Whooping cough has re-emerged in many places where it was previously eliminated, including California and the United Kingdom. Exactly why this happened isn’t clear, and it hasn’t happened everywhere. The re-emergence of previously eliminated “childhood” infections like whooping cough in places where vaccines are in wide use is one of the main motivations for this study. The goals of our studies are to develop the basic theory of the forecastability of re-emerging diseases like whooping cough and to create software for anticipating re-emergence before it occurs.