Figure 7.

Fitting the simple SEIR model with a negative binomial error structure (<method1>=3 and <dist1>=3) to the early phase of the fall wave of the 1918 influenza pandemic in San Francisco (17-day calibration period). 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. The model is well calibrated to the data with the resulting 95% prediction interval covering 94.1% of the data points. The transmission rate parameter was estimated at 0.77 (95% CI: 0.74, 0.80). The solid red line is the median model fit. The gray lines correspond to the model fits associated with the 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).