pascalantwi/Malaria-Spatio-Temporal-Ghana-Study

# Spatio-Temporal Generalized Linear Modeling of Climatic Influences on Malaria Incidence in Ghana ## Overview This repository contains the complete R code for the MSc thesis titled **"Spatio-Temporal Generalized Linear Modeling of Climatic Influences on Malaria Incidence in Ghana (2020--2024)"**. The analysis applies a Bayesian spatio-temporal Negative Binomial model estimated via Integrated Nested Laplace Approximation to examine the lagged effects of nine climatic predictors on monthly malaria incidence across Ghana's 16 administrative regions. --- ## Repository Contents | File | Description | |---|---| | `malaria_spatio_temporal_analysis.R` | Complete analysis pipeline | | `README.md` | Repository documentation | --- ## Analysis Pipeline The script proceeds through the following sequential stages: 1. **Data Loading and Merging** — Malaria incidence data from DHIMS-2 and climatic data from Visual Crossing merged by region, month, and year 2. **Exploratory Visualisation** — Monthly malaria incidence and rainfall plots for all 16 regions 3. **Lag Determination** — Pearson correlation analysis for nine climatic predictors at lags 0 to 3 months 4. **Multicollinearity Diagnostics** — Two-stage procedure comprising inter-lag correlation screening and Generalised Variance Inflation Factor analysis 5. **Poisson and Negative Binomial Models** — Overdispersion testing, model fitting, and Poisson versus Negative Binomial comparison 6. **Bayesian Spatio-Temporal Model** — INLA model with CAR spatial prior, RW1 temporal prior, and spatio-temporal interaction term 7. **Prior Sensitivity Analysis** — Three prior sensitivity tests and two structural specification tests with WAIC, DIC, and Log CPO comparison 8. **CPO Model Validation** — Conditional Predictive Ordinate statistics, PIT histogram, and Kolmogorov-Smirnov calibration test 9. **Risk Mapping** — Annual posterior relative risk maps for 2020--2024 10. **Exceedance Probability Maps** — Posterior probabil …