Immunity can impose a reproduction-survival tradeoff on human malaria parasites

Summary

• This repository contains (primarily MATLAB) codes and associated data for the paper "Immunity can impose a reproduction-survival tradeoff on human malaria parasites".
• To reproduce figure X from the paper, run the script Figure_X.m in MATLAB (download the entire folder first so that you have all the necessary supporting functions and scripts).

User guide

• The file run_full_model.m runs a single simulation of the within-host model.
• The parameters are set globally by calling the file baseline_parameter_set.m
• Time stepping schemes for the within-host dynamics are contained in the function within_host_model.m.
• To generate the fitness landscape for fixed (constant) transmission investment (c) strategies run the script run_withinhost_constant_strats.m
• For optimizing nonconstant/age-varying strategies, i.e. transmission investment c is a function of age of infection, use run_strategy_optimization.m being careful to ensure that the spline and discretization settings in this script match those in withinhost_model_optimization.m
• The file run_evaluate_strategy.m computes the fitness of a given strategy by running the model once.
• Splines are imported for various mesh spacings from text files labelled 'basisMatrix...txt' and new sets of splines can be generated by running CodeToGenerateBasisMatrix.R in R.
• The folder 'sensitivity_results' contains optimal strategy weights for a range of different parameter regimes (this data is shown in supplementary figures to the paper).