Kooijman, S.A.L.M. (2006) Making sense of ecotoxicological test results: towards application of process-based models. Ecotoxicology, 15, 305-314.
14. Jager, T., Crommentuijn, T., van Gestel, C.A.M. & Kooijman, S.A.L.M. (2004) Simultaneous modeling of multiple end points in life-cycle toxicity tests. Environmental Science & Technology, 38, 2894-2900.
15. Klanjscek, T., Caswell, H., Neubert, M.G. & Nisbet, R.M. (2006) Integrating Dynamic Energy Budgets into matrix population models. Ecological Modelling, 196, 407-420.
16. Klok, C. & de Roos, A.M. (1996) Population level consequences of toxicological influences on individual growth and reproduction in Lumbricus rubellus (Lumbricidae, Oligochaeta). Ecotoxicology and Environmental Safety, 33, 118-127.
17. Kooijman, S.A.L.M. (2001) Quantitative aspects of metabolic organization; a discussion of concepts. Philosophical Transactions of the Royal Society B, 356, 331-349.
18. Kooijman, S.A.L.M. (2010) Dynamic Energy Budget theory for Metabolic Organisation. Cambridge University Press, Cambridge.
19. Kooijman, S.A.L.M., Hoeven, N.V.D. & Werf, D.C.V. (1989) Population consequences of a physiological model for individuals. Functional Ecology, 3, 325-336.
20. Kooijman, S.A.L.M. & Metz, J.A.J. (1984) On the dynamics of chemically stressed populations: the deduction of population consequences from effects on individuals. Ecotoxicology and Environmental Safety, 8, 254-274.
21. Kooijman, S.A.L.M., Sousa, T., Pecquerie, L., Van der Meer, J. & Jager, T. (2008) From food-dependent statistics to metabolic parameters, a practical guide to the use of Dynamic Energy Budget theory. Biological Reviews, 83, 533-552.
22. Luke, S., Cioffi-Revilla, C., Panait, L., Sullivan, K. & Balan, G. (2005) MASON: a multiagent simulation environment. Simulation, 81, 517-527.
23. Nikolai, C. & Madey, G. (2009) Tools of the trade: a survey of various agent based modeling platforms. Journal of Artificial Societies and Social Simulation, 12, 2. http://jasss.soc.surrey.ac.uk/12/2/2.html.
24. Nisbet, R.M., Muller, E.B., Lika, K. & Kooijman, S.A.L.M. (2008) From molecules to ecosystems through Dynamic Energy Budget models. Journal of Animal Ecology, 69, 913-926.
25. Railsback, S.F. & Grimm, V. (2012) Agent-based and Individual-based Modeling: A Practical Introduction. Princeton University Press, Princeton, N.J.
26. Railsback, S.F., Lytinen, S.L. & Jackson, S.K. (2006) Agent-based simulation platforms: review and development recommendations. Simulation, 82, 609-623.
27. Sæther, B.E. & Bakke, Ø. (2000) Avian life history variation and contribution of demographic traits to the population growth rate. Ecology, 81, 642-653.
28. Sousa, T., Domingos, T. & Kooijman, S.A.L.M. (2008) From empirical patterns to theory: a formal metabolic theory of life. Philosophical Transactions of the Royal Society B, 363, 2453-2464.
29. Stillman, R.A. & Goss-Custard, J.D. (2010) Individual-based ecology of coastal birds. Biological Reviews, 85, 413-434.
30. Van der Meer, J. (2006) An introduction to Dynamic Energy Budget (DEB) models with special emphasis on parameter estimation. Journal of Sea Research, 56, 85-102.
31. Wilensky, U. (1999) NetLogo. http://ccl.northwestern.edu/netlogo/. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.