Alex Lancaster asked: At 04:28 AM 3/26/03 -0800: I'm looking for papers that compare and constrast ABM/IBM to classical models (ecological or otherwise) such as Lotka-Volterra predator-prey dynamics, or otherwise help provide a bridge from classical equation-based models to ABM/IBM (e.g. setting up an ABM/IBM in a "special case" mode to reproduce known classical dynamics). If there's anybody out there who can recommend papers on ABM/IBM that would be general enough to digest, but with reference to ecology, please let me know. Here are some answers I pasted out of modelling@swarm.org. Alex, If you're looking for a paper that compares an IBM approach specifically to classical Lotka-Volterra predator-prey dynamics, you might take a look at: Wilson, W.G., de Roos, A.M., and E. McCauley. 1993. Spatial instabilities within the diffusive Lotka-Volterra system: individual-based simulation results. Theoretical Population Biology. 43(1): 91-127. Don't know if it's general enough for your purposes, but it might provide some useful ideas. This one also make some specific comparisons, but with age-structured populations: McCauley, E., Wilson, W.G., and A.M. de Roos. 1993. Dynamics of age-structured and spatially structured predator-prey interactions: individual-based models and population-level formulations. American Naturalist. 143(3): 412-442. Cheers, Ho Jung Alex, On the specific topic you mentioned (compare and constrast ABM/IBM to classical models), I suggest you might include the paper by Lorenz Fahse, Christian Wissel, and Volker Grimm "Reconciling classical and individual-based approaches in theoretical population ecology: a protocol for extracting population parameters from individual-based models" published in American Naturalist 152:838-852 (Dec. 1998) available through Jstor. Volker Grimm and colleagues have published alot more on this topic since then, but that paper lays out a good framework for the topic you mentioned. Note that Eli Meir has been working on a whole book on this topic as well, based around what he has learned from developing Ecobeaker - I don't think the book is out yet though. Regarding what pre-dated Swarm, you should realize that Swarm has been around in one form or another for a long time - I first saw a demo of it when we invited Dave Hiebeler here for a visit in mid-1994, at which time it was still at such a stage that we decided for the ATLSS project to develop our own C++ code. Good luck preparing for the exams! Best regards, Lou Gross Alex: Here are a couple more papers that do the compare and contrast-- Janusz Uchmanski is a real pioneer in this field but unfortunately in Poland it is very hard for him to travel so few people know him. Uchmanski, J. 1999. What promotes persistence of a single population: an individual-based model. Ecological Modelling 115:227-241. (A very simple single-species, single-resource model; examines effects on population dynamics of stepwise increases in complexity- from "classical" towards IBM.) Grimm, V., and J. Uchmanski. 2002. Individual variability and population regulation: a model of the significance of within-generation density dependence. Oecologia 131:196-202. Abstract: Most models of theoretical population ecology consider population density as a state variable and thus ignore the fact that populations are composed not of identical average individuals but of individuals which are usually different. However, this individual variability may be important for population regulation. We there-fore analysed an individual-based population model which explicitly describes within-generation processes, i.e. individual growth, starvation, and resource dynam-ics. The results show that if population dynamics are dominated by slow changes in resource level, the popu-lation size in the model undergoes wide oscillation, often leading to extinction. If, on the other hand, fast within-generation processes predominate, such as starvation and sudden drops in resource levels, the population fluctu-ates to a limited extent around an average. Within-gener-ation density dependence may thus be an important mechanism which is largely ignored in classic time-dis-crete state-variable models. We conclude that the indi-vidual- based approach provides important insights into the hierarchical organization of population dynamics, i.e. the relationship between fast processes at the individual level and slower processes at the population level. -------------------- Doug Donalson said: Here is a paper that might be useful to you. It compares the results of a PDE model to those of an equivelent ABM. Nisbet, R. M., Diehl, S., Cooper, S. D., Wilson, W. G., Donalson, D. D., Kratz, K., Primary productivity gradients and short-tern population dynamics in open systems. Ecological Monographs 67: 535-553, 1997. You might want to think about the following when approaching your orals: The biggest argument against ABMs in Ecology has been the assumption that adding more parameters means that the model becomes less accurate. This is not true. (I call it " !(The Emperor's New Clothes) " argument). If you pretend it is no longer there, you don't have to think aboit it.) It comes from the fact that as you move to simpler model classes, say from a CA based representation of a system to an ODE based representation of the same system, the interactions appear to become more simple and thereby more tractable. However, this is an illusion. All of the mechanisms that are explicitly represented in the CA still exist in the ODE, they are just subsumed in the implicit structure of the model. Over and over I have the same discussion with eco-modelers. "Tell me, if you think movement might be important in this system than how can you believe that a model that has instant teleportation of all agents to new random locations every millisecond (the well-mixed ODE assumption) can be more accurate than a model where you can explore the dynamical responses to different possible spatial movement scenarios (including the well-mixed assumption) and better understand how spatial movement might effect the overall system dynamics." You can extend this argument to things like "logistic growth", which becomes quite interesting when you try to implement it in a spatially explicit model, or some of the functional responses (like the Holling Type 3 functional response.) One of the things I am sending you is a book chapter that is in the publication cycle at present that discusses how using different model classes (ODE, SBD, CA, and ABM) to explore the same system can greatly improve both the verification and validation processes in model development. I actually have a much better (modified) version of this chapter but it is still is prep and not at the point where it would do you any good. It explores how different spatial assumptions (for example grid-based vs. continuous space) change system dynamics in a model of mussels and their predators, sea stars. Anyway, I'll get those out to you ASAP. (A great philosophical question is, "What does ASAP mean to a procrastinator?") Cheers, D4 -------------------- Alex, you could also take a look at Ezequiel Di Paolo's paper on ecological symmetry breaking where he compares an ABM and EBM of the same system and concludes that they give substantially different results due to their different representations of space. Di Paolo, E. (2000) Ecological Symmetry Breaking can Favour the Evolution of Altruism in an Action-response Game. Journal of Theoretical Biology 203, 2, pp. 135-152 Enjoy your viva, James --- Dr James A R Marshall Complex Systems Modelling --------------------------- Hi Alex, This paper has nothing about ecology, but much about bridging equation-based and A/IBM models. I hope it will be useful. On The Transition to Agent-Based Modeling: Implementation Strategies from Variables to Agents / Laszlo Gulyas Social Science Computer Review, Volume 20, No. 4, Winter, 2002 Regards, Gulya ------------------------ 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 115:129-148 *Great section in here on "Why individual-based modelling?" Lomnicki, A. 1999. Individual-based models and the individual-based approach to population ecology. Ecological Modelling 115: 191-198 *Focused on population ecology And then a great monograph (in my opinion) for ecological modellers before comps: Rigler, F. H. and R. H. Peters 1995. Science and Limnology. Excellence in Ecology series, volume 6. Ecology Institute, Oldendorf/Luhe, Germany. *I know you don't have time to really get into this but it's worth a skim-over And as an afterthought: Levin, S.A., B. Grenfell, A. Hastings, A.S. Perelson. Mathematical and computational challenges in population biology and ecosystems science. Science. 275: 334-343 1. Liu, J. and P. S. Ashton. 1998. FORMOSAIC: An individual-based spatially explicit model for simulating forest dynamics in landscape mosaics. Ecological Modelling 106:177-200. 2. Liu, J., J. B. Dunning, and H. R. Pulliam. 1995. Potential impacts of a forest management plan on Bachman's Sparrows (Aimophila aestivalis): Linking a spatially-explicit model with GIS. Conservation Biology 9: 62-79. 3. Liu, J. and P. S. Ashton. 1995. Individual-based simulation models for forest succession and management. Forest Ecology and Management 73:157-175.