Verrah/HIV-TB-Kenya-Spatiotemporal

Data, code, and codebook for: Bayesian joint spatiotemporal modelling of HIV and TB in Kenya (PLOS ONE 2020) # Bayesian Joint Spatio-Temporal Modelling of HIV and TB in Kenya (2012–2017) ## Publication This repository contains the data, code, and documentation supporting: > Otiende, V.A., Achia, T.N., & Mwambi, H.G. (2020). **Bayesian hierarchical modeling of joint spatiotemporal risk patterns for Human Immunodeficiency Virus (HIV) and Tuberculosis (TB) in Kenya.** *PLOS ONE*, 15(7), e0234456. doi.org ## Repository Contents | File | Description | |---|---| | `pone_0234456_s005.csv` | HIV new diagnoses and projected populations by county, 2012–2017 | | `pone_0234456_s004.csv` | TB new notifications and projected populations by county, 2012–2017 | | `pone_0234456_s001.R` | Original R analysis script | | `HIV_TB_Kenya_Analysis.Rmd` | Cleaned and fully documented R Markdown analysis script | | `HIV_TB_Kenya_Codebook.pdf` | Codebook in ACM journal style (PDF) — all variables, derived measures, and model indices | | `HIV_TB_Kenya_Codebook.tex` | LaTeX source file for the codebook | ## How to Reproduce the Analysis ### Prerequisites Install R (≥ 4.0) and the following packages: ```r install.packages(c( "sp", "sf", "rgdal", "spdep", "maptools", "spacetime", "maps", "mapdata", "RColorBrewer", "lattice", "latticeExtra", "gridExtra", "grid", "car", "epitools", "DCluster", "plotrix", "knitr" )) # INLA requires a separate installation: install.packages("INLA", repos = c(getOption("repos"), INLA = "inla.r-inla-download.org"), dep = TRUE) ``` ### Steps 1. Clone this repository: ```bash git clone github.com ``` 2. Open `HIV_TB_Kenya_Analysis.Rmd` in RStudio and click **Knit** > **Note:** The INLA model chunk is cached. First run will take approximately 20–40 minutes. ## Data Sources - **HIV/TB case counts:** Kenya Ministry of Health, National Disease Surveillance Programme - **Population projections:** Kenya National Bureau of Statistics (KNBS). www.knbs.or.ke ## …