https://github.com/FrancoisBlanquart/selection_variant
Tip revision: a242a18349393e2e98d353a879ef9e66e99f21c1 authored by François Blanquart on 13 December 2021, 07:50:23 UTC
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README.md
# Selection for infectivity profiles in slow and fast epidemics
This is the code and data used to investigate the selection for SARS-CoV-2 variants depending on their infectivity profile.
## Codes
### simulation_study_v3.R
Conducts the simulation study to verify inference.
### inference_UK_v3.R
Conducts the inference on UK data.
### get_clean_data.R
Cleans the data on cases number and frequency dynamics.
### functions_v3.R
Auxiliary functions.
### inference_functions.R
Functions needed for inference.
### conceptual_figures_v2.R
Draw conceptual figures of the paper.
### simulate_v2.cpp
Code doing the epidemiological simulations in cpp
### source_simulation_parameters.R
R code sourcing the parameters for simulations.
### spatial_correlation.R
Code cleaning the spatial frequency of Delta across EU countries.
### inference_results_v2.RData
Results of the inference method on Alpha and Delta variant data.
## Data sources
### cleaned_UK_cases.csv
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
### cleaned_UK_frequencies.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.
### cleaned_UK_frequencies_period2.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 17.
### delta_frequencies_EU.csv
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
### spatial_variation_EU.csv
Cleaned delta frequencies across EU countries at the time when the frequency passes 50%, used for inference.