This repository has all code and data required to generate the results reported in Investigating methods for using genetic data to estimate the association between host factors and being an infection source with application to probing the association between HIV infection and tuberculosis transmission.
Files used to generate simulated TB-like outbreaks are located in the simulation folder. These files were written to be run on a computing cluster using the Slurm scheduler. Pre-processed results assessing odds ratio estimation pipeline performance reported in the manuscript are stored in the simulation results folder, and can be visualized using the available R code.
Code used to calculate the true odds ratios of interest using Monte Carlo simulation are available in the monte carlo folder.
Code used to summarise the characteristics of simulated TB-like outbreaks are located in the simulation summary folder
SNP Data and associated metadata used in the real data results portion of the manuscript are in the data folder. BEAST2 .xml files and maximum clade credibility trees are located in the BEAST2 folder. R code for the creation of clusters by SNP cutoff, as well as analysis and visualization of real data are located in the real data analysis folder.