sarpong-md/africa-diseases-surveillance.github.io

An R-Analysis tracking Mpox and Measles in Sub Saharan Africa. # Africa Disease Surveillance — Mpox & Measles A fully reproducible R project tracking **mpox** (monkeypox) and **measles** across African countries using publicly available WHO and Our World in Data sources. Includes a complete data pipeline (download → clean → visualize), six publication-ready figures, and a rendered HTML report available via GitHub Pages. --- ## Live Report > 📊 **View the full report** > *(Update the link above after enabling GitHub Pages — see Publishing below)* --- ## Project Structure ``` africa-disease-surveillance/ ├── R/ │ ├── 00_setup.R # Install packages and create directories │ ├── 01_download.R # Download raw CSVs from public sources │ ├── 02_clean.R # Filter to Africa, standardize column names │ ├── 03_visualize.R # Generate and save all 6 figures │ └── 04_run_all.R # Master script: runs 00 → 01 → 02 → 03 ├── data_clean/ # Africa-filtered CSVs (committed to git) ├── data_raw/ # Downloaded source files (gitignored — re-downloaded by script) ├── figures/ # Saved PNG figures (committed to git) ├── docs/ # Rendered HTML report (for GitHub Pages) ├── africa_surveillance_report.qmd # Full Quarto report with code explanations ├── africa_disease_surveillance.Rproj ├── .gitignore └── README.md ``` --- ## Quick Start **Prerequisites:** R ≥ 4.2, internet access. Quarto CLI only needed for re-rendering the report. ```r # 1. Open africa_disease_surveillance.Rproj in RStudio # (this sets the working directory to the project root) # 2. Run the complete pipeline source("R/04_run_all.R") # 3. (Optional) Re-render the HTML report quarto::quarto_render( "africa_surveillance_report.qmd", output_file = "index.html", quarto_args = c("--output-dir", "docs") ) ``` --- ## Data Sources | Dataset | Source | License | |---------|--------|---------| | Mpox confirmed cases & deaths (daily, by country) | Our World in Data / WHO GitHub | CC BY …