Java class package for IBM (Individual-Based Modeling) of meta-populations in remote Indigenous communities.
This model has been utilized in various projects, including investigations into the impact of mobility on STI transmission, the dynamics of syphilis outbreaks, and the spread of COVID-19 in these communities.
As this model is no longer in active development, detailed documentation for the full usage of each simulation type is limited (and often unnecessary as it is largely replaced by later models). However, additional usage information is available upon request.
- Ben Hui ([email protected])
To run the model, the typical approach is to execute the main method from the Simulation_Remote_MetaPopulation class, using a command such as:
java sim.Simulation_Remote_MetaPopulation basedir other_arguments
where
- basedir: The working directory for the model, containing the required PROP file (simSpecificSim.prop)
- other_arguments: Additional simulation-specific arguments (if needed).
The simSpecificSim.prop is a XML file formatted according to the java.util.Properties class specifications. It uses methods such as loadFromXML(InputStream) and storeToXML(OutputStream, String, String) to define text-based settings for the model simulation.
Some general settings are described in the SimulationInterface class in the Package_BaseModel, while others are simulation-specific.
The behavior of the simulation depends on the settings in the simSpecificSim.prop file, specifically the value of the PROP_RMP_SIM_TYPE parameter:
- PROP_RMP_SIM_TYPE = 0: Simulates the transmission of gonorrhoea and chlamydia in remote Indigenous communities.
- PROP_RMP_SIM_TYPE = 1: Simulates the transmission of syphilis in remote Indigenous communities.
- PROP_RMP_SIM_TYPE = 2: Performs model optimisation using the Simplex method.
- PROP_RMP_SIM_TYPE = 3: Generates a population representing a remote community and stores the output as zip files.
- PROP_RMP_SIM_TYPE = 4: Performs model optimization using a genetic algorithm (GA).
- PROP_RMP_SIM_TYPE = 5: Simulates the transmission of COVID-19 in remote Indigenous communities.
Journal paper
- Hui BB, Ward JS, Guy R, Law MG, Gray RT, Regan DG. Impact of Testing Strategies to Combat a Major Syphilis Outbreak Among Australian Aboriginal and Torres Strait Islander Peoples: A Mathematical Modeling Study. Open Forum Infect Dis. 2022;9(5):ofac119.
- Hui BB, Brown D, Chisholm RH, Geard N, McVernon J, Regan DG. Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities. BMC Infect Dis. 2021;21(1):929.
- Hui BB, Ryder N, Su J-Y, Ward J, Chen MY, Donovan B, et al. Exploring the benefits of molecular testing for gonorrhoea antibiotic resistance surveillance in remote settings. PloS one. 2015;10(7):e0133202.
Report
- Hui B; Regan D; Gray R, 2019, Modelling of the infectious syphilis outbreak in Indigenous Australians: guidance for Multi-Jurisdictional Syphilis Outbreak Working Group. (https://www.kirby.unsw.edu.au/research/reports/modelling-infectious-syphilis-outbreak-indigenous-australians)
The project was funded to provide guidance to the Multi-Jurisdictional Syphilis Outbreak Working Group (MJSO) and the AHPPC Enhanced Response Governance Group (the Governance Group) to assist in the roll out of the national Enhanced Response and developing activity work plans in Aboriginal Community Controlled Health Services and other settings. The MJSO and Governance Group provided surveillance data and feedback on the modelling methods and characteristics of the scenarios implemented. The working group consists of the following members:
Governance Group:
Prof Brendan Murphy, Chief Medical Officer (CMO) for the Australian Government;
Ms Celia Street, First Assistant Secretary, Office of Health Protection (OHP), Department of Health (DoH);
Dr Nathan Ryder, Chair of Multi-jurisdictional Syphilis Outbreak (MJSO) Working Group;
Dr Dawn Casey, National Aboriginal Community Controlled Health Organisation (NACCHO);
Dr Russell Waddell, South Australia Department of Health;
Dr Sonja Bennett, Queensland Department of Health;
Dr Hugh Heggie, Northern Territory Department of Health;
Dr Paul Armstrong, Western Australia Department of Health;
Prof James Ward, University of Queensland
MJSO – represented organisations:
Australian Government Department of Health
National Aboriginal Community Controlled Health Organisation
Aboriginal Medical Services Alliance Northern Territory
Northern Territory Department of Health
Queensland Aboriginal and Islander Health Council
Queensland Department of Health
Cairns and Hinterland Health and Hospital Service (Qld)
Townsville Health and Hospital Service (Qld)
Aboriginal Health Council of Western Australia
Western Australia Department of Health
Pilbara Public Health Unit (WA)
Kimberley Public Health Unit (WA)
Aboriginal Health Council of South Australia
South Australia Health and Medical Research Institute
South Australia Department of Health
Kirby Institute, UNSW Sydney
Victorian Department of Health and Human Services
NSW Ministry of Health