Phylogenetic and epidemiologic data relating to age-specific HIV incidence and transmission in Rakai, Uganda, 2003-2018.

This repository contains the data for the analyses presented in the paper Growing gender inequity in HIV infection in Africa: sources and policy implications by M. Monod, A. Brizzi, R. Galiwango, R. Ssekubugu, Y. Chen, X. Xi et al. available in the pre-print https://doi.org/10.1101/2023.03.16.23287351 

We thank all contributors, program staff and participants to the Rakai Community Cohort Study; all members of the PANGEA-HIV consortium, the Rakai Health Sciences Program, and CDC Uganda for comments on an earlier version of the manuscript.

We also extend our gratitude to the Imperial College Research Computing Service and the Biomedical Research Computing Cluster at the University of Oxford for providing the computational resources to perform this study. Additionally, we thank the Office of Cyberinfrastructure and Computational Biology at the National Institute for Allergy and Infectious Diseases for data management support; and Zulip for sponsoring team communications through the Zulip Cloud Standard chat app. 

All analysis code is available from https://github.com/MLGlobalHealth/phyloSI-RakaiAgeGender.