Fig. 3: Joint estimation of the basic reproduction number (R0) and the timing of the index case (t0) using simulated data, and comparison against PhyDyn.
From: Epidemiological inference for emerging viruses using segregating sites
a The log-likelihood surface based on the segregating site trajectory shown in Fig. 2b is shown over a range of R0 and t0 parameter combinations. The log-likelihood value shown in each cell is the mean log-likelihood value calculated from 20 SMC simulations. Blank cells yielded mean log-likelihood values of negative infinity. The red boundary shows the set of (R0, t0) values that fall within the 95% confidence region. Parameter combinations within the red boundary have mean log-likelihood values that fall within 2.996 units of the highest mean log-likelihood value, based on a chi-squared distribution with 2 degrees of freedom. b Joint density plot for R0 and the time of the most recent common ancestor (tMRCA), as estimated using PhyDyn6 on the same set of 500 sampled sequences. Dashed red line in the joint density plot shows the 95% HPD interval of the joint density.
