COVID-19 Vaccine Simulation

This is a simulation package written in Python 3 for understanding the upcoming vaccine adoption from the behavioural aspect. This is a agent-based modelling and incorporates game theoretical measures, longitudinal social network and local majority rules.

The work is published under a capstone project under Master of Complex System provided by Centre of Complex Systems, University of Sydney. This work is still work in progress with additional functions adding here soon. 😆

Getting Started

You may need the following Python libraries

• numpy
• networkx
• matplotlib

These libraries are the common external libraries. In case you need to install them, use

pip install numpy

pip install networkx

pip install matplotlib

Install

1. Install all required package as previous.
2. Fork this repository.
3. To start simulation, you will open the main.py file in the repository (See usage below). I recommend to open the command line first and open in there.

Once you have opened main.py, you will see the interface like this.

First use

4. At this point, the command prompt will ask you to input the parameters.

• Number of people (N)
• Simulation time (T)
• Adoption rate (α)
• Infection rate (β)
• Recovery rate (γ)
• Rate to resuscept (φ)
• Removal rate (δ)

5. After that you are in the main portal of the software. Input the command (case insensitive) to continue.

• LOOK - View contact network.
• MODE - Change mode settings.
• RUN/ START - Start the simulation.
• SETTING - Set simulation settings.
• OTHER SETTING - Set auxiliary simulation parameters.
• SUMMARY - Print the simulation parameters.
• QUIT/ Q - Quit the software.

Advanced Usage

python3 main.py [(N) (T) (α) (β) (γ) (φ) (δ)] ...\n\
  [-m]  <modes_config>] [-f (filename)] [-verbose | --v] [run]

Example usage:

py main.py 10 3 0.8 0.3 0.5 0.1 0.005

By adding 'run' at the end, the simulation will run automatically.

py main.py 10 3 0.8 0.3 0.5 0.1 0.005 run

If you did not use run at the end, you will arrive to the interface. The program will ask your command prompt (capitals does not matter).

• LOOK - View contact network.
• MODE - Change mode settings.
• RUN/ START - Start the simulation.
• SETTING - Set simulation settings.
• OTHER SETTING - Set auxiliary simulation parameters.
• SUMMARY - Print the simulation parameters.
• QUIT/ Q - Quit the software.

Mode

This simulation can be customised by setting different modes. You may set them via express mode or under MODE command. This simulation offers the following modes:

• 01 Living in city/rural
• 02 Travelled back from overseas
• 04 Bounded rationality of vaccine
• 05 Edit contact network
• 07 Age distribution
• 08 Gender distribution
• 10 Type of vaccine
• 11 Stop transmissability/ reduce severity
• 12 Cost of vaccine
• 13 Accessibility to vaccine
• 14 Side effects of vaccine
• 20 Intimacy game
• 21 Local majority rule
• 22 Stubbon to take vaccine
• 23 Stubbon to against vaccine
• 24 Contrary to social groups
• 31 Medication incorporated
• 43 Advanced immunity period settings
• 51 Erdos-Renyi topology
• 52 Scale free network
• 53 Small world topology
• 54 Lattice network

You should see the following:

The interface will ask you to input the modes you wish to change them.

• Input the ones you wish to add, separate them by space.
• If you want to remove a mode, use the command -dp and input the modes you wish to remove after this (separate modes by spaces). For example, 1 2 3 -dp 99 100 will create modes 1, 2 and 3 and removes modes 99 and 100.

After that you will enter setting the configuration of the modes, and they will ask you if you want to return to the main portal or the mode menu. When a mode is activated, you will see a X mark next to the mode selection.

Note: Not all modes have been equipped. You will not see anything if you tried to set up those.

Note: The removal function does not remove the relevant attributes, it may not behave as expected.

Contributing

Pull requests are welcome! 🚀🚀

For major changes, please open an issue first to discuss what you would like to change. Please make sure to update tests as appropriate.

License

This work is licensed under Creative Commons Attribution-ShareAlike 4.0 International.

Further Reading

• Idea of mode 20 comes from
  • Bhattacharyya, S., A. Vutha, and C. T. Bauch (2019). “The impact of rare but severe vaccine adverse events on behaviour-disease dynamics: a network model.” en. In: Scientific reports 9.1, p. 7164. issn: 2045-2322. url: http://search.proquest.com/docview/2231910970/.
• Local majority rule comes (modes 21 - 24) comes from
  • Galam, S. (2012). Sociophysics : A Physicist’s Modeling of Psycho-political Phenomena. en. 1st ed. Bibliographic Level Mode of Issuance: Monograph. Springer. isbn: 9781461420323.
  • Galam, S. and F. Jacobs (2007). “The role of inflexible minorities in the breaking of democratic opinion dynamics”. In: Physica A: Statistical Mechanics and its Applications 381, pp. 366–376.

Other references of this model are located in the capstone project report.