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 metadata for the repository.
• zenodo.json: Metadata file for depositing the repository to Zenodo.
• LICENSE: Creative Commons Attribution 4.0 International License.
• README.md: This document.

Prerequisites

• R (version >= 4.3.2)
• RStudio (optional, recommended)
• Required R packages (specified in requirements.txt):
  • metafor (>= 3.0-2)
  • ggplot2 (>= 3.3.0)
  • dplyr (>= 1.0.0)
  • readr (>= 1.3.1)

To install packages, open R and run: ```r install.packages(c("metafor", "ggplot2", "dplyr", "readr"))

```

Data Extraction

1. Template: Use data/data_extraction_with_guide.csv. This CSV contains column headers and guide text for each field.
2. Example: data/data_extraction_example.csv shows a filled example for one outbreak (Gulu 2000).
3. Fill-in: Populate rows for each included study/outbreak. Each column is defined in the guide embedded in the template.

Analysis & Reproducibility

R Script: meta_analysis.R

The code/meta_analysis.R script performs all analyses:

1. Load Data: Reads data/data_extraction_with_guide.csv.
2. Data Cleaning: Filters outbreaks with complete data for CFR calculation and timeliness metrics.
3. CFR Calculation: Computes CFR as Deaths / Confirmed_Cases.
4. Transformation: Applies Freeman-Tukey double-arcsine transformation for meta-analysis.
5. Meta-Analysis:
   • Pooled CFR using a random-effects model.
   • Generates a forest plot (figures/forest_plot_cfr.png).
6. Meta-Regression:
   • Regression of transformed CFR on diagnostic delay (Days_FirstCase_to_SpecimenCollection).
   • Regression of transformed CFR on MoH response delay (Days_Onset_of_IndexCase_to_MoHResponse).
   • Saves bubble plots to figures/.

To run, set your working directory to the repository root and execute: r source("code/meta_analysis.R")

Generating Figures

The R script will save figures to the figures/ directory: - forest_plot_cfr.png - bubble_plot_delay_vs_cfr.png - bubble_plot_onset_to_response.png

Ensure the figures/ folder exists before running the script.

Session Information

Reproducibility is enhanced by capturing the R session details. The code/session_info.R script outputs the session info to session_info.txt. Run: r source("code/session_info.R") This file records package versions and R environment details.

How to Cite

Please use the following citation when referencing this repository:

Paasi, George; Okwware, Sam; Olupot-Olupot, Peter (2025). Ebola Outbreak Meta-Analysis Data and Code. Zenodo. https://doi.org/10.5281/zenodo.15537213

For software citation, refer to CITATION.cff.

License

This repository is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). See LICENSE for details.

Zenodo Deposition

Metadata for Zenodo is provided in zenodo.json. Once the repository is finalized: 1. Zip the repository or link directly to GitHub. 2. Submit to Zenodo using the zenodo.json metadata. 3. Ensure DOI: 10.5281/zenodo.15564078 is minted and matches.

Contact Information

For questions, issues, or contributions, please open an issue on the GitHub repository:

https://github.com/gpaasi