===== CST-317: Introduction to Earth System Modelling (INPE Course 2013) =====

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.dpi.inpe.br/gilberto/cursos/cst-317-2013/luaforterrame-version2.pdf|Lua for TerraME: A Short Introduction}}
  * {{http://www.dpi.inpe.br/gilberto/papers/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-317-2013/lecture-introd.ppt|Introduction}}| | | |
|2  |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-lua-terrame-basics.ppt|Lua for TerraME}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-introduction.zip|Lua scripts}}     | nil, number, boolean, string, table. function    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-lua_programs.pdf|Lua exercises}} |
|3  |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-systems-theory.ppt|Systems Theory}}      | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-systems.zip|Water in the tub}}    | Cell, Event, Timer, Observer    | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-systems_theory.pdf|The City and the Dam}}|
|4   |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-feedbacks.ppt|Feedbacks}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-feedbacks.zip|Feedbacks}}          |                                                | |
|5  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-epidemics.ppt|Epidemics}}                       |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-epidemics.zip|Epidemics}}          |                                                 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-epidemics.pdf|Epidemics scenarios}}|                                             
|6 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-resources.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-317-2013/exercise-resources.pdf|Renewable Resources}} |                          
|7 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-daisyworld.ppt|Daisyworld}}              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/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-317-2013/exercise-predator-prey.pdf| Fitting Predator Prey Models}} |
|9 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-cellular-automaton.ppt|Cellular Automaton}}	              | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-life.zip|Game of Life}}	              |CellularSpace, Neighborhood, Legend | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-cellular-automata.pdf|Variations on the Game of Life}}|
|9a| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-fire-in-the-forest.ppt|Fire in the Forest (CA example)}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-fire-in-the-forest.zip|Fire in the forest}}|                  | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-fire-in-the-forest.pdf|Fire Scenarios}}|
|10| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-hydrological-model.ppt|Hydrological Models}}   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/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-317-2013/code-runoff.zip|Source code}}|                                            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-hydro-models.pdf|Hydrological Modelling}} |
|11 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-deforestation-1-introd.ppt|Deforestation-part1}}     |  |                                               | |
|11a | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-deforestation-2-database.ppt|Deforestation-part2}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/data-amazonia.zip|Deforestation data}}  |                             | |
|11b | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/lecture-deforestation-3-modelling.ppt|Deforestation-part3}}     | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/amazonia-database.zip|Databases}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-deforestation.zip|Scripts}}  | Trajectory                            | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/exercise-deforestation.pdf|Deforestation Model}} + {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-modelling-deforestation.zip|Scripts}}|
|12 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/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-317-2013/lecture-game-theory.ppt|Game Theory}}             | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/code-game-theory.zip|Prisioner's Dilemma}}     |                   | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2013/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}} |
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===== 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.

| Christiane e Anahi | {{http://www.leg.ufpr.br/~pedro/final-projects/Balzter-97.pdf|H. Balzter, P. W. Braun, W. Köhler (1998) Cellular automata models for vegetation dynamics. Ecological Modelling 107(2-3):113-125}}|
|  | {{http://www.leg.ufpr.br/~pedro/final-projects/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}}|
| Felipe | {{http://www.leg.ufpr.br/~pedro/final-projects/Chase-91.pdf|Chase, C. (1992) Fluvial landsculpting and the fractal dimension of topography. Geomorphology, 5(1-2):39-57.}}|
|  | {{http://www.leg.ufpr.br/~pedro/final-projects/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.leg.ufpr.br/~pedro/final-projects/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.leg.ufpr.br/~pedro/final-projects/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}}|
|Jaidson e Rafael  | {{http://www.leg.ufpr.br/~pedro/final-projects/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}}|
|Ana Gabriela e Lucinéia  | {{http://www.leg.ufpr.br/~pedro/final-projects/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.leg.ufpr.br/~pedro/final-projects/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.}}|
|Carla e Ian | {{http://www.leg.ufpr.br/~pedro/final-projects/Avolio-00.pdf|M.V. Avolio, S. Gregorio, F. Mantovani, A. Pasuto, R. Rongo, S. Silvano, W. Spataro (2000) Simulation of the 1992 Tessina landslide by a cellular automata model and future hazard scenarios. International Journal of Applied Earth Observation and Geoinformation 2(1):41–50}}|
| Sandro e Lira | {{http://www.leg.ufpr.br/~pedro/final-projects/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.leg.ufpr.br/~pedro/final-projects/joana_barros.pdf|Barros, J. Urban Growth in Latin American Cities. PhD thesis, CASA/UCL}} |
| Lis e Ana Paula | Cycles in Predator and Prey Populations, Chapter 20 of A. Ford, Modeling the Environment|