Tracking and predicting the African COVID-19 pandemic

This code is a modification of the model and visualization found in "Pan-African evolution of within- and between-country COVID-19", Proceedings of the National Academy of Sciences (PNAS), July 13, 2021 118 (28) e2026664118, https://www.pnas.org/content/118/28/e2026664118. with GitHub code here.

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.