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--- cst-317:classes2016 [2016/08/19 09:36]
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+++ cst-317:classes2016 [2017/05/05 17:22]
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 |1  |{{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2015/lecture-introd.ppt|Introduction}}| | | | |
 |2  |{{:cst-317:1-lua-for-terrame.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 | {{:cst-317:exercicios-lua.pdf|Lua exercises}} |
-|3  |{{:cst-317:2-system-dynamics.ppt|Systems Dynamics}}      | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Tub.lua|Tub]] (sysdyn) | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/tub-scenarios.lua|tub-scenarios]] (sysdyn) | Model, Event, Timer, Chart | {{:cst-317:exercise1.pdf|Water in the Dam}} |
+|3  |{{:cst-317:2-system-dynamics.ppt|Systems Dynamics}}      | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Tub.lua|Tub}} (sysdyn) | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/tub-scenarios.lua|tub-scenarios}} (sysdyn) | Model, Event, Timer, Chart | {{:cst-317:exercise1.pdf|Water in the Dam}} |
-|4  | {{:cst-317:3-feedbacks.ppt|Feedbacks}} | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Coffee.lua|Coffee]], [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PopulationGrowth.lua|PopulationGrowth]] (sysdyn) | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/coffee-scenarios.lua|coffee-scenarios]], [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-1]], [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-2]] (sysdyn) | Environment, instance of Model |
+|4  | {{:cst-317:3-feedbacks.ppt|Feedbacks}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Coffee.lua|Coffee}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PopulationGrowth.lua|PopulationGrowth}} (sysdyn) | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/coffee-scenarios.lua|coffee-scenarios}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-1}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/population-scenarios-1.lua|population-scenarios-2}} (sysdyn) | Environment, instance of Model |
-|5  | {{:cst-317:4-epidemics.ppt|Epidemics}} | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/SIR.lua|SIR]] (sysdyn) | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-1.lua|infection-scenarios-1]], [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-2.lua|infection-scenarios-2]], [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-3.lua|infection-scenarios-3]] (sysdyn) | |
+|5  | {{:cst-317:4-epidemics.ppt|Epidemics}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/SIR.lua|SIR}} (sysdyn) | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-1.lua|infection-scenarios-1}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-2.lua|infection-scenarios-2}}, {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/examples/infection-scenarios-3.lua|infection-scenarios-3}} (sysdyn) | |
-|6  | {{:cst-317:5-predator-prey.ppt|Predator-Prey}} | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PredatorPrey.lua|PredatorPrey]] (sysdyn) | | |
+|6  | {{:cst-317:5-predator-prey.ppt|Predator-Prey}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PredatorPrey.lua|PredatorPrey}} (sysdyn) | | |
-|7  | {{:cst-317:6-daisyworld.ppt|Daisyworld}} | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Daisyworld.lua|Daisyworld]] (sysdyn) | [[https://raw.githubusercontent.com/pedro-andrade-inpe/calibration/master/examples/daisy-calibration.lua|daisy-calibration]] (calibration)| MultipleRuns (calibration) |
+|7  | {{:cst-317:6-daisyworld.ppt|Daisyworld}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/Daisyworld.lua|Daisyworld}} (sysdyn) | {{https://raw.githubusercontent.com/pedro-andrade-inpe/calibration/master/examples/daisy-calibration.lua|daisy-calibration}} (calibration)| MultipleRuns (calibration) |
-|8  | {{:cst-317:7-calibration.ppt|Calibration}} | [[https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PredatorPrey.lua|PredatorPrey]] (sysdyn) | | | {{:cst-317:exercise2.pdf|Exploring SIR Model}}|
+|8  | {{:cst-317:7-calibration.ppt|Calibration}} | {{https://raw.githubusercontent.com/gilbertocamara/sysdyn/master/lua/PredatorPrey.lua|PredatorPrey}} (sysdyn) | | | {{:cst-317:exercise2.pdf|Exploring SIR Model}}|
-|9 | {{:cst-317:8-cellular-automaton.ppt|Cellular Automata}}	              | [[https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Life.lua|Life]] (ca)         |      |Cell, CellularSpace, Neighborhood, Map, Random | |
+|9 | {{:cst-317:8-cellular-automaton.ppt|Cellular Automata}}	              | {{https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Life.lua|Life}} (ca)         |      |Cell, CellularSpace, Neighborhood, Map, Random | |
-|10| {{:cst-317:9-fire-in-the-forest.ppt|Fire in the Forest}}             | [[https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Fire.lua|Fire]] (ca) |      |             | {{:cst-317:exercise3.pdf|Fire in the Forest}}|
+|10| {{:cst-317:9-fire-in-the-forest.ppt|Fire in the Forest}}             | {{https://raw.githubusercontent.com/pedro-andrade-inpe/ca/master/lua/Fire.lua|Fire}} (ca) |      |             | {{:cst-317:exercise3.pdf|Fire in the Forest}}|
-|11| {{:cst-317:10-runoff.ppt|Runoff}} | [[https://raw.githubusercontent.com/TerraME/terrame/master/packages/terralib/examples/runoff.lua|Runoff]] (terralib) | | |
+|11| {{:cst-317:10-runoff.ppt|Runoff}} | {{https://raw.githubusercontent.com/TerraME/terrame/master/packages/terralib/examples/runoff.lua|Runoff}} (terralib) | | |
 |12| {{:cst-317:11-geospatial-data.ppt|Geospatial data}} | | | Project, Layer (terralib) | |
 |13| {{:cst-317:12-deforestation.ppt|Deforestation}}   | {{:cst-317:deforestation.zip|}}| | Trajectory | {{:cst-317:exercise4.pdf|Deforestation}}, {{:cst-317:exercise4.zip|database}}|
-|14| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/lecture-agent-based-modelling.ppt|Agent-Based Modelling}}   | | | Agent, Society, Group| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/exercise5.pdf|Butterfly Model}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/butterfly_paper.pdf|Butterfly Model Paper}}|
+|14| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/lecture-agent-based-modelling.ppt|Agent-Based Modelling}}   | | | Agent, Society, Group| {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/exercise5.pdf|Butterfly Model}}, {{http://www.dpi.inpe.br/gilberto/cursos/cst-317-2016/butterfly_paper.pdf|Butterfly Paper}}|
+|15| {{:cst-317:14-sugarscape.ppt|Sugarscape}}| | | |
+|16| {{:cst-317:15-predator-prey.ppt|Predator Prey}} | {{https://raw.githubusercontent.com/pedro-andrade-inpe/logo/master/lua/PredatorPrey.lua|PredatorPrey}}| | |
 ===== Additional Reading =====
@@ Line 41: / Line 44: @@
 ===== Papers for Final Projects =====
-The final project consists of an implementation and discussion of one of the following papers.
+The final project consists of an implementation and discussion of one of the models available
+[[http://www.easterbrook.ca/steve/2013/01/simple-climate-models-to-play-with-in-the-classroom/|here]]
+or 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/Crooks2016ConflictDiamonds.pdf|Pires, B. and Crooks, A.T. (2016), The Geography of Conflict Diamonds: The Case of Sierra Leone}} (see also the model in the {{https://www.openabm.org/model/4955/OpenABM site)}} |
-|  | {{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}}|
+| Diogo, Rolf e João | {{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.}}|
+| Cassia e Kelly| {{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}} |
-|  | {{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.|
+| Frederico e André | {{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.}}|
@@ Line 65: / Line 67: @@
 | | {{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)}}|
+| | Almeida, Rodolfo Maduro, and Elbert EN Macau. "Stochastic cellular automata model for wildland fire spread dynamics." Journal of Physics: Conference Series. Vol. 285. No. 1. IOP Publishing, 2011.|
+| | de Bakker MP, de Jong K, Schmitz O, Karssenberg D. Design and demonstration of a data model to integrate agent-based and field-based modelling. Environmental Modelling & Software. 2017 Mar 31;89:172-89.|
+| |[[https://en.wikipedia.org/wiki/Brian%27s_Brain|Brian's Brain]]  |
+| | Fisch, Robert, Janko Gravner, and David Griffeath. "Threshold-range scaling of excitable cellular automata." Statistics and Computing 1.1 (1991): 23-39. |
+| | Fisch, Robert. "Clustering in the one-dimensional three-color cyclic cellular automaton." The Annals of Probability (1992): 1528-1548. |
+| | [[https://qlfiles.net/the-ql-files/next-nearest-neighbors-cellular-automata/|Li, Wentian. "Complex patterns generated by next nearest neighbors cellular automata." Computers & Graphics 13.4 (1989): 531-537.]] |
+| | Chate, H. & Manneville, P. (1990). Criticality in cellular automata. Physica D (45), 122-135.|
+| | Li, W., Packard, N., & Langton, C. (1990). Transition Phenomena in Cellular Automata Rule Space. Physica D (45), 77-94. |
+| | [[https://en.wikipedia.org/wiki/Belousov–Zhabotinsky_reaction|Belousov–Zhabotinsky reaction]]|
+| | Colasanti, R. L., R. Hunt, and L. Watrud. "A simple cellular automaton model for high-level vegetation dynamics." Ecological Modelling 203.3 (2007): 363-374.|
+===== Papers for Final Projects: Secondary Choices =====
+You can also choose from the following papers if you did not find a suitable paper in the above list.
+|  | {{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/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.openabm.org/model/3163/version/2/view|S Bergin (2012). Torsten Hägerstrand’s Spatial Innovation Diffusion Model. Available in CoMSES Computational Model Library.}}|
+| Ricardo, Ana e Karina | {{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}}|
+|  | {{:env-model:classes:first2014:finalproject:jager-amblard-attitude-change.pdf|Jager, Wander, and Frédéric Amblard. "Uniformity, bipolarization and pluriformity captured as generic stylized behavior with an agent-based simulation model of attitude change." Computational & Mathematical Organization Theory 10.4 (2005): 295-303.}}|

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