Completion of example model data chapter

So its been a while since my last blog post. On a personal note I have been busy with Christmas and my young daughter and we have also just moved house again - all of which have distracted me from doing the finishing touches to my PhD. I have also just applied for a NERC grant with cardiff University. That was a terrific amount of work in a short space of time, for which I am not going to know the outcome until June!

With all that going on, I'm surprised to have got so far with things.

To make a general update:

I have now completed my third data chapter - the big beast of a chapter that describes my entire model in detail and publishes the model outcomes, sensitivity analysis and validation with empirical data. What a feat! At every turn I felt like mistakes were arising and the model seemed to crash every time I tried to improve things and make output more ecologically realistic. But time waits for no-one and some sage advice form my supervisor has allowed me to close the door on the continually effort for improvement and concentrate on getting it done and moving on to the landscape analysis.

Some bits and pieces from this chapter:

1. territories and population size. females in red, males in blue.

population remains fairly stable, increasing slightly to fill the useable space and has some good stats for individuals inside and outside of the protected areas. agents are younger in the matrix than inside the protected area, have lower energy reserves and less fecundity.

2. Population stats, protected vs non-protected areas

I still have some issues with validation via the empirical data with the number and distribution of agents being captured by model camera traps not matching the empirical data. The fine and local scale movement of agents does not seem to be adequately captured by the model, but considering the landscape scale nature of the simulation and the scale of movements and number of individuals, then its not surprising to get some scaling issues. A higher resolution landscape and were individuals would allow for a bit more work to be done in this area, but this was not the focus of the piece of work so I'm not too worried. As long as the population level events are being captured, and match the empirical population data then I believe we can be happy with the outcome of the model so far.

Its not my intention to get a model that fully encapsulate the complexity of real individual jaguar movements, as this is going to be pretty much impossible. The need to reduce model complexity, but increase model realism is always going to be a battle. We just have to hope that we reduce model complexity in the right places that model outcomes are not adversely affected. 

The next, and last(!) chapter of my thesis will take a look at this by using the model to investigate connectivity and landscape utilisation in a population of jaguars in a far more fragmented area of Belize.  This should give me a better idea of the issues with the model and how these need to be addressed (if any exist).

For now, I'm pleased to have got this chapter done and happy to be moving onto the last phase of my PhD. The end is in sight!