Repast demo and tutorial

I have gotten to the point in the current version of my model where sending a both run of simulations of to IRIDIS the southampton uni supercomputer is becoming more and ore necessary. I'm struggling to get a run of 20 years in my simulation at the moment to check for stability of population and territories etc and its taking ages.
One run, depending on the number of agents and amount of reproduction (hence new agents), can take anywhere from half an hour to about 2 hours. I'm also having problems with memory where the simulation breakdown at that start of a new run due to being out of memory. Am currently trying to fix this problem.

Anyway, on my way to discovering if its possible to export a repast batch and pass it to IRIDIS I have come across a nice Repast demo that I wish had been around two years ago when I was starting to think about potential agent based simulation software and 18 months ago when i was struggling with my first attempts with repast.

Demo is based on a population of 'bugs' that move around and eat food from the landscape. Coincidentally amazingly relevant to my own model. I might try the demo and see if I can steal any ideas for better coding/construction of the model/GUI.

Demo can be found here: http://code.google.com/p/repast-demos/wiki/StupidModel
and an output of the GUI:

Biological principles underpinning Jaguar ABM

After some careful consideration of the need for a good biological foundation to my ABM, my supervisors and I agreed to implement some well-known population dynamics theory into key processes of the way the model and the agents undertake tasks.

Key factors: the jaguars - how they decide when and how often to move, and how they consume food across the landscape, and the food itself - food represents prey species and how will this respond to consumption?

Some sample prey species shown here, armadillo, coati, kinkajou, white-lipped peccary.

 


For my agents (jaguars), the key factor governing the way they move in the model is energy. Starting from an initial maximum energy state, they 'use-up' energy in a similar way to calorific expenditure in real animals. Moving and simply existing causes a steady loss of energy. Agents however need energy to survive and so must replenish this lost energy by consuming food. In this respect, low energy creates a greater need for the agent to change location to find an alternative, and potentially greater, food source. But of course real predators suffer a density-dependent relationship with prey and so based on some estimate of attack rate, a, handling time, b, and prey density, N, agents consume food based on the Holling Type 11 response:

Prey must then respond to being consumed, and are considered to regenerate according to a standard logistic growth function:

where, r is the intrinsic growth rate, K is carrying capacity and N is current prey density. For simplification, all prey species have been combined into a single food source and evenly distributed across the landscape, with K varying only with habitat type.

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.

Outline of Thesis (July 2012)

A recent meeting with my supervisors generated some good discussion about where my PhD is going and what I should be thinking about in terms of my final PhD thesis.
Having already been mandated to complete both a 6-month and a 10-month report, I feel like I have the bare bones of my thesis laid out already, with some chapters and details requiring further definition.

As of this week, my thesis already comprises a introductory chapter (literature review) and two data chapters. Im currently working on the third data chapter which I expect to finish in time for the upcoming transfer report and viva. With this in mind, and following clarification of what I hope to achieve by the end of my PhD, my thesis will be as follows:

1. Introductory chapter - to be completed. A short 5-8 page introduction to project and motivation/methods.
2. Literature Review - completed, but needs refining.
3. Exploring and Integrating Least-Cost Models and Agent-Based Simulations in Fragmented Landscapes - completed, but needs some refining to aid potential publication
4. An Agent-Based Model of Jaguar Movement Through Conservation Corridors - completed and published.
5. Integrating and Validating an Agent-Based Model of Jaguar Movements with real-life GIS and Camera-Trap Data Collected in Cockscomb Basin Wildlife Sanctuary, Belize - currently in progress
6. Analysis of real-world corridor designs based on an agent-based model of jaguar movements in Belize - next step, transferring validated jaguar model to corridor area in central belize.
7. An analysis of the potential future impacts of increased human activities and major environmental events on jaguar movements in Belize - last step given enough time (!), Potential impacts and factors are wide-ranging and will depend on discussions with Bart and Beccie and findings from previous work.
8. General Discussion - final section, generally quite short - 6-8 pages, covering limitations and implications of current work and section of future work (although this needs to be specific and achievable).

Chapters 3, 4, 5, 6 and 7 are data chapters. Chapter 7 is best-case scenario and I would like to get this far, but some of this may be combined into chapter 6 if there is not enough time for a stand-alone chapter.

Some sample pages from my thesis to date.....