bioepirnet-lab/malaria-spatiotemporal-model-nigeria

Code for the study “Spatio-Temporal and Mathematical Modeling of Malaria Burden and Intervention Efficacy in Nigeria”, including R (INLA Bayesian spatio-temporal model) and Python (ODE transmission model) implementations. # Spatio-Temporal and Mathematical Modeling of Malaria Burden and Intervention Efficacy in Nigeria This repository contains the **R and Python code** for the study: **"Spatio-Temporal and Mathematical Modeling of Malaria Burden and Intervention Efficacy in Nigeria."** The manuscript has been **submitted and is currently under review at *Communications in Statistics – Case Studies and Data Analysis*.** The repository provides reproducible implementations of the statistical and mathematical models used in the study, including: - **R code** implementing the Bayesian spatio-temporal statistical model using **INLA** - **Python code** implementing the **ODE-based malaria transmission model** These models are used to analyze malaria prevalence patterns and evaluate the potential impact of interventions across Nigeria. --- # Overview The study combines two complementary modeling approaches. ## 1. Bayesian Spatio-Temporal Statistical Model (R – INLA) This model analyzes malaria prevalence among children under five using **Nigeria Malaria Indicator Survey (NMIS)** data from: - 2010 - 2015 - 2021 The statistical model evaluates the influence of demographic, socioeconomic, and environmental factors on malaria prevalence while accounting for spatial and temporal dependencies. ## 2. Mathematical Transmission Model (Python – ODE System) A compartmental model describing malaria transmission dynamics between humans and mosquitoes. The model explores the impact of interventions such as: - Seasonal Malaria Chemoprevention (SMC) - Vaccination - Bed net use - Environmental factors (e.g., irrigation and mosquito breeding sites) --- # Repository Structure ```text malaria-spatiotemporal-model-nigeria/ ├── code/ │ ├── spatiotemporal_malaria_inla_model.R │ └── malaria_transmission_ode_model.py └── README.md ``` ## Statistical Model The statistical analysis uses a **Bayesian hierarchical spatio-temporal model** where malaria infection status is modeled at the individua …