Thanks, I was not aware of the SIR model. Regarding your original question... if you can identify individual regions where the model can be applied, maybe you

Thanks, I was not aware of the SIR model. Regarding your original question... if you can identify individual regions where the model can be applied, maybe you could use Markov chains to model the transitions between states in each region. I am not qualified enough to do that, but I imagine that the result would be a few endemic nodes where the disease is always present (with different degrees of intensity over time) and from where outbreaks get sporadically "exported" to disease free nodes.