A method for representing and developing process models

Ecological Complexity

Volumn 4, Issue 1-2, 2007, Pages 1-12

  Borrett, Stuart R ^a   Bridewell, Will ^a   Langley, Pat ^a   Arrigo, Kevin R ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Ecosystem; Machine learning; Process based models; Ross Sea; System identification; Uncertainty

Indexed keywords

EID: 34247537497     PISSN: 1476945X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecocom.2007.02.017     Document Type: Note

References (73)

1. Abarca-Arenas L.G., and Ulanowicz R.E. The effects of taxonomic aggregation on network analysis. Ecol. Model. 149 (2002) 285-296
2. Abrams P.A. Why predation rate should not be proportional to predator density. Ecology 74 (1993) 726-733
3. Abrams P.A. The impact of habitat selection on the spatial heterogeneity of resources in varying environments. Ecology 81 (2000) 2902-2913
4. Ahl V., and Allen T.F.H. Hierarchy Theory: A Vision, Vocabulary, and Epistemology (1996), Columbia University Press, New York
5. Allen T.F.H., and Starr T.B. Hierarchy: Perspectives for Ecological Complexity (1982), University of Chicago Press, Chicago
6. Allesina S., Bodini A., and Bondavalli C. Ecological subsystems via graph theory: the role of strongly connected components. Oikos 110 (2005) 164-176
7. Arrigo K.R., and Tagliabue A. Iron in the Ross Sea: 2. Impact of discrete iron addition strategies. J. Geophys. Res. Oceans 110 (2005) C03010
8. Arrigo K.R., Worthen D.L., and Robinson D.H. A coupled ocean-ecosystem model of the Ross Sea: 2. Iron regulation of phytoplankton taxonomic variability and primary production. J. Geophys. Res. Oceans 108 (2003) 73231
9. Asgharbeygi N., Bay S., Langley P., and Arrigo K. Inductive revision of quantitative process models. Ecol. Model. 194 (2006) 70-79
10. Beck M.B. Water-quality modeling: a review of the analysis of uncertainty. Water Resour. Res. 23 (1987) 1393-1442
11. Borrett, S.R., Fath, B.D., Patten, B.C., 2007. Functional integration of ecological networks through pathway proliferation. J. Theor. Biol. 245, 98-111, doi:10.1016/j.jtbi.2006.09.024.
12. Bossel H. Real-structure process description as the basis of understanding ecosystems and their development. Ecol. Model. 63 (1992) 261-276
13. Brando V.E., Ceccarelli R., Libralato S., and Ravagnan G. Assessment of environmental management effects in a shallow water basin using mass-balance models. Ecol. Model. 172 (2004) 213-232
14. Brugnach M. Process level sensitivity analysis for complex ecological models. Ecol. Model. 187 (2005) 99-120
15. Cale W.G., Henebry G.M., and Yeakley J.A. Inferring process from pattern in natural communities: can we understand what we see?. Bioscience 39 (1989) 600-605
16. Cale W.G., and Odell P.L. Concerning aggregation in ecosystem models. In: Halfon E. (Ed). Theoretical Systems Ecology (1979), Academic Press, New York 55-77
17. Carpenter S.R., Cole J.T., Essington T.E., Hodgson J.R., Houser J.N., Kitchell J.F., and Pace M.L. Evaluating alternative explantations in ecosystem experiments. Ecosystems 1 (1998) 335-344
18. Carpenter S.R., Cottingham K.L., and Stow C.A. Fitting predator-prey models to time series with observation errors. Ecology 75 (1994) 1254-1264
19. Carpenter S.R., Kitchell J.F., and Hodgson J.R. Cascading trophic interactions and lake productivity: fish predation and herbivory can regulate lake ecosystems. Bioscience 35 (1985) 634-639
20. Clark J.S., Carpenter S.R., Barber M., Collins S., Dobson A., Foley J.A., Lodge D.M., Pascual M., Pielke R., Pizer W., Pringle C., Reid W.V., Rose K.A., Sala O., Schlesinger W.H., Wall D.H., and Wear D. Ecological forecasts: an emerging imperative. Science 293 (2001) 657-660
21. Costanza R., and Ruth M. Using dynamic modeling to scope environmental problems and build consensus. Environ. Manage. 22 (1998) 183-195
22. Ford E.D. Scientific Method for Ecological Research (2000), Cambridge University Press, Cambridge, New York
23. Galbraith K.A., Arnold G.W., and Carbon B.A. Dynamics of plant and animal production of a subterranean clover trifolium-subterraneum pasture grazed by sheep. 2: Structure and validation of the pasture growth model. Agricult. Syst. 6 (1980) 23-43
24. Gardner R.H., Cale W.G., and O'Neill R.V. Robust analysis of aggregation error. Ecology 63 (1982) 1771-1779
25. George D., Saito K., Langley P., Bay S., and Arrigo K. Discovering ecosystem models from time-series data. Proceedings of the Sixth International Conference on Discovery Science (2003) 141-152
26. Gold H.J. Mathematical Modeling of Biological Systems: An Introductory Guidebook (1977), Wiley, New York
27. Grant W.E., Pedersen E.K., and Marin S.L. Ecology and Natural Resource Management: Systems Analysis and Simulation (1997), John Wiley and Sons, Inc., New York
28. Gurney W.S.C., and Nisbet R.M. Ecological Dynamics (1998), Oxford University Press, New York
29. Hilborn R., and Mangel M. The Ecological Detective: Confronting Models with Data (1997), Princeton University Press, Princeton, NJ
30. Hornberger G.M., and Spear R.C. Eutrophication in Peel Inlet-1. The problem-defining behavior and a mathematical model for the phosphorus scenario. Water Res. 14 (1980) 29-42
31. Jørgensen S.E. Models as instruments for combination of ecological theory and environmental practice. Ecol. Model. 75-76 (1994) 5-20
32. Jørgensen S.E. Integration of Ecosystem Theories: A Pattern. third ed. (2002), Kluwer Academic Publishers, Dordrecht
33. Jørgensen S.E., and Bendoricchio G. Fundamentals of Ecological Modelling. third ed. (2001), Elsevier, New York
34. Jost C., and Arditi R. Identifying predator-prey processes from time-series. Theor. Popul. Biol. 57 (2000) 325-337
35. Jost C., and Arditi R. From pattern to process: Identifying predator-prey models from time-series data. Popul. Ecol. 43 (2001) 229-243
36. Krupnick, A., Morgenstern, R., Batz, M., Nelson, P., Burtraw, D., Shih, J.-S., McWilliams, M., 2001. Not a sure thing: making regulatory choices under uncertainty. Resources for the future, Washington, DC, 2006. Accessed at: http://www.rff.org/rff/News/Features/Not-a-Sure-Thing.cfm.
37. Korfmacher K.S. The politics of participation in watershed modelling. Environ. Manage. 27 (2001) 161-176
38. Landsberg J.J., and Waring R.H. A generalized model of forest productivity using simplified concepts of radiation-use efficiency carbon balance and partitioning. Forest Ecol. Manage. 95 (1997) 209-228
39. Langley P. The computational support of scientific discovery. Int. J. Hum. Comput. Stud. 53 (2000) 393-410
40. Langley P., George D., Bay S., and Saito K. Robust induction of process models from time-series data. Proceedings, 20th International Conference on Machine Learning, vol. 1 (2003) 432-439
41. Langley P., Sánchez J., Todorovski L., and Džeroski S. Inducing process models from continuous data. Proceedings of the 19th International Conference on Machine Learning (2002) 347-354
42. Langley P., Shiran O., Shrager J., Todorovski L., and Pohorille A. Constructing explanatory process models from biological data and knowledge. Artif. Intell. Med. 37 (2006) 191-201
43. Langley P., Simon H.A., Bradshaw G.L., and Żytkow J.M. Scientific Discovery: Computational Explorations of the Creative Processes (1987), MIT Press, Cambridge, MA
44. Levins R. The strategy of model building in population biology. Am. Sci. 54 (1966) 421-431
45. Levins R. Formal analysis and the fluidity of science-a response. Q. Rev. Biol. 68 (1993) 547-555
46. Loehle C. Errors of construction, evaluation, and inference: a classification of sources of error in ecological models. Ecol. Model. 36 (1987) 297-314
47. Loehle C. Hypothesis testing in ecology: Psychological aspects and the importance of theory maturation. Q. Rev. Biol. 62 (1987) 397-409
48. Machamer P., Darden L., and Craver C.F. Thinking about mechanisms. Philos. Sci. 67 (2000) 1-25
49. Maguire L.A. Interplay of science and stakeholder values in Neuse River total maximum daily load process. J. Water Resour. Plann. Manage. 129 (2003) 261-270
50. McMurtrie R.E. Forest productivity in relation to carbon partitioning and nutrient cycling: a mathematical model. In: Cannell M.G.R., and Jackson J.E. (Eds). Attributes of Trees as Crop Plants. Institute of Terrestrial Ecology (1985), Natural Environment Research Council, Abbots Ripton, Huntington, UK
51. Melillo J.M., McGuire A.D., Kicklighter D.W., Moore B., Vorosmarty C.J., and Schloss A.L. Global climate change and terrestrial net primary production. Nature 363 (1993) 234-239
52. National Geographic Society. Field Guide to the Birds of North America. third ed. (1999), National Geographic, Washington, DC
53. O'Neill R.V., DeAngelis D.L., Waide J.B., and Allen T.F.H. A Hierarchical Concept of Ecosystems (1986), Princeton University Press, Princeton, New Jersey
54. Oreskes N. Evaluation (not validation) of quantitative models. Environ. Health Perspect. 106 (1998) 1453-1460
55. Oreskes N., Shraderfrechette K., and Belitz K. Verification, validation, and confirmation of numerical-models in the earth-sciences. Science 263 (1994) 641-646
56. Orzack S.H., and Sober E. A critical assessment of Levins's the strategy of model-building in population biology (1966). Q. Rev. Biol. 68 (1963) 533-546
57. Osidele O.O., and Beck M.B. Food web modelling for investigating ecosystem behaviour in large reservoirs of the south-eastern United States: lessons from Lake Lanier, Georgia. Ecol. Model. 173 (2004) 129-158
58. Pulliam H.R., and Danielson B.J. Sources, sinks, and habitat selection-a landscape perspective on population-dynamics. Am. Nat. 137 (1991) S50-S66
59. Rastetter E.B., King A.W., Cosby B.J., Hornberger G.M., O'Neill R.V., and Hobbie J.E. Aggregating fine-scale ecological knowledge to model coarser-scale attributes of ecosystems. Ecol. Appl. 2 (1992) 55-70
60. Reckhow K.H. Water quality simulation modeling and uncertainty analysis for risk assessment and decision making. Ecol. Model. 72 (1994) 1-20
61. Reynolds J.H., and Ford E.D. Multi-criteria assessment of ecological process models. Ecology 80 (1999) 538-553
62. Sage R.W., Patten B.C., and Salmon P.A. Institutionalized model-making and ecosystem-based management of exploited resource populations: a comparison with instrument flight. Ecol. Model. 170 (2003) 107-128
63. In: Saltelli A., Chan K., and Scott E.M. (Eds). Sensitivity Analysis (2000), John Wiley and Sons, Chichester, U.K.
64. Sánchez J.N., and Langley P. An interactive environment for scientific model construction. Proceedings of the Second International Conference on Knowledge Capture (2003) 138-145
65. Simioni G., Le Roux X., Gignoux J., and Sinoquet H. Treegrass: A 3-D, process-based model for simulating plant interactions in tree-grass ecosystems. Ecol. Model. 131 (2000) 47-63
66. Spear R.C., and Hornberger G.M. Eutrophication in peel inlet-2. Identification of critical uncertainties via generalized sensitivity analysis. Water Res. 14 (1980) 43-49
67. Tagliabue A., and Arrigo K.R. Anomalously low zooplankton abundance in the Ross Sea: an alternative explanation. Limnol. Oceanogr. 48 (2003) 686-699
68. Tagliabue A., and Arrigo K.R. Iron in the Ross Sea: 1. Impact on CO2 fluxes via variation in phytoplankton functional group and non-Redfield stoichiometry. J. Geophys. Res. Oceans 110 (2005) 03009
69. Todorovski L., Bridewell W., Shiran O., and Langley P. Inducing hierarchical process models in dynamic domains. Proceedings of the 20th National Conference on Artificial Intelligence (2005) 892-897
70. Underwood A.J. Experiments in Ecology: Their Logical Design and Interpretation Using Analysis of Variance (1997), Cambridge University Press, Cambridge; New York
71. Whipple S.J., Patten B.C., and Verity P.G. Life cycle of the marine alga Phaeocystis: a conceptual model to summarize literature and guide research. J. Mar. Syst. 57 (2005) 83-110
72. Worthen D.L., and Arrigo K.R. A coupled ocean-ecosystem model of the Ross Sea. Part 1: Interannual variability of primary production and phytoplankton community structure. In: DiTullio G.R., and Dunbar R.B. (Eds). Biogeochemistry of the Ross Sea. Antarctic Research Series vol. 78 (2003), American Geophysical Union, Washington, DC
73. Zeigler B.P. Theory of Modelling and Simulation. second ed. (1974), Robert E. Krieger Publishing Company, Malabar, Florida