The various models for assessment of test, trace, isolation and quarantine (TTIQ) are contained in the external repository ttiq-simulation.
The script to reproduce the work from LGAs is contained in contact_matrices_australia/lgas.R. The work-from-home effect can be calculated using contact_matrices_australia/wfh.R. Maps can be drawn using contact_matrices_australia/mapping.R.
The script to produce the effects on transmission potential by area is in contact_matrices_australia/nt_aboriginal_communities.R
The transmission model and clinical pathways model are located in remote_communities_transmission_model and remote_communities_clinical_pathways_model respectively. Please see the separate READMEs for each model (located here and here) for more specific information on these models.
The COVASIM model used for the Schools substream is in schools_abm. Please see the readme in that repository for details on exactly how to run that model.
The quarantine model is contained in quarantine_abm. This agent based model is what is used to generate the breach events from the quarantine system to be seeded in the community.
The population level model is contained in population_abm_package3. This model takes outputs from the quarantine ABM, transforms them into an appropriate format (using create_arrivals_linelist.R) and seeds infections in the community.
The script to update estimates of infectiousness and susceptibility by age is in contact_matrices_australia/calibrate_settings.R
The software to extrapolate age-structured contact matrices based on demographic information is available ain the repo njtierney/conmat. This commit gives the version used in the final reports.