Schiff-Lab/COVID19-HHH4-Africa

# Tracking and predicting the African COVID-19 pandemic ### Please Note: You are at the page that discusses the code required to reproduce the findings in the published paper "Pan-African evolution of within- and between-country COVID-19", *Proceedings of the National Academy of Sciences* (PNAS), July 13, 2021 118 (28) e2026664118, pnas.org. If you are interested in current daily data predictions, please use the 'daily' branch of this GitHub site at Updated Daily Code, or the updated daily Shiny App. This code was tested with R version 3.6.3 on Ubuntu 18.04 LTS and Windows and version 4.0.2 on Mac OS A visualization of the model inputs and published results can be found at our R-shiny server Set the working directory to the one with these source files, and run these files: - `01_data-processing-model.R`: cleans and processes the input data in `data/original` and gets it ready for modelling. The output of this script goes into the `data/processed` folder. - `01_data-processing-plot.R`: cleans and processes the input data in `data/original` and gets it ready for plotting. The output of this script goes into the `data/processed` folder. - `02_modelfitting.R`: uses the processed data to fit the models and saves them in `output/models/`. Summary tables are also produced and saved in `output/tables`. - `03_figures-model.R`: uses fitted model to create figures in the `figs` folder. - `03_figures_aux.R`: use processed data and fitted model to create other figures in the `figs` folder. The `R` folder contains the `functions.R` file that has a set of costum functions needed to run the code.