This repository contains the data and code needed to replicate the analyses in the manuscript "Population dynamics of HIV drug resistance among pre-treatment and treatment-experienced PLHIV during treatment scale-up in Uganda: a population-based longitudinal study". The raw data is located in the ./data directory and the ./scripts/run_all.sh shell script runs all of the analyses. All code was written by Michael A. Martin, PhD who can be reached at [email protected] with any questions about the code. Inquiries about the research itself can be directed Dr. M. Kate Grabowski, PhD at [email protected], who is corresponding author on the manuscript.
The analysis is all run in the R programming language with the following packages:
- tidyverse v.2.0.0
- cowplot v.1.1.1
- geepack v.1.3.9
- ggpattern v.1.0.1
- ggplo2 v.3.4.3
- ggrepel v.0.9.3
- haven v.2.5.3
- mtest v.0.9.40
- Readxl v.1.4.3
- sandwich v.3.0.2
- patchwork v. 1.1.3