## What to do

### Task 1:

- Set the model parameters such that it corresponds to the following setting:
  - 1000 susceptible hosts and 1 infected host of type 1.
  - 200 susceptible hosts and 1 infected host of type 2.
  - Simulation duration approximately 5 years.
  - Assume that transmission from host 1 to 1 is 0.002, from host 2 to 2 is 0.01. No transmission from one host type to the other.
  - Assume that the duration of the infectious period is 1 month long for both types.
  - Assume nobody dies due to disease, and immunity does not wane.
  - No waning immunity or natural births/deaths.
- With parameters set to correspond to the scenario just described, run the simulation and ensure you get outbreaks in both populations with 20% susceptibles left at the end.

### Task 2:

- Set the transmission rate from host 1 to host 1 to 0.001. Rest as before. Run the simulation.
- Now set the transmission rate from host 2 to host 1 to 0.001. You should see an outbreak in both populations. This is an example of a core group driving the dynamics. Contemplate what the core group does.

### Task 3:

- Keep all settings as before, but set initial number of infected type 1 hosts to 0.
- Contemplate what you expect to see, run simulation, see if your expectations are confirmed.
- Now set initial number of infected type 1 hosts back to 1, infected type 2 hosts to 0.
- Contemplate what you expect to see, run simulation, see if your expectations are confirmed.

### Task 4:

- Set the transmission rate from host 1 to host 1 to 0. Same for the transmission rate between type 2 hosts.
- Set the transmission rate from host 2 to host 1 to 0.01, from host 1 to host 2 to 0.002. Those are the same values used on task 1 for transmission among the same hosts.
- Set number of initial infected of type 1 and 2 both to 1.
- Contemplate what you expect to see, run simulation, see if your expectations are confirmed.
- Now set the transmission rate from host 1 to host 2 to 0.01, from host 2 to host 1 to 0.002. Again, think about your expectations, run simulation and check.

### Task 5:

- Repeat the previous task, with only infected of type 1 initially present.
- Contemplate what you expect to see, run simulation, see if your expectations are confirmed.

### Task 6:

- Repeat the previous task, with only infected of type 2 initially present.
- Contemplate what you expect to see, run simulation, see if your expectations are confirmed.

### Task 7:

- Set everything as in task 1, but with waning immunity for both types at a rate 0.2.
- Run simulation, confirm that both populations reach a steady endemic state.
- Set transmission from type 2 to type 1 to 0.005, run simulation and see what changes.
- Set transmission from type 1 to type 2 to 0.005, other cross-transmission back to 0. Run simulation and see what changes.

### Task 8:

- With the settings you just had, turn off waning immunity for type 1, run simulation and see what you get.
- Turn waning immunity for type 1 back on and turn off for type 2, run simulation and see what you get.

### Task 9:

- Keep exploring. Think of a real ID where accounting for 2 types of hosts is important, see if you can use the simulation to approximate and explore that ID.