Repo for publicly shareable code for the publication "Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts" (Ferretti & Wymant et al, Nature, 2023, https://www.nature.com/articles/s41586-023-06952-2).
The main analysis can be run by launching the script mock_configuration.R (replacing the configuration therein with the appropriate configuration) then launching RunMainAnalyses.R.
Running the secondary analyses for the paper (generate_statistics_for_paper_risk.R and plots_for_paper_risk.R) can be very slow due to the Maximum Likelihood analyses.
Data not included in this repo. See the original publication for details on data access.