Analysis code for:
A viral perspective on worldwide non-pharmaceutical interventions against COVID-19
Jean-Philippe Rasigade, Anaïs Barray, Julie Teresa Shapiro, Charlène Coquisart, Yoann Vigouroux, Antonin Bal, Grégory Destras, Philippe Vanhems, Bruno Lina, Laurence Josset, Thierry Wirth.
R software (tested on Windows 10 with v3.6.1).
Packages
- ape
- data.table
- lubridate
- survival
- coxme
- stringr
- beeswarm
- plotrix
- wordcloud
A workstation with at least 24 CPU cores is recommended to run scripts involving mixed-effect models. Use the special flag rebuild = FALSE to bypass these computations.
Scripts should be run individually in the following order:
These scripts perform alignment operations, especially between country identifiers; and extraction of branch length data.
- S1_dataprep_countries.R
- S2_dataprep_tree.R
- S3_dataprep_branch_lengths.R
- S4_dataprep_npis.R
These scripts generate the results and figures of the study.
- A1_descriptive_stats_by_country.R
- A2_branch_length_distribution.R
- A3_divergence_rates_per_country.R
- A4_npi_timing.R
- A5_npi_univariate.R
- A6_npi_multivariate.R
- A7_SIR_models.R
- Z1_flowchart.R
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