Malaria_Vaccine-Averted_Burden

This repository contains the data and code used in the manuscript "Malaria Vaccine Impact on Cases, Drug Resistant Cases, and Deaths in Africa: A Modeling Study". The model projects health burden averted with a vaccine similar to RTS,S administered yearly to one-year-olds in the WHO Africa Region from 2021-2030.

FOLDERS

1. Code: Python code for analysis and R code for figures
2. Data: Input data files (Sources in Malaria_Data.py)
3. Results: Generated .csv, .tiff, and .pdf files

WORKFLOW

1. Update OneDrive = "[Main file path]" in all Python and R scripts.

2. Malaria_Data.py reads files from the Data folder and outputs Data/malaria_df.csv, runs Malaria_Imputate.py, and outputs Results/Malaria_Data.csv and Pop1_byCountry.csv for analysis.

3. Malaria_Imputate.py reads Data/malaria_df.csv and uses multivariate regression to impute missing values for treatment received rate, delayed parasite clearance rates, and treatment failure rates (Supplementary Tables 5 and 6). This script generages Results/Malaria_Imputation.png (Supplementary Figures 1 and 2) and Data/malaria_imputed.csv, which is used by Malaria_Data.py.

4. Malaria_PE.py reads Results/Malaria_Data.csv, runs the model to produce point estimates by country-year, and outputs Results/Malaria_PE.csv and Results/Malaria_Country_Parameters.csv (Supplementary Tables 3 and 4).

5. Malaria_MC.py reads Results/Malaria_Data.csv and Results/Malaria_PE.csv, generates uncertainty intervals using Monte Carlo simulation (1,000 iterations), and outputs results by country-year in Results/Malaria_MC.csv.

6. Malaria_Post.py reads Results/Malaria_MC.csv and outputs Results/Malaria_byCountry.csv, Results/Malaria_byCountry_per1000.csv (Supplementary Tables 8-12), Results/Malaria_Total_per1000.csv, and Results/Malaria_byYear.csv'.

7. Malaria_LineGraphs.R reads Resutls/Malaria_byYear.csv and outputs Malaria_CasesAvt_byYear.tiff (Figure 2), Malaria_ResCasesAvt_byYear.tiff (Figure 3), Malaria_DeathsAvt_byYear.tiff (Figure 4), Malaria_ResCases_byDPC.tiff (Figure 5), Malaria_CasesAll_byYear.tiff (Supplementary Figure 3), Malaria_ResCasesAll_byYear.tiff (Supplementary Figure 4), and Malaria_DeathsAll_byYear.tiff (Supplementary Figure 5) in the Results folder.

8. Malaria_Map_Cases.R reads Results/Malaria_ByCountry.csv and files in "Data/CreateChoroplethPlotFiles" to generate Malaria_Map_Cases.pdf (Supplementary Figure 6). Similarly, Malaria_Map_ResCases.R ouptus Malaria_Map_ResCases.pdf (Supplementary Figure 7), and Malaria_Map_Deaths.R outputs Malaria_Map_Deaths.pdf (Supplementary Figure 8) in the Results folder.