anchitapuri/cameroon_chik_onnv

Spatial Modelling of CHIK and ONNV in Cameroon # Analysis for ONNV and CHIKV in Cameroon A statistical framework using multi-pathogen serology data to simultaneously reconstruct cross-reactivity patterns and infer individual- and population-level infection histories. In addition, this repository includes spatial modelling of CHIKV and ONNV transmission across Cameroon. All analysis was conducted in R (R version 4.4.1). Bayesian analysis was conducted using the R Interface to CmdStan (cmdstan-2.38.0). Spatial analysis was conducted using R-INLA (INLA_24.06.27). # Pre processing data District level geometery from: - Caedistricts179_region.shp (179 districts, 183 geometeries (MANOKA == 5 geometries) - cmr_admin3.shp (360 districts) - Districts not present in either were spatially assinged to their nearest shapefile polygon - Population weighted centroids calculated for each districts, and used for downstream analysis # MultiSero Model - Model (MultiSero_Model.stan) used to jointly inferred pathogen-specific prevalence estimates and between-pathogen cross-reactivity - Analysis in `R/MultiSero_Fitting.R` # Spatial Analysis - To explore the variability of ONNV prevalence across Cameroon, applied a spatially explicit catalytic model with a Bayesian framework implemented using INLA - Analysis for this part in `R/INLA_SpatialPrediction.R`