[BorisVSchmid]

That indeed could be. We didn't test mixed models of transmission, but we took the first step here by testing all three models independently.

Xavier Didelot did some work on testing mixed models for two cities, 17th century Eyam and 19th century Cairo. He did have to further simplify the models though - there are some restrictions on how many floating parameters you can have while the models are trying to converge to the parameter set that results in the best match with the observations.

Epidemiological analysis of the Eyam plague outbreak of 1665–1666: http://rspb.royalsocietypublishing.org/content/283/1830/2016...

Model-based analysis of an outbreak of bubonic plague in Cairo in 1801: http://rsif.royalsocietypublishing.org/content/14/131/201701...