All non-genomic analyses can be replicated in R using the "XDR_Typhoid_Analysis.Rmd" markdown file and data from the "Air Travel Data" and "Country Data" folders.
S. typhi genomes from the Wong et al. and Carey et al. papers can be downloaded from the Pathogenwatch repository.
Our phylogeographic analysis can be replicated in BEAST using the xml files in the "XML" folder.
Log files containing BEAST glm estimates for the effect of air travel volume and shared country borders on the rate of H58 lineage movement are given in the "LogOutput" folder. These files can be analyzed using Tracer.