What to do
Task 1:
- Run the simulation with a population size of 1000, 1 initially infected host, simulation duration 100 days, recovery rate gamma=0.5 per day, and infectiousness beta=0.001. You will get an outbreak of some - currently unspecified - infectious disease.
- Record the number and fraction of susceptible/infected/recovered remaining at the end of the outbreak.
- From the graph, get a (rough) estimate of the day at which the outbreak peaks.
- Contemplate the fact that the outbreak ends even though there are still a good number of susceptible remaining, i.e. not everyone got infected.
- Run the simulation again, with the same values you just had. Does anything change? Why (not)?
Task 2:
- Double the value of the transmission rate, beta. Leave everything else the same.
- What do you expect to get for the number/fraction of S/I/R at the end of the outbreak and the time at which the outbreak peaks?
- Run the simulation with the doubled transmission rate, record the same values (final S/I/R and outbreak peak) as above.
- Compare your expectations with the results. How do they agree/disagree? Does it make sense? Anything surprising happening?
Task 3:
- Now, double the rate of recovery (gamma), leave everything as in #2.
- How do you expect the results to change? (Try to make your prediction as precise/quantitative as you can)
- Run the simulation with these new parameter settings, record the same values as above.
- Compare your expectations with the results. How do they agree/disagree? Does it make sense? Anything surprising happening?
Task 4:
- Now, double the number of susceptibles (i.e. the population size), leave everything as in #3.
- How do you expect the results to change?
- Run the simulation with these new parameter settings, record the same values as above.
- Compare your expectations with what results. How do they agree/disagree? Does it make sense? Anything surprising happening?
Task 5:
- Keep playing around with changing any of the parameters and starting conditions.
- Every time, think about what you expect to get, then run the simulation, compare your expectations with the results. Then make sense of it.
- What is the minimum and maximum number of outbreaks you can get? Why is that?