This is the code and data used to investigate the selection for SARS-CoV-2 variants depending on their infectivity profile.
Conducts the simulation study to verify inference.
Conducts the inference on UK data.
Cleans the data on cases number and frequency dynamics.
Auxiliary functions.
Functions needed for inference.
Draw conceptual figures of the paper.
Code doing the epidemiological simulations in cpp
R code sourcing the parameters for simulations.
Code cleaning the spatial frequency of Delta across EU countries.
Results of the inference method on Alpha and Delta variant data.
Clean UK cases used for inference. These data are available from https://api.coronavirus.data.gov.uk/v2/data?areaType=region&metric=newCasesBySpecimenDate&format=csv
Clean UK SGTF frequencies used for inference. These data are available from https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201 Data underlying technical briefing 9.
Clean UK SGTF frequencies used for inference. These data are available from https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201 Data underlying technical briefing 17.
Delta frequencies across EU countries and across dates. These data are available from the ECDC website at https://www.ecdc.europa.eu/en/publications-data/data-virus-variants-covid-19-eueea
Cleaned delta frequencies across EU countries at the time when the frequency passes 50%, used for inference.