Malaria No More

Code used to produce data for Malaria No More artwork.

Quick start

Download site file and vaccine coverage inputs

Contact Lydia for these filepaths. These files should be saved in src/model_country/.

Run workflow.R

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.

Directory

.
├── 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