The scripts pre and post are self-explanatory for time varying parameters. When fitting models with time varying infectivity parameters we actually fit I post and the ratio m = I pre /I post we called infectivity factor. This is a within species ratio, a parameter directly fitted by the models, unlike the between species infectivity ratio additionally calculated as explained later in the text (see Parameter estimates section). Note that all models above treat the epidemic as fully observed, i.e. infection times are assumed to be known (when in fact only estimated infection times are known -see Sensitivity Analysis section), and only IPs are assumed to be infectious.