Not sure about individual-scale models, but Markov Chains are common in Mathematical Ecology. You can do quite a lot in animal group modeling with transition matrices and basic probability theory. This is a good book if you can get it cheap (like most monograph textbooks): http://www.amazon.com/Introduction-Stochastic-Processes-Biol...

Also, props to submission author Victor Powell. Those force-directed graphs are visually interesting, add to the article, and are even responsive (try changing the window size).