Thick red lines are R t1 t0 (d) estimated from observed data, thin red lines mark the 95% confidence interval, dashed cyan lines mark the 95% significance intervals, and distributions of R t1 t0 (d) estimated from simulated epidemics are shown in shaded gray. doi:10.1371/journal.pcbi.1003587.g005 from the ''full'' estimation, cf. solid gray line in Figures 3D, H) , and estimating only a, b 0 , and e.