ThieryM95/SP_resistance_data_and_visualisation: Update revision

This is the first release of the data and code to visualise the data for:

Seasonal malaria chemoprevention potentially remains effective with the spread of Plasmodium falciparum parasites resistant to sulfadoxine-pyrimethamine: a modelling study.

Thiery Masserey1,2, Tamsin Lee1,2, Sherrie L Kelly1,2, Ian M Hastings3, Melissa A Penny1,2 1 Swiss Tropical and Public Health Institute, Basel, Switzerland 2 University of Basel, Basel, Switzerland
3 Liverpool School of Tropical Medicine, Liverpool, UK Correspondence to: Prof Melissa A. Penny, melissa.penny@unibas.ch

In the study mentioned above, we have developed a disease modelling approach with emulator-based global sensitivity analysis to quantify the influence of multiple factors on the spread of Plasmodium falciparum parasites resistant to sulfadoxine-pyrimethamine (SP) (quintuple mutant) and predicted the time needed for the quintuple mutant to spread from 1% to 50% of inoculations for several SMC deployment strategies. We also estimated the impact of this spread on SMC effectiveness against clinical malaria. This analysis was performed using an individual-based malaria model (https://github.com/SwissTPH/openmalaria/wiki).

This repository contains the data generated during this study and the R scripts used to visualise the data. The repository is structured based on the figure's name in the manuscript. Each figure has a folder with its name. The folder contains the data and code used to generate the figure and a PDF version of the plot.

Note that the plotting code uses the folder structure and working directories used by the researchers. The file paths will have to be adjusted to replicate figures.