This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
cst-317:classes2015 [2015/08/14 10:13] gilberto |
cst-317:classes2015 [2016/07/17 17:04] gilberto |
||
---|---|---|---|
Line 5: | Line 5: | ||
Professors: [[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]], Pedro R. Andrade | Professors: [[http://www.dpi.inpe.br/gilberto|Gilberto Câmara]], Pedro R. Andrade | ||
- | ===== References ===== | + | ===== References =====http://www.geoinformatics.cc/doku.php?id=cst-317:classes2015&do= |
* Modeling the Environment (2nd edition), Andrew Ford. Island Press, 2010. | * Modeling the Environment (2nd edition), Andrew Ford. Island Press, 2010. | ||
Line 23: | Line 23: | ||
|5 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-epidemics.ppt|Epidemics}} |Epidemics | sysdyn | | | |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}} | | |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-317-2013/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}} | | + | |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-317-2014/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}}| | + | |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-317-2014/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}}| | + | |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-317-2014/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}} | | + | |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-317-2014/lecture-deforestation-1-introd.ppt|Deforestation-part1}} | | | | | + | |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-317-2014/lecture-deforestation-2-database.ppt|Deforestation-part2}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/data-amazonia.zip|Deforestation data}} | | | | + | |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-317-2014/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}}| | + | |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-317-2014/lecture-agent-based-modelling.ppt|Agent-based modelling}} | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/code-butterfly.zip|ButterflyModel}}| Agent, Society | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/exercise-segregation.pdf| Segregation Models}} | | + | |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-317-2014/code-barros-model.zip|BarrosModel}}| | | | + | | | | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/code-barros-model.zip|BarrosModel}}| | | |
- | |13 | {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2014/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}} | | + | |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-317-2013/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}} | | + | |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 ===== | ===== Additional Reading ===== | ||
Line 40: | Line 40: | ||
* W. von Bloh. Daisyworld: a tutorial approach to geophysiological modelling [[http://www.pik-potsdam.de/~bloh/]] | * 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.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-317-2015/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-317-2013/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. | + | * {{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 ===== | ===== Papers for Final Projects ===== | ||
Line 48: | Line 48: | ||
| | {{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/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/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/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/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}}| |
- | |Marcos Sanches, Diego Jatobá | {{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//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//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//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/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/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/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/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}}| |
- | |Phillip Edson, Raquel Melo | {{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/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/Nakanishi-90.pdf|H. Nakanishi (1990) Cellular-automaton model of earthquakes with deterministic dynamics. Phys. Rev. A 41:7086–7089}}| | + | | | {{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}}| |
- | |Raquel Carvalho | {{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.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}} | | | | {{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| | | Iane | Cycles in Predator and Prey Populations, Chapter 20 of A. Ford, Modeling the Environment| | ||
Line 69: | Line 69: | ||
| | {{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/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/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).}}| | ||
- | |Marcio, Eduardo | {{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.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/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 | | | {{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 |