HopkinsIDD/geotargeting_ocv_ssa

The impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa: a modeling study # The impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa: a modeling study This repository provides the source code and supplementary material for a modeling study on the impact of geographic targeting of oral cholera vaccination in sub-Saharan Africa. ## Source The source code for the primary models presented in the manuscript may be found in `source/`. The codes here demonstrate the specific settings and parameters in our models. Please note that the input data to run the source code are not posted in this repository, but descriptions for accessing this data exist at the top of each R script. Descriptions of the files are as follows: 1. `generate_all_rasters_parallel.R`: Projects population at 5km x 5km scale for all study countries from 2018-2030. Crops and disaggregates incidence rate rasters for all study countries from Lessler and Moore et al., Lancet, 2018. 1. `generate_wash_targets.R`: Processes 1km x 1km rasters on access to improved water and sanitation from Pullan et al., PLOS Medicine, 2014 into lists of targeted districts for water, sanitation, and WASH based vaccine deployment strategies for a given parameter set. 1. `run_model_nonwash.R`: Run model for untargeted and burden based vaccine deployment strategies, for a given parameter set. 1. `run_model_wash.R`: Run model for water and sanitation related vaccine deployment strategies, for a given parameter set. 1. `process_all_models.R`: Processes non-wash and wash model outputs into non-cumulative and cumulative results (over study period years) and calculates confidence intervals for all parameter sets together. 1. `make_main_plots.R`: Plot subpanels of main manuscript Figures 1 and 2. 1. `make_main_plots_fig3.R`: Plot subpanels of main manuscript Figure 3. 1. `utils_mods.R`: Utilities for targeting vaccine, modeling the health impacts of vaccination campaigns, and processing model output data. 1. `utils_figs.R`: Utilities for making the main manuscript figures. 1. `ut …