The plots show the correlation between inferred and true quantities. The three colors show different sample sizes used to infer variant frequency: 1000 daily, 10,000 daily, and 1000 daily grouped by week (7000 weekly). The left panels show the R advantage, the right panels the mean generation time (mgt). Top, middle, and bottom panels show inference for large, medium, and small variability in R0,H(t). The simulations are initialized with and . For the inference of the R advantage, we used a variant relative mean generation time of (also inferred by the model), while for the inference of relative mean generation time we used the following combinations: ; ; ; We used a greater R advantage when the mean generation time is unchanged or longer to ensure the emerging variant reaches a significant frequency over the 80 days time period considered. For each parameter combination, 10 replicate simulations were drawn with the same parameters, hence the same deterministic epidemiological dynamics, but with different random error on data (Poisson error on cases number and binomial error on frequencies).