abidv/DTTC-SACEMA-South-Africa-TB-model

Transmission dynamic model of tuberculosis in South Africa ## DTTC-SACEMA South Africa Tuberculosis Model This repository provides the R code for a deterministic, compartmental transmission-dynamic model of the tuberculosis (TB) epidemic in South Africa. The model was developed through a collaboration between the Desmond Tutu TB Centre (DTTC) and the South African Centre for Epidemiological Modelling and Analysis (SACEMA), and builds on an earlier version developed between 2017 and 2020. The model structure and underlying assumptions are described in detail in the accompanying publication. In brief, the model incorporates established TB transmission dynamics alongside additional features to represent transitions and losses along the TB care cascade. It distinguishes between subclinical and clinical TB disease states and further differentiates individuals based on their care-seeking status. HIV infection, disease progression, and antiretroviral therapy are also explicitly modelled. ## Related publication **Impact of prolonged tuberculosis healthcare service disruptions following the COVID-19 pandemic in South Africa – a mathematical modelling study*** Authors: Abigail K. de Villiers, Sue-Ann Meehan, Muhammad Osman, Rory Dunbar, James A. Seddon, Cari van Schalkwyk, Gerald J. Maarman, Karen Du Preez, Anneke C. Hesseling, Florian M. Marx, for the DTTC-SACEMA TB Modelling Group ## License Impact of prolonged tuberculosis healthcare service disruptions following the COVID-19 pandemic in South Africa – a mathematical modelling study © 2025 by Abigail K. de Villiers, Florian M. Marx is licensed under CC BY-NC-SA 4.0. Unless otherwise noted, all content associated with this work is licensed under CC BY-NC-SA 4.0. To view a copy of this license, visit [Creative Commons BY-NC-SA 4.0. ## Directory structure ``` . ├── code ├── makefile ├── INPUTS ├── OUTPUTS ``` - *code* : model R code - *makefile* : (optional) script to run the model using the makefile system - *INPUTS* : excel sheet containing all input data - *OUTPUTS* …