mundialis/RVF_Mauritania

Repository for modeling of Rift Valley Fever (RVF) in Mauritania # RVF_Mauritania Repository for modeling of Rift Valley Fever (RVF) in Mauritania. The analysis includes - calculation of potential risk areas (suitability maps), depending on environmental conditions and - calculation of spillover potential, depending on the suitability maps and livestock and animal data. ## Calculation of potential risk areas - Tool for Analysis: Maxent - Used within GRASS GIS - Installation with `r.maxent.setup`: - Note: need to have java installed - Analysis - Define configuration file: potential_risk_areas_config.cfg - Train model: potential_risk_areas_train.sh - Apply model: potential_risk_areas_predict.sh ### Analysis procedure: #### Input - Prepared disease data and covariates - Defined within config - For different data versions see table potential_risk_areas_data_versions #### Train model: - Script: potential_risk_areas_train.sh - AOI/Region setting - Use all given positive and negative samples -> AOI defined by them (Covariates only sampled at negative/positive result coordinates) - Model options: Usage of monthly disease data - Option 1: single model - Combine all given positive and negative samples from all months/years - Sample covariates for all given positive and negative results (i.e. create monhtly SWD files) and combine them --> use this as input to train one single model - Option 2: monthly models - Train monthly models (for which enough positive (and negative) samples given) - For different model versions see table potential_risk_areas_model_versions #### Apply model - Script: potential_risk_areas_predict.sh - Apply model to all monthly data - From 2019-2023, see also `PREDICTION` section within config ## Calculation of spillover potential The spillover potential calculation follows Hardcastle et al. 2020 with two differences: - the geographic units are not administrative areas but pixels - livestock movement from Jahel et al. 2020 is included The main script is spillover_risk.sh which includes livestock movement: the num …