Performance of One- versus Two-Dose Oral Cholera Vaccine Campaigns in Response to Outbreaks S3 Text: Overview of Stochastic Models and Fit

Country-wide data from the 2008-2009 cholera epidemic in Zimbabwe came from the authors of Reyburn et al.4 Country-level data was used in this exercise due to the unavailability of adequate city-level data, as in the other illustrative examples. We fit this model with maximum-likelihood via iterated filtering (using the mif2 algorithm, an improved version of that described in Ionides et al5) starting at the first week of the data. We fit two parameters in this model, the transmission rate (β), and the duration of infectiousness (1/γ), and three initial conditions, the number of infectious (I(0)), exposed (E(0)), and susceptible (S(0)) individuals at the time the first case was observed. Other parameters were based on published literature or expert opinion. Parameter values are shown in Table S3-1.