Tutorial. Setting simulation parameters.

Transmission, recovery, sampling rates.

In the file .rt we need to set transmission, recovery (getting uninfectious), sampling and mutation rates. First, let’s choose to measure time in days.

Assume that a patient becomes uninfectious within 10 days on average. Remember, that sampling an individual also means that this person becomes uninfectious. So, the sum of recovery and sampling rates is 1/10=0.1.

If 1 in 100 cases are sampled, then the recovery rate to sampling rate ratio is 99:1. Hence, recovery rate is 0.099 and sampling rate is 0.001.

Now, if in the absence of immune individuals in the population (e.g., in the beginning of the pandemic) an infectious person transmits the disease to 2.5 individuals on average, the birth rate is 2.5*0.1=0.25.

Migration matrix.

Assume that there are 10 populations, and that an average individual from the first population spends on average 10 days per year outside of its population of origin. The chance to travel to any destination is the same. Then the migration probability to travel to a particular destination is