lagzini/SIR-Ebola-DA-MCMC-Code

MATLAB code for Bayesian and frequentist inference in partially observed stochastic SIR epidemic models, with application to Ebola in Sierra Leone. # SIR-Ebola-DA-MCMC-Code MATLAB code supporting the manuscript: **"Bayesian and Frequentist Inference for Partially Observed Stochastic SIR Epidemic Models with Application to Ebola in Sierra Leone"** ## Description This repository contains the MATLAB code and data supporting the simulation study and the real-data application presented in the manuscript. The implemented methodology focuses on statistical inference for partially observed stochastic SIR epidemic models. In particular, the repository includes: - Simulation of stochastic SIR epidemic trajectories using Gillespie's stochastic simulation algorithm. - Bayesian inference using a data-augmentation Markov chain Monte Carlo (DA-MCMC) algorithm. - Reconstruction of latent infectious trajectories under partial observation. - Estimation of the basic reproduction number \(R_0\). - Frequentist estimation for comparison with the Bayesian approach. - Application to data from the 2014–2016 Ebola outbreak in Sierra Leone. ## Repository Structure SIR-Ebola-DA-MCMC-Code/ │ ├── README.md ├── LICENSE │ ├── simulation/ │ ├── simulation_SIR_DA_MCMC.m │ └── gillespie_SIR.m │ └── real_data/ ├── DA_MCMC_Ebola_Sierra_Leone.m ├── ebola_daily_data_full.xlsx └── sierra_leone_real_values.xlsx ## File Description ### Simulation - **`simulation/simulation_SIR_DA_MCMC.m`** Main MATLAB script for the simulation study of the partially observed stochastic SIR epidemic model. It implements the DA-MCMC inference procedure and estimates the basic reproduction number \(R_0\). - **`simulation/gillespie_SIR.m`** MATLAB implementation of Gillespie's stochastic simulation algorithm for generating sample paths of the stochastic SIR epidemic model. ### Real-Data Application - **`real_data/DA_MCMC_Ebola_Sierra_Leone.m`** Main MATLAB script for the statistical analysis of the 2014–2016 Ebola outbreak in Sierra Leone using the proposed inference methodology. - **`real_data/ebola_daily_data_full.xlsx`** Data file containing the Ebola …