Dunsin11/kagera-cholera-sitrep

End-to-end public health data analysis pipeline in R. Covers linelist cleaning, deduplication, epidemic curve generation, attack rates per 1,000 population, case fatality rates, and age-sex stratification across five districts in Kagera Region, Tanzania. # Kagera Cholera Project ## Overview This project presents an epidemiological analysis of a cholera outbreak in the Kagera region. Using R, this analysis investigates case distribution, mortality, and disease burden across districts to support evidence-based public health response and decision-making. ## Author **Dunsin Adetuberu** | Epidemiologist ## Objectives - Investigate the distribution of cholera cases across Kagera districts - Calculate Case Fatality Rate (CFR) overall and by district - Identify high-burden areas to guide targeted interventions - Generate a reproducible epidemiological report ## Data Source - District Health Information System 2 (DHIS2) ## Methods & Tools | Tool | Purpose | |---|---| | R | Data analysis and statistical computing | | tidyverse | Data cleaning and manipulation | | dplyr | Data wrangling and aggregation | | lubridate | Date handling | | readr | Data import | | Quarto | Reproducible report generation | ## Key Analyses - Data cleaning and standardisation - Descriptive epidemiology (cases by district, age, sex) - Case Fatality Rate (CFR) calculation overall and stratified by district - Epidemic curve generation - District-level summary statistics ## Key Findings - A total of **542 cholera cases** were recorded across Kagera districts - **20 deaths** were recorded giving an overall CFR of **4%** - District-level analysis revealed variation in disease burden and mortality across the region ## Repository Structure ``` Kagera-Cholera-Project/ ├── Kagera Cholera Project.qmd # Main analysis script (Quarto) ├── kagera_cholera_linelist.csv # Dataset ├── Kagera Cholera Project.Rproj # RStudio project file └── README.md ``` ## How to Run 1. Clone this repository 2. Open `Kagera Cholera Project.Rproj` in RStudio 3. Install required packages: ```r install.packages(c("tidyverse", "lubridate", "readr")) ``` 4. Open and render `Kagera Cholera Project.qmd` ## Contact For questions or collaboration, reach out via GitHub: @Dunsin11