As a final check of the method, epidemics within a community of 2,000 households were simulated using an individual based stochastic model (see Appendix S1). I choose R G = 1.21 as inferred from an epidemic growth rate of r = 0.20 per day, and the other parameters as described above. The exponential rate of growth was then re-estimated directly from the simulated incidence timeseries to be r = 0.19 (Figure 4) , close to the predicted value of r = 0.20. This provides further support for the validity of this method, especially since no restrictions were placed on re-infection of households within this small simulated community.