Figure 5.

Fitting the simple SEIR model with Poisson error structure (<method1>=1 and <dist1>=1) to the early phase of the fall wave of the 1918 influenza pandemic in San Francisco. The upper panel provides the empirical distributions of model parameters along with their 95% CIs that correspond with the model fit shown in the bottom panel. Overall, the model provides a good fit to data. However, the 95% prediction interval only covers about 65% of the data points. The transmission rate parameter was estimated at 0.77 (95% CI: 0.75, 0.79). The solid red line is the median model fit. The gray lines correspond to the model fits obtained from 300 bootstrap realizations. In contrast, the cyan lines indicate the predictive uncertainty around the model fit, which are used to derive the 95% prediction intervals (dashed lines), with Poisson error structure.