Neisseria gonorrhoeae Transmission Model

This repository contains an individual-based mathematical model of Neisseria gonorrhoeae transmission among Aboriginal and Torres Strait Islander peoples living in remote areas of Australia. The model is used to assess the impact of vaccination in controlling N. gonorrhoeae prevalence among this population.

Key Features

Programming Languages

• Python (currently version 3.11.5): Main model implementation.
• R: Model fitting.

Main Model Components

• N. gonorrhoeae infection dynamics: ng.py
• Vaccination dynamics: vaccination.py
• Demographics: generate_population.py and population_dynamics.py
• Sexual partnership dynamics: partners.py
  • Sexual behaviour data is based on the GOANNA Study.

Usage Instructions

Model Fitting

Use the R script driver_calibration.R to fit the model to the age and sex-specific prevalence reported in the STRIVE Study.

Running Vaccination Scenarios

1. Execute driver_vaccine_scenario.py to run vaccination scenarios.
2. Define vaccination scenarios in vax_example.py.

Data

The model parameterisation data is located in the data folder.

Contributors to this Modelling Project:

The code for this project was originally developed by Nicolas Rebuli (School of Population Health/Kirby Institute, UNSW Sydney) and later taken over and modified by Thilini Padeniya (Institute for Biomedicine and Glycomics, Griffith University).

Other Contributors:

• Ben Hui (Kirby Institute, UNSW Sydney)
• David Regan (Kirby Institute, UNSW Sydney)
• James Wood (School of Population Health, UNSW Sydney)
• Kate Seib (Institute for Biomedicine and Glycomics, Griffith University)