Spatially-explicit agent-based model of jaguar movement - Overview of model

So my first week back at work after maternity leave has been spent getting re-acquainted with my model and preparing to write the next chapter for my thesis. I've found several articles which use ABMs to look at the response of populations to some form of landscape change, and whilst these are different to mine in key aspects, they nonetheless provide me a good overview of how others have gone about doing similar work.

Some papers to mention:

• Parry et al (2007) Aphid population response to agricultural ;landscape change: A spatially-explicit, individual-based model. Ecological Modelling 199 451-463
• Wang & Grimm (2007) Home range dynamics and population regulation: An individual-based model of the common shrew Sorex araneus. Ecological Modelling 205 397-409
• Pitt et al (2003) An individual-based model of canid populations: modelling territoriality and social structure. Ecological Modelling 166 109-121

Grimm has been quite prolific in producing individual-based models in ecology and a great paper by Grimm (and plenty of others) outlines a standard procedure for describing these type of models, so I'll be sticking to this and following the seven elements they outline:

1. Purpose,
2. State Variables and Scales,
3. Process and Overview and Scheduling,
4. Design Concepts,
5. Initialisation,
6. Input, and
7. Submodels.

Parry et al (2007) start from the protocol but provide information flow diagrams that make it easy to follow the model steps and simplify model procedures, so I've incorporated three flow diagrams into the Grimm protocol, as you can see below:

 Fig 1. Overview of model process

 Fig 2. Overview of agent process

Fig 3. Overview of movement process of agents

Fig 3 is undoubtedly quite complicated and probably subject to some change, but the current version of my model follows these steps quite literally. And I have to say it was quite difficult getting a fairly simplified(!) version of the movement process. A flow diagram is definitely the best way of presenting this information in my thesis chapter and hopefully will ease attempts at future publications as I'm following Ecological Modelling formats.

Other people using ABMS for spatially explicit ecological modelling

I recently went to a talk by Lael Parrot who was visiting Southampton University for the week. Not a name I had heard of before but I'm quite surprised at this now considering she is involved in very similar work to me!

The most relevant paper I found from her was the one she talked about at the seminar she gave:

Anwar, S.M., Jeanneret, C.A., Parrot, L. & Marceau, D.J. (2007) Conceptualization and implementation of a multi agent model to simulate whale-wathcing tours in the St. Lawrence Estuary in Quebec, Canada. Environmental Modelling and Software 22 1775-1787.

Not only was this paper spatially explicit and employed agent-based modelling, but it was done using the Repast Simphony toolkit!! Finally, an ecological example of someone doing a peer-reviewed and published piece of research using Repast.

I've not yet management to dive into the paper in depth but some of the simulations Lael showed during her talk have me very impressed - linking the repast output with GIS data and creating some pretty good looking 3D models of the system. They also re-integrated the model output with the original GIS data to do some spatial analysis and statistics, so I wonder whether this might also be my best option... definitely something to look into in more detail.

Its a much bigger model than mine will be so I have no doubt that I'll be able to pick up some interesting tips from Lael and the paper. I'll report back with any useful bits of information.

Book

An interesting new book but Alison Heppenstall, Andrew Crooks, Linda See and Mike Batty
"Agent-Based Model of Geographical Systems"

as stated on Andrew Crooks' blog 'GIS and agent-based modelling':

[the book] brings together a comprehensive set of papers on the background, theory, technical issues and applications of agent-based modelling (ABM) within geographical systems. This collection of papers (see below) is an invaluable reference point for the experienced agent-based modeller as well those new to the area. Specific geographical issues such as handling scale and space are dealt with as well as practical advice from leading experts about designing and creating ABMs, handling complexity, visualising and validating model outputs. With contributions from many of the world’s leading research institutions (see map below), the latest applied research (micro and macro applications) from around the globe exemplify what can be achieved in geographical context.

This book is relevant to researchers, postgraduate and advanced undergraduate students, and professionals in the areas of quantitative geography, spatial analysis, spatial modelling, social simulation modelling and geographical information sciences.

Book Contents:

Part 1: Computational Modelling: Techniques for Simulating Geographical Systems

1. Perspectives on Agent-Based Models and Geographical Systems.
2. A Generic Framework for Computational Spatial Modelling.
3. A Review of Microsimulation and Hybrid Agent Based Approach.
4. Cellular Automata in Urban Spatial Modelling.
5. Introduction to Agent-Based Modelling.

Part 2: Principles and Concepts of Agent-Based Modelling.

6. Agent-Based Models - Because they're Worth it?
7. Agent-Based Modelling and Complexity.
8. Designing and Building an Agent-Based Model.
9. Modelling Human Behaviour in Agent-Based Models.
10. Calibration and Validation of Agent-Based Models of Land Cover Change.
11. Networks in Agent-Based Social Simulation.

Part 3: Methods, Techniques and Tools for the Design and Construction of Agent-Based Models: 

12. The Integration of Agent-Based Modelling and Geographical Information for Geospatial Simulation.
13. Space in Agent-Based Models.-
14. Large Scale Agent-Based Modelling: A Review and Guidelines for Model Scaling.
15. Uncertainty and Error.-
16. Agent-Based Extensions to a Spatial Microsimulation Model of Demographic Change.
17. Designing, Formulating, and Communicating Agent-Based Models.-
18. Agent Tools Techniques and Methods for Macro and Microscopic Simulation.

Part 4: Fine-Scale, Micro Applications of Agent-Based Models: 

19. Using Agent-Based Models to Simulate Crime.
20. Urban Geosimulation.
21. Applied Pedestrian Modelling.
22. Business Applications and Research Questions using Spatial Agent-Based Models.
23. Using Agent-Based Models for Education Planning. Is the UK Education System Agent Based?
24. Simulating Spatial Health Inequalities.
25. ABM of Residential Mobility, Housing Choice and Regeneration.-
26. Do Land Markets Matter? A Modelling Ontology and Experimental Design to Test the Effects of Land Markets for an Agent-Based Model of Ex-urban Residential Land-Use Change.
27. Exploring Coupled Housing and Land Market Interactions Through an Economic Agent-Based Model (CHALMS).

Part 5: Linking Agent-Based Models to Aggregate Applications Macro:

28. Exploring Urban Dynamics in Latin American Cities using an Agent-Based Simulation Approach.
29. An Agent-Based/Network Approach to Spatial Epidemics.
30. An Agent-Based Modelling Application of Shifting Cultivation.
31. Towards New Metrics for Urban Road Networks. Some Preliminary Evidence from Agent-Based Simulations.
32. A Logistic Based Cellular Automata Model for Continuous Urban Growth Simulation: A Case Study of the Gold Coast City, Australia.
33. Exploring Demographic and Lot Effects in an ABM/LUCC of Agriculture in the Brazilian Amazon.
34. Beyond Zipf: An Agent Based Understanding of City Size Distributions.
35. The Relationship of Dynamic Entropy Maximising and Agent Based Approaches in Urban Modelling.
36. Multi-Agent System Modelling for Urban Systems: The Series of SIMPOP Models.
37. Reflections and Conclusions: Geographical Models to Address Grand Challenges

Looks particularly interesting but I'll be waiting to hear a few more reviews before I take the plunge and buy it on impulse. Very interesting though....

VERY relevant paper from 2001

I just found an extremely relevant paper form 2001 where someone has actually implemented an agent-based model of panther movements to explore the feasibility of re-introducing panthers to a location in Northern Florida.

The paper doesn't explicitly acknowledge its agent-based modelling methodology, but it definitely uses ABMs to model panthers moving around a real landscape. There are many similarities to my work here. The exact methodology does differ but is essence they have panthers looking at neighbouring cells, choosing a location and moving to that location, based on habitat, prey resource, roads and human density, whilst simultaneously interacting with other panthers in the area.

This is THE paper to reference.

And I am one very happy camper! :)

Reference:
Cramer, P.C. & Portier, K.M. (2001) Modelling Florida panther movements in response to human attributes of the landscape and ecological settings. Ecological Modelling 140: 51-80
(available from ScienceDirect, or Mendeley).