sap00k/COVID19-ABM-Maputo

Agent based model of COVID 19 transmission and intervention scenarios in Maputo City, Mozambique. # COVID19 ABM Maputo This repository contains the code, model outputs and manuscript materials for an agent based model of COVID 19 transmission in Maputo City, Mozambique. ## Study objectives The model evaluates how population mobility, location closures and different levels of compliance could influence COVID 19 transmission and the number of reported active cases. ## Repository structure - `R/`: ordered scripts for data preparation, calibration, validation, final refitting and intervention scenarios - `data/`: input and processed data permitted for public distribution - `output/`: calibration, validation, final refit and scenario results - `manuscript/`: LaTeX manuscript, figures and tables - `docs/`: model and parameter documentation ## Reproducing the analysis Run the scripts in the following order: 1. `R/01_prepare_data.R` 2. `R/02_calibrate_validate.R` 3. `R/03_refit_all_data.R` The second script performs temporal calibration and validation. The third script refits the model using all available observations and generates the parameters used in the intervention scenarios. ## Software requirements The analysis was conducted in R. Package names and tested versions will be added after verification of the final project environment. ## Data availability Aggregated data and model outputs that can be distributed publicly are provided in this repository. Any restricted source data are described in the manuscript and are not redistributed here. ## Citation Citation information will be updated after publication of the manuscript and creation of the associated Zenodo record. ## License The code is distributed under the MIT License. Data and third party materials may be subject to separate terms.