Skip to content

Impact of non-pharmaceutical interventions on the spread of the Covid-19 pandemic

License

Notifications You must be signed in to change notification settings

rasigadelab/covid-npi

Repository files navigation

covid-npi

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.

medRXiv preprint manuscript

Requirements

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.

Usage

Scripts should be run individually in the following order:

Pre-treatment scripts

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

Analysis scripts

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

Flowchart of selection steps

  • Z1_flowchart.R

About

Impact of non-pharmaceutical interventions on the spread of the Covid-19 pandemic

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages