This repository contains all the scripts that were developped to produce the work "Scripts used for the study "Phylodynamics of SARS-CoV-2 in France, Europe and the world in 2020". You can contact the authors if you need some helps to use the scripts for your own projects.
Large metadata can be shared on demand. In the Data/ subdirectory, you will find the epidemiological data (i.e., the daily and weekly number of SARS-CoV-2-related deaths) per country and French administrative regions .

All the scripts to generate the datasets can be found in the subdirectory Dataset_generation.

All the scripts from identifying exchange events to plots can be found in the subdirectory Phylodynamics.

To use these scripts, you need the following programs:

- R version 4.0.4
- List of R packages: adephylo, tidyverse, lubridate, glue, ape, phytools, tidytree, ggplot2, treeio, data.table, dplyr, ggtree, zoo, ggpubr

If you use or adapt some scripts for your own work, please cite:

In preparation.