Analysis code for Wastewater surveillance predicts Mpox outbreak dynamics in a resource-limited urban setting

Wastewater-Based Epidemiological Surveillance of Mpox Virus (MPXV) in Kampala Metropolitan Area, Uganda — February to September 2025

This repository contains the statistical analysis pipeline for a wastewater-based epidemiological (WBE) surveillance study of Mpox virus across four treatment facilities in the Kampala metropolitan area over 32 consecutive weeks (Epidemiological Weeks 6–37, 2025).

Study Overview

Objective: Evaluate whether MPXV genomic copies detected in wastewater (WW) correlate with and lead clinical mpox positivity rates in Kampala, Uganda, and quantify the early-warning potential of wastewater surveillance across four sites.

The code performs descriptive statistics, Shapiro–Wilk normality testing, Wilcoxon tests with Holm correction, Quenouille-adjusted effective sample size estimation, Spearman correlation, ±4-week lead–lag analysis with BH correction, Theil–Sen regression with bootstrap confidence intervals, and exploratory GEE modelling.

All figures and supplementary tables are generated programmatically to ensure full reproducibility.