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CST-317: Introduction to Earth System Modelling (INPE Course 2016)

References

Classes

Title Models Scenarios Concepts Exercises
1 Introduction
2 Lua for TerraME Lua scripts nil, number, boolean, string, table, function Lua exercises
3 Systems Dynamics Tub (sysdyn) tub-scenarios (sysdyn) Model, Event, Timer, Chart Water in the Dam
4 Feedbacks Coffee, PopulationGrowth (sysdyn) coffee-scenarios, population-scenarios-1, population-scenarios-2 (sysdyn) Environment, instance of Model
5 Epidemics SIR (sysdyn) infection-scenarios-1, infection-scenarios-2, infection-scenarios-3 (sysdyn)
6 Predator-Prey PredatorPrey (sysdyn)
7 Daisyworld Daisyworld (sysdyn) daisy-calibration (calibration) MultipleRuns (calibration)
8 Calibration PredatorPrey (sysdyn) Exploring SIR Model
9 Cellular Automata Life (ca) Cell, CellularSpace, Neighborhood, Map, Random
10 Fire in the Forest Fire (ca) Fire in the Forest
11 Runoff Runoff (terralib)
12 Geospatial data Project, Layer (terralib)
13 Deforestation deforestation.zip Trajectory Deforestation, database
14 Agent-Based Modelling Agent, Society, Group Butterfly Model, Butterfly Paper
15 Sugarscape
16 Predator Prey PredatorPrey

Additional Reading

Papers for Final Projects

The final project consists of an implementation and discussion of one of the models available here or the following papers.

Pires, B. and Crooks, A.T. (2016), The Geography of Conflict Diamonds: The Case of Sierra Leone (see also the model in the OpenABM site)
Diogo, Rolf e João 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
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
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
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
Cassia e Kelly 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.
H. Nakanishi (1990) Cellular-automaton model of earthquakes with deterministic dynamics. Phys. Rev. A 41:7086–7089
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
Barros, J. Urban Growth in Latin American Cities. PhD thesis, CASA/UCL
Frederico e André Sex, Culture and Conflict in SugarScape. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.
Trade in SugarScape. From J Epstein, R. Axtell, Growing Artificial Societies: Social Science from the Bottom Up. MIT Press, 1996.
S Heckbert (2013). MayaSim: An agent-based model of the ancient Maya social-ecological system. Available in CoMSES Computational Model Library.
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.
J Pepper and B Smuts (2000). The evolution of cooperation in an ecological context: an agent-based model. Replicated in CoMSES Computational Model Library.
K Kahn (2013) A model of the Spanish Flu Pandemic. Available in CoMSES Computational Model Library.
Schindler J (2012) A simple Multi-Agent System of the Tragedy Of the Commons. Available in CoMSES Computational Model Library.
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.
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).
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.
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
S. Hoya White, A. Martín del Rey, G. Rodríguez Sánchez(2007), Modeling epidemics using cellular automata. Applied Mathematics and Computation, 186(1):193-202
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.
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.
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.
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.
Scherer A. & McLean A., (2002) Mathematical models of vaccination, British Medical Bulletin 2002;62 187-199.

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.

H. Balzter, P. W. Braun, W. Köhler (1998) Cellular automata models for vegetation dynamics. Ecological Modelling 107(2-3):113-125
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.
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
S Bergin (2012). Torsten Hägerstrand’s Spatial Innovation Diffusion Model. Available in CoMSES Computational Model Library.
Ricardo, Ana e Karina D. L. Dunkerley (1997) Banded vegetation: development under uniform rainfall from a simple cellular automaton model. Plant Ecology 129(2):103-111
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
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.