. ReMASTER parameters for outbreak simulations for the Scenario Testing section.

The ‘Main Scenarios’ include the Baseline, Sampling and Transmission. Here constant rates were used for each reaction. In the ‘sampling’ scenario, the rate of sampling was increased 10-fold on day 35. In the transmission scenario, the rate of transmission was increased 3-fold on day 100. For the noise scenarios, either transmission or sampling rates were changed at regular intervals (intervals drawn from a Poisson distribution with rate 6 for the transmission noise, and every 7 days for the observation noise). We added increased noise by drawing interval rate values from distributions with increasing standard deviations. (XLSX)