You are in [[http://www.geoinformatics.cc | Geoinformatics - Creative Commons]] :: Introduction to Earth System Science Modelling :: Classes 2015 ===== CST-317: Introduction to Earth System Modelling (INPE Course 2015) ===== Professors: [[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]], Pedro R. Andrade ===== References =====http://www.geoinformatics.cc/doku.php?id=cst-317:classes2015&do= * Modeling the Environment (2nd edition), Andrew Ford. Island Press, 2010. * Thinking in Systems, Donella Meadows, Chelsea Green Publishing, 2008. * Nonlinear Dynamics And Chaos, Steven Strogatz, Westview Press, 2014. * Simulation for the Social Scientist, Nigel Gilbert & Klaus Troitzsch, Open University Press, 2005. * Complex Adaptive Systems: An Introduction to Computational Models of Social Life, John H. Miller & Scott Page, Princeton University Press, 2007. * Agent-based models of geographical systems, editors: Heppenstall, A.J., Crooks, A.T., See, L.M., Batty, M., Springer-Verlag, 2012. ===== Classes ===== ^Topic ^ Title ^ Models ^ TerraME Packages ^ Exercise | |1 |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-introd.ppt|Introduction}}| | | | |2 |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-lua-terrame-basics.ppt|Lua for TerraME}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-introduction.zip|Lua scripts}} | nil, number, boolean, string, table. function | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-lua_programs.pdf|Lua exercises}} | |3 |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-systems-theory.ppt|Systems Theory}} | LinearGrowth, LimitedGrowth, PopulationGrowth | sysdyn | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/assignment-1.pdf|Adjusting Limited Growth Model}}| |4 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-mono-lake.ppt| Renewable Resources }} | Mono Lake | sysdyn, sci | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/assignment-2.pdf|The Tucannon Salmon Model}}| |5 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-epidemics.ppt|Epidemics}} |Epidemics | sysdyn | | |6 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-daisyworld.ppt|Daisyworld}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-daisyworld.zip|Daisyworld model}} | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-daisyworld.pdf| Daisyworld}} | |8 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-predator-prey.ppt|Ecological Models}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-predator-prey.zip|Predator Prey Models}} | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-predator-prey.pdf| Fitting Predator Prey Models}} | |9 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-cellular-automata.ppt|Cellular Automata}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lifemodel.lua|Game of Life}} |CellularSpace, Neighborhood, Legend | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-cellular-automata.pdf|Variations on the Game of Life}}| |9a| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-fire-in-the-forest.ppt|Fire in the Forest (CA example)}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-fire-in-the-forest.zip|Fire in the forest}}| | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-fire-in-the-forest.pdf|Fire Scenarios}}| |10| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-hydrological-model.ppt|Hydrological Models}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/data-cabeca_de_boi-mdb.zip|Database}}, {{http://www.dpi.inpe.br/terraview/dow/terraView420.exe|TerraView}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-runoff.zip|Source code}}| | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-hydro-models.pdf|Hydrological Modelling}} | |11 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-deforestation-1-introd.ppt|Deforestation-part1}} | | | | |11a | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-deforestation-2-database.ppt|Deforestation-part2}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/data-amazonia.zip|Deforestation data}} | | | |11b | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-deforestation-3-modelling.ppt|Deforestation-part3}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/amazonia-database.zip|Databases}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-deforestation.zip|Scripts}} | Trajectory | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-deforestation.pdf|Deforestation Model}} + {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-modelling-deforestation.zip|Scripts}}| |12 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-agent-based-modelling.ppt|Agent-based modelling}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-butterfly.zip|ButterflyModel}}| Agent, Society | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-segregation.pdf| Segregation Models}} | | | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-barros-model.zip|BarrosModel}}| | | |13 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-game-theory.ppt|Game Theory}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-game-theory.zip|Prisioner's Dilemma}} | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-game-theory.pdf| Variations on Prisioner's Dilemma}} | |14 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-cooperation.ppt|Evolution of Cooperation}} |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-cooperation.zip|Code Evolution of Cooperation}} | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/exercise-evolution-cooperation.pdf| Cooperation Models}} | \\ ===== Additional Reading ===== * {{http://www.leg.ufpr.br/~pedro/final-projects/Wood-08.pdf|Wood, A. J., G. J. Ackland, J. G. Dyke, H. T. P. Williams, and T. M. Lenton (2008), Daisyworld: A review, Rev. Geophys., 46, RG1001}}. * W. von Bloh. Daisyworld: a tutorial approach to geophysiological modelling [[http://www.pik-potsdam.de/~bloh/]] * {{http://www.leg.ufpr.br/~pedro/final-projects/Schelling-71.pdf|Schelling, T. C. (1971). Dynamic models of segregation. Journal of mathematical sociology, 1(2), 143-186.}} (check also for its variations in the literature) * {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lenton1998.pdf|Timothy M. Lenton(1998). Gaia and Natural Selection. Nature 394, 439-447 (30 July 1998)}} * {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/games_on_grids.pdf| Nowak MA & Sigmund K (2000), Games on Grids}}. In: The Geometry of Ecological Interactions: Simplifying Spatial Complexity, eds. Dieckmann U, Law R & Metz JAJ, pp. 135–150. Cambridge UniversityPress. ===== Papers for Final Projects ===== The final project consists of an implementation and discussion of one of the following papers. | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Balzter1998.pdf|H. Balzter, P. W. Braun, W. Köhler (1998) Cellular automata models for vegetation dynamics. Ecological Modelling 107(2-3):113-125}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Silvertown1992.pdf|J. Silvertown, S. Holtier, J. Johnson and P. Dale (1992) Cellular Automaton Models of Interspecific Competition for Space-The Effect of Pattern on Process. Journal of Ecology, 80(3):527-533}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Berjak2002.pdf|S. G. Berjak, J. W. Hearne (2002) An improved cellular automaton model for simulating fire in a spatially heterogeneous Savanna system. Ecological Modelling 148(2):133–15}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers//Dunkerley1997a.pdf|D. L. Dunkerley (1997) Banded vegetation: development under uniform rainfall from a simple cellular automaton model. Plant Ecology 129(2):103-111}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers//Dunkerley1997b.pdf|D.L Dunkerley (1997) Banded vegetation: survival under drought and grazing pressure based on a simple cellular automaton model. Journal of Arid Environments 35(3):419–428}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Sirakoulis2000.pdf|G.Ch Sirakoulis, I. Karafyllidis, A. Thanailakis (2000) A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecological Modelling 133(3): 209–223}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Beauchemina2005.pdf|C. Beauchemina, J. Samuelb, J. Tuszynskia (2005) A simple cellular automaton model for influenza A viral infections. Journal of Theoretical Biology 232(2) 223–234}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Medeiros2011.pdf|Medeiros, L. C., Castilho, C. A. R., Braga, C., de Souza, W. V., Regis, L., Monteiro, A. M. V. (2011). Modeling the dynamic transmission of dengue fever: investigating disease persistence. PLOS neglected tropical diseases, 5(1), e942.}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Nakanishi1990.pdf|H. Nakanishi (1990) Cellular-automaton model of earthquakes with deterministic dynamics. Phys. Rev. A 41:7086–7089}}| | | {{http://www.hks.harvard.edu/netgov/files/fellows/onnela_j/papers/A7.pdf| R. Toivonen, J. Onnela, J. Saramaki, J. Hyvonen, K. Kaski (2006) A model for social networks. Physica A: Statistical Mechanics and its Applications 371(2):851–860}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers//joana_barros.pdf|Barros, J. Urban Growth in Latin American Cities. PhD thesis, CASA/UCL}} | | Iane | Cycles in Predator and Prey Populations, Chapter 20 of A. Ford, Modeling the Environment| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/gas_book_chap3.pdf|Sex, Culture and Conflict in SugarScape}}. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/gas_book_chap4.pdf|Trade in SugarScape}}. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.| | | {{http://www.openabm.org/model/3163/version/2/view|S Bergin (2012). Torsten Hägerstrand’s Spatial Innovation Diffusion Model. Available in CoMSES Computational Model Library.}}| | | {{http://jasss.soc.surrey.ac.uk/16/4/11.html|S Heckbert (2013). MayaSim: An agent-based model of the ancient Maya social-ecological system.}}{{http://www.openabm.org/model/3063/version/4/view| Available in CoMSES Computational Model Library.}}| | |{{http://www.openabm.org/model/3705/version/2/view| R Axelrod (1997). “The dissemination of culture - A model with local convergence and global polarization.” Journal of Conflict Resolution 41: 203-226.Replicated in CoMSES Computational Model Library.}}| | | {{http://www.openabm.org/model/3377/version/1/view|J Pepper and B Smuts (2000). The evolution of cooperation in an ecological context: an agent-based model. Replicated in CoMSES Computational Model Library.}}| | | {{http://www.openabm.org/model/3890/version/2/view|K Kahn (2013) A model of the Spanish Flu Pandemic. Available in CoMSES Computational Model Library.}}| | | {{http://www.openabm.org/model/3051/version/1/view|Schindler J (2012) A simple Multi-Agent System of the Tragedy Of the Commons. Available in CoMSES Computational Model Library.}}| | | {{http://www.openabm.org/model/2762/version/1/view| A K Knittel, R Riolo and R Snow (2011). Development and evaluation of an agent-based model of sexual partnership. Adaptive Behavior (available at CoMSES Computational Model Library.}}|. | | {{http://www.openabm.org/model/2274/version/2/view| M Janssen and N.D. Rollins (2012). Evolution of cooperation in asymmetric commons dilemmas. Journal of Economic Behavior and Organization, 81: 220-229. Available in CoMSES Computational Model Library).}}| | | {{http://www.openabm.org/model/2222/version/2/view|Axtell, Epstein, et al. (2002) Population Growth and Collapse in a Multi-Agent Model of the Kayenta Anasazi in Long House Valley. PNAS 99(3): 7275-7279. Replicated in M Janssen and available in CoMSES Computational Model Library.}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Bandini2007.pdf|S Bandini, F Celada, S Manzoni, G Vizzari (2007). Modelling the immune system: the case of situated cellular agents, Natural Computing, 6(1):19-32.}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Yassemi2008.pdf|S. Yassemi, S. Dragićevića, M. Schmidt(2008), Design and implementation of an integrated GIS-based cellular automata model to characterize forest fire behaviour , Ecological Modelling, 210(1–2), 71–84}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Sirakoulis2000.pdf|G.Ch Sirakoulis, I. Karafyllidis, A. Thanailakis (2000) A cellular automaton model for the effects of population movement and vaccination on epidemic propagation. Ecological Modelling 133(3): 209–223}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/White2007.pdf|S. Hoya White, A. Martín del Rey, G. Rodríguez Sánchez(2007), Modeling epidemics using cellular automata. Applied Mathematics and Computation, 186(1):193-202}}| | | {{http://www.dpi.inpe.br/gilberto/cursos/papers/Feitosa2012.pdf| F. Feitosa, A.M. Monteiro, Urban Conventions and Residential Location Choice. CAMUSS Conference (Cellular Automata Modeling forUrban and Spatial Systems 2012)}}|