rhea-dsouza1/infectious-disease-modelling

Stochastic (event-driven) epidemic model evaluating the impact of different vaccination coverage levels on canine rabies outbreak size in Tanzania # Stochastic Transmission Model of Canine Rabies Outbreaks A stochastic (event-driven) epidemic model evaluating the impact of different vaccination coverage levels on canine rabies outbreak size in Tanzania, originally developed as university coursework and cleaned up here to show the core model clearly. ## Background Canine rabies is close to 100% fatal once symptomatic, and dogs are the primary transmission route to humans in endemic regions — Tanzania included. Understanding how vaccination coverage affects outbreak dynamics has direct public health relevance for designing vaccination campaigns. ## Model **SEID(V)** compartmental structure: **S**usceptible → **E**xposed (infected, not yet infectious — rabies has a variable incubation period) → **I**nfectious → **D**ead, with an optional **V**accinated compartment. Parameters (birth/death rates, incubation rate, transmission rate, disease-induced death rate) were estimated from a real canine rabies contact-tracing and monthly case-report dataset from two Tanzanian districts (Ngorongoro and Serengeti), using: - Maximum likelihood estimation and Poisson regression (cross-validated against R's `glm()`) to estimate exponential growth rates from case report time series - Direct estimation from contact-tracing data for incubation/infectious period parameters - R0 (basic reproductive number) back-calculated from the fitted growth rate and estimated generation time ## Why stochastic, not just deterministic A deterministic model (a system of ODEs) always produces the same outbreak trajectory from the same starting conditions. Real outbreaks don't work that way — especially early on, when case numbers are low, random chance in whether any given infectious contact actually transmits the disease matters a great deal. The same starting conditions can lead to an outbreak fizzling out entirely, or to sustained spread, purely by chance. This project implements the **Gillespie algorithm** (the standard method for exact s …