A practical generation interval-based approach to inferring the strength of epidemics from their speed

Sang Woo Park; David Champredon; Joshua S. Weitz; Jonathan Dushoff

The moment-matching method (approximating R based on estimated mean and variance of the generation interval) has an appealing simplicity, and works well for all of the actual disease parameters we tested (the breakdown for rabies distributions occurs for values of R well above observed values). We therefore wanted to compare its robustness given small sample sizes along with that of the more sophisticated maximum likelihood method. Fig. S3 shows results of this experiment. When sample size is limited, estimates using MLE tend to be substantially close to the known true values in these experiments. As we increase sample size, our estimates become narrower. We also find that using the gamma approximated speed-strength relationship gives narrower estimates than the two naive estimates even when the sample size is extremely small (n = 10). It is important to note that Fig. S3 only conveys uncertainty in the estimate of coefficient of variation of generation interval distributions. Estimation of mean generation interval will introduce additional uncertainty into estimates of the reproductive number. Relative length of generation interval (ρ)