A. Explanation of the data points used by EpiFusion; B. the key parameters of the EpiFusion particle filter.

Gamma, phi and psi are fit by MCMC, either as constant values over time or in epochs by either fixing or fitting change times and interval values. Beta must vary over time and can either be fit using (i) a random walk within the particle filter, (ii) linear splines within the particle filter, (iii) MCMC fitting in epochs by fixing or fitting change times and interval values, or (iv) MCMC fitting the parameters of a logistic function which defines beta over time; C. Other key terms in the EpiFusion particle filtering algorithm, in order of appearance in the text.