gpaasi/ebola-uganda-outbreak-timeliness-cfr

Data and code for a systematic review and meta‐analysis of Ebola outbreak case‐fatality ratios in Uganda (2000–2023), examining how diagnostic and response delays affect mortality. # Uganda Ebola Outbreak Meta-Analysis (Review Paper) This repository contains all data extraction sheets, R scripts, and analytic outputs for the review paper: **"The impact of diagnostic delays and timeliness of response on Ebola disease outbreak-level case-fatality ratios in Uganda (2000–2023)."** --- ## Table of Contents 1. Project Overview 2. Repository Structure 3. Prerequisites 4. Data Extraction 5. Analysis & Reproducibility - R Script: meta_analysis.R - Generating Figures - Session Information 6. How to Cite 7. License 8. Zenodo Deposition 9. Contact Information --- ## Project Overview This project synthesizes data from seven laboratory-confirmed Ebola virus disease (EBOD) outbreaks in Uganda between 2000 and 2023. Using a rapid systematic review and meta-analysis, we quantify outbreak-level case-fatality ratios (CFRs) and investigate how diagnostic and response delays impact CFRs. Analyses were conducted in R (version 4.3.2) using the `metafor` package for meta-analysis and `ggplot2` for visualization. --- ## Repository Structure ``` / ├── README.md ├── LICENSE ├── CITATION.cff ├── requirements.txt ├── zenodo.json ├── data/ │ ├── data_extraction_with_guide.csv │ ├── data_extraction_example.csv ├── code/ │ ├── meta_analysis.R │ └── session_info.R └── figures/ ├── forest_plot_cfr.png ├── bubble_plot_delay_vs_cfr.png └── bubble_plot_onset_to_response.png ``` - **data/**: Contains the data extraction template (`data_extraction_with_guide.csv`) and a filled example file (`data_extraction_example.csv`) illustrating structure. - **code/**: - `meta_analysis.R`: Main R script performing meta-analysis, meta-regression, and saving figures. - `session_info.R`: Script capturing the R session environment for reproducibility. - **figures/**: Placeholder folder where generated figures (e.g., forest plots, bubble plots) will be saved. - **requirements.txt**: Lists R package dependencies required to run the analysis. - **CITATION.cff**: Citation metadat …