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You are in [[http://www.geoinformatics.cc | Geoinformatics - Creative Commons]] :: Introduction to Earth System Science Modelling :: Classes 2014

===== CST-317: Introduction to Earth System Modelling (INPE Course 2014) =====

Professors: [[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]], Pedro R. Andrade

===== References =====

  * Modeling the Environment (2nd edition), Andrew Ford. Island Press, 2010.
  * Thinking in Systems, Donella Meadows, Chelsea Green Publishing, 2008.
  * Dynamic Modeling of Environmental Systems, Michael L. Deaton & James J. Winebrake. Springer, 2000.
  * 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.
  * Cities and Complexity. Michael Batty. MIT Press, 2007.

===== Software Description  =====

The models described in this course will be developed using [[http://www.terrame.org | TerraME]]. TerraME is an extension of the [[http://www.lua.org|Lua]] language. Some useful documents about TerraME:

  * {{http://www.terrame.org/luaforterrame-version2.pdf|Lua for TerraME: A Short Introduction}}
  * {{http://www.terrame.org/terrame_ems_post_print.pdf|TerraME paper on EMS journal}}
  * [[http://www.lua.org/spe.html| Introduction to Lua]]

Students should read the TerraME EMS paper first, to get a sense of the language. Then they should read the Lua papers, to learn about programming in Lua.

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===== Classes =====

^Topic ^  Title	                  ^  Models                  ^ TerraME Types ^ Exercise |
|1  |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-introd.ppt|Introduction}}| | | |
|2  |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-lua-terrame-basics.ppt|Lua for TerraME}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/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-317-2014/lecture-systems-theory.ppt|Systems Theory}}      | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-systems.zip|Water in the tub}}    | Cell, Event, Timer, Observer    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-systems_theory.pdf|The City and the Dam}}|
|4   |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-feedbacks.ppt|Feedbacks}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-feedbacks.zip|Feedbacks}}          |                                                | |
|5  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-epidemics.ppt|Epidemics}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-epidemics.zip|Epidemics}}          |                                                 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-epidemics.pdf|Epidemics scenarios}}|                                             
|6 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-mono-lake.ppt| Renewable Resources }}                       | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-resources.zip|Mono Lake Example}}         |          |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-resources.pdf|Renewable Resources}} |                          
|7 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-daisyworld.ppt|Daisyworld}}              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-daisyworld.zip|Daisyworld model}}      |                               | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-daisyworld.pdf| Daisyworld}} |
|8 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-predator-prey.ppt|Ecological Models}}              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-predator-prey.zip|Predator Prey Models}}      |                               | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-predator-prey.pdf| Fitting Predator Prey Models}} |
|9 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-cellular-automata.ppt|Cellular Automata}}	              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lifemodel.lua|Game of Life}}	              |CellularSpace, Neighborhood, Legend | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-cellular-automata.pdf|Variations on the Game of Life}}|
|9a| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-fire-in-the-forest.ppt|Fire in the Forest (CA example)}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-fire-in-the-forest.zip|Fire in the forest}}|                  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-fire-in-the-forest.pdf|Fire Scenarios}}|
|10| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-hydrological-model.ppt|Hydrological Models}}   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/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-317-2014/exercise-hydro-models.pdf|Hydrological Modelling}} |
|11 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-deforestation-1-introd.ppt|Deforestation-part1}}     |  |                                               | |
|11a | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/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-317-2014/lecture-deforestation-3-modelling.ppt|Deforestation-part3}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/amazonia-database.zip|Databases}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-deforestation.zip|Scripts}}  | Trajectory                            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-deforestation.pdf|Deforestation Model}} + {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-modelling-deforestation.zip|Scripts}}|
|12 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-agent-based-modelling.ppt|Agent-based modelling}}    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-segregation-model.zip|SegregationModel}}|       Agent, Society      | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-segregation.pdf| Segregation Models}} |
|13 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/lecture-game-theory.ppt|Game Theory}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-game-theory.zip|Prisioner's Dilemma}}     |                   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-game-theory.pdf| Variations on Prisioner's Dilemma}} |
|14 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-cooperation.ppt|Evolution of Cooperation}}              |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-cooperation.zip|Code Evolution of Cooperation}}     |            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/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-317-2013/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-317-2013/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/Silvertown-92.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/Berjak-01.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//Dunkerley-96.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//Dunkerley-96-b.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/Sirakoulis-00.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/Beauchemina-05.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/Medeiros-11.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/Nakanishi-90.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}} |
|  | 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)}}|
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