HIV-transmission-PoissonProcess

Code for Inferring HIV Transmission Patterns from Viral Deep-Sequence Data via Latent Spatial Poisson Processes

List of scripts:

• main.py: the main file to run for real data analysis (Case Study section in paper)
• utilsHupdate.py: all utility functions (imported by main.py)
• utilsHupdatePrev.py: utility functions used for simulation code (in server_main_simulations.py)
• server_main_simulations.py: simulation code (run on a Slurm-system server)
• process_simulations.py: code for post-processing simulation experiment results
• real-data-plots.R: code for making various real data plots (used for Data and Case Study sections in paper)
• process-simulations.R: R code for post-processing simulation results and making plots

An anonymized real data table is included in Rakai_data_processed.csv.

To run the code, you may first install Anaconda and then install all the dependencies by running

conda env create --file dependencies.yml