AlinaRosalbe/SCIRS-Meningitis-Model-Africa

This project implements an age-structured SCIRS model for meningococcal meningitis in Africa, combining deterministic and stochastic approaches to capture both average epidemic trends and outbreak variability. # SCIRS-Meningitis-Model-Africa This repository presents an age-structured SCIRS model for meningococcal meningitis in the African meningitis belt, developed by Yuyue Yuan under the Research Mentor Dr. Mark Asare Owusu. The project integrates both deterministic and stochastic modeling approaches to analyze epidemic dynamics, extinction probabilities, and outbreak variability. By comparing these two frameworks, the study provides a comprehensive understanding of long-term equilibrium behavior, uncertainty in transmission, and implications for meningitis control strategies across diverse population structures. ## 🧠 Project Overview The **SCIRS model** (Susceptible–Carrier–Infectious–Recovered–Susceptible) represents the transmission dynamics of *Neisseria meningitidis*. This study explores both deterministic and stochastic formulations of the model using age-structured data from the African meningitis belt. - **Deterministic Model:** Captures average epidemic trends, equilibrium behavior, and long-term dynamics using ODEs. - **Stochastic Model:** Introduces randomness to capture extinction probabilities, outbreak variability, and covariance-driven shifts in equilibrium levels. Together, these complementary approaches help assess how uncertainty and demographic structure influence disease persistence and control outcomes. --- ## 🧩 Requirements This project was developed and tested in **R (version ≥ 4.3)**. Before running the model, ensure the following packages are installed: ```R # Core dependencies install.packages(c("tidyverse", "ggplot2", "cowplot", "scales", "wesanderson", "ggpubr", "rootSolve", "deSolve")) # Modeling and simulation frameworks install.packages("drat") drat::addRepo("mrc-ide") install.packages(c("odin", "dust", "mcstate", "odin.dust"))