This repository accompanies a manuscript investigating the genomic and epidemiological features of ciprofloxacin non-susceptible Salmonella Typhi in Blantyre, Malawi.
The "raw" data file is not made available due to potentially sensitive information. Therefore, a series of summary files have been generated for your convenience, and are stored in the data directory.
Therefore, you should be able to just clone the repo, change the working directory to the cloned repo, and run the pefloxacin_typhi_analysis_and_figures.Rmd script, which does the analyses and plots the figures.
If you just want to see the details of the code without running it, you can download the pefloxacin_typhi_analysis_and_figures.html file and view it in a browser.
pefloxacin_typhi_data_cleaning.Rmd is for taking the various raw data sources and producing two datasets for further analysis/plotting. These are saved in data directory
pefloxacin_typhi_functions.R has various helper functions to reduce the amount of code in pefloxacin_typhi_data_cleaning.Rmd and pefloxacin_typhi_analysis_and_figures.Rmd
pefloxacin_typhi_analysis_and_figures.Rmd is for running the association models and producing graphs, it reads in the data from data dir.