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.....

Distance to urban areas in GIS

I've just finished the last updates to my GIS data for using in my ABM and I generated such a cool picture that I thought I would share:

This is a combination of the distance to the main urban areas and distance to tarmac roads. I removed all of the tracks and trails from my road file as this layer is supposed to represent a general cost layer where proximity to humans is detrimental to jaguars and they would rather be in the low cost areas to the far left and upper regions of the map.

Some things to remember where trying to generate these types of maps:
1. the euclidean distance method seems to be the most appropriate:

                 Spatial Analyst - Distance - Euclidean Distance

2. this method can be used on shape file data or on raster data making it a pretty flexible function
3. the output will only be generate for the exact extent of the data you are performing the function on. For instance, if you have polyline data, then the distance will extend only until the smallest rectangle that includes all the lines, and NOT the surrounding NoData areas. Therefore you need to do the distance function on a larger dataset and then clip it to the area you want if this is a problem.
4. In my case, this was not possible so I converted my polyline shape file (roads) to a raster first, then extended the extent to the area required by my model and then performed the distance function.
5. To get the map above, I combined distance maps for urban areas and roads.
6. My urban areas were actually polygons and the distance function worked just fine with this.
7. As I said earlier, I decided to remove the small roads and tracks from my roads dataset before calculating the distances as these do not impact negatively on the movement of my agents (jaguars).
8. Once I had the two datasets that were each of the correct size and extent, I simply added the layers together:

                  Spatial Analyst - Math - Plus

9. Adding the two layers together creates a new layer that matches the size of the smallest input raster, so I actually added together the roadProximity file (purely for the model area) together with the urbanProximity file for the whole of Belize. 

changing extent of GIS file

Another update to my GIS information:

For some reason some of the methods I've outlined in my earlier post (1/12/2011) don't necessarily work !

So, an update to extending the extent of a file is as follows:

This seems pretty impossible to do with shape file, be it a feature, polygon, polyline or point. This makes life more difficult than it needs to be (typical), so the only alternative at the moment is to

1. convert the shape file to a raster

2. Via spatial analyst toolbar (View - Toolbars - Spatial Analyst)

Options - Analysis Extent - same as Layer "TotalClip" (or whatever the file of the right size is, and this needs to be a shape file) - snap extent to 'total area' (this needs to be a raster file).

3. The above method seems to work most effectively at getting the extent of the file to the required area, so its good to ensure you have both a shape file and a raster of the required area.

4. Now all that needs to be done is to add the raster you want to extend to the raster of the required area. In my case this is adding 'finalRoads' to 'totalarea'.

         totalarea has a value of 1 for every cell within the layer as its only purpose is to show the extent of the area I want to use in my simulations.

        Spatial Analyst toolbar - Raster Calculator - [finalRoads] + [totalarea] - evaluate

5. A new temporary file is now created called Calculation and this needs to be made permanent:

       right click on Calculation - Data - Make Permanent - then go to appropriate folder and name the file (allRoads in my case) - save

6. This new permanent file does not get automatically added, so this needs to be manually added if required.

7. For some reason, some of the classes change slightly (all mine increased by 1). The raster can be reclassified from either the temporary Calculation file or the permanent new allRoads file. Reclassifying the Calculation file means that a permanent reclassified file gets created so you no longer need to make the Calculation file permanent.