tadema00/lassa-rci-nigeria

Project Repository: Lassa Fever RCI Nigeria (2012–2025) This repository hosts a production-grade, fully reproducible Python pipeline dedicated to calculating and modeling the Reporting Completeness Index (RCI) for Lassa fever surveillance in Nigeria across a 14-year timeline. # Lassa Fever Reporting Completeness — Nigeria 2012–2025 Reproducible analysis code for: > **A Mortality-Based Reporting Completeness Index for Lassa Fever Surveillance in Nigeria, 2012–2025** > > *Manuscript submitted to Epidemiology & Infection (Cambridge University Press)* --- ## Overview This repository contains the complete analysis pipeline that reproduces every quantitative result, figure, and supplementary table in the manuscript. Given the four input data files, running `scripts/run_pipeline.py` end-to-end regenerates every number in the paper. ### Key methodological contributions | Component | Description | |---|---| | **Reporting Completeness Index (RCI)** | Deaths-based back-calculation (Eq 1), extending Simons (2022) | | **Monte Carlo uncertainty** | N = 10,000 draws from truncated-normal CFR (Eq 3–4) | | **Five CFR scenarios** | 10%, 15%, 16.5% (reference), 20%, 25% | | **Non-parametric trend** | Mann–Kendall τ, Spearman ρ, Sen's slope + bootstrap CI | | **Change-point detection** | Binary segmentation, L2 cost, F-test α = 0.05 | | **Outlier detection** | Grubbs test + robust z-score (MAD-based) | | **Random Forest** | TimeSeriesSplit CV (primary); shuffled K-fold (upper bound) | | **State validation** | Edo and Ondo States, 2018–2025 | --- ## Repository Structure ``` lassa-rci-nigeria/ │ ├── README.md ├── LICENSE ├── requirements.txt ├── environment.yml │ |─── data/raw/ | |── ncdc_weekly.xlsx # Sourced from Emmanuel's Kaggle dataset (CC BY 4.0) | |── simons_annual.xlsx # Sourced from David Simons' GitHub (MIT) | |── LICENSE_NCDC.txt | ├── LICENSE_SIMONS.txt | |── edo_weekly.xlsx # Curated by author from NCDC reports (Public Domain/CC BY) | └── endo_weekly.xlsx # Curated by author from NCDC reports (Public Domain/CC BY) | ├── src/ # One module per analytical section │ ├── config.py # All constants, paths, CFR scenarios │ ├── data_cleaning.py …