All the metadata used in this study are available in the metadata subdirectory.
Two main scripts were produced:
- script_epidemio_Africa.R : this short script allows to visualize the number of SARS-CoV-2 positive cases and related deaths in 2020 and 2021 in Africa and Senegal. We also calculate the proportion of observations in Senegal at the African scale.
- script_Senegal.R : this script allows to reproduce all of the figures that were created for this work. It covers the proportion of lineages over time and cities of Senegal, as well as the frequency of mutations for each gene and/or for each lineage.
These scripts can be downloaded and executed in R.
submitted