Code used to produce data for Malaria No More artwork.
Contact Lydia for these filepaths. These files should be saved in src/model_country/
.
This script contains the orderly2::orderly_run()
function, which is used to run the model_country orderly report. The parameters for this report are as follows:
- iso3c: country code for country to model
- scenario: scenario to run for Malaria No More runs.
Options:
- vaccine_scaleup: includes vaccine scale-up of 80% coverage for R21 vaccine starting in 2023, where the vaccine is administered to all admin-1 units in the country.
- no-vaccination: no vaccine scale-up, interventions remain constant through 2040.
- new_tools: incorporates a blood-stage vaccine (IE RH5) in 2029, which we presume has 60% efficacy against cases not prevented by R21 vaccination. Operationalised as an increase in vaccine efficacy with no other changes to R21 parameters. Also reduces carrying capacity by 50% in 2029, as a crude attempt to model the introduction of gene drive technologies that may reduce mosquito populations in malaria-endemic regions.
Models are run from 2000-2040 for all malaria-endemic countries in Sub-Saharan Africa at the admin-1 level. The modelled population size is 50,000, with a burn-in period of 15 years.
Outputs will be saved to the archive\model_country
directory, with site-level incidence and mortality rates saved to outputs.rds
for every country/scenario combination.
.
├── ethiopia # Ethiopia test case
| ├── ethiopia_recalibration.R # Ethiopia EIR recalibration
├── plots # Plots of model output
├── src # Coding scripts
| ├── model_country # Country runs
| ├── MNM_functions.R # Model run functions
| ├── model_country.R # Model run script
| ├── postprocess # Post-processing
| ├── compare_ethiopia_versions.R # ETH comparison
| ├── postprocess.R # Post-processing functions
├── country_shapefiles.R # GADM shapefiles
├── data_and_libraries.R # R packages and paths to load
├── ethiopia_recalibration.R # Ethiopia EIR recalibration
├── export_shapefiles.R # Exporting GADM and MAP .rds as .shp
├── ITN_vs_PfPR_plot.R # Site ITN use vs. PfPR
├── malariaatlasproject.R # Shapefiles of MAP CI data Pf & Pv
├── model_outputs.R # Key script for ICL model results
├── seasonality curves.R # Creating seasonality weights for each site
├── site_files.R # Calculating lives saved from site file data
├── test_carrying_capacity.R # Testing the cc function in malariasim
├── WHO_elimination.R # WHO decade of elimination maps
├── WMR cases and deaths.R # Test script for saving shp files
├── WMR lives saved.R # Cumulative lives saved: WMR 2023
├── workflow.R # Key script for running models
├
├── .gitignore # gitignore file
├── malaria_no_more.Rproj # R.Studio project file
└── README.md # Project overview