malaria_recomb_MDR

Investigating the effect of recombination on the rate of emergence of multi-drug resistance under different treatment strategies in Malaria.

A stochastic, agent-based model, built in C++. Complete description of model architecture

Includes python scripts for simple inference and visualizations in data/plotting/.

Compile

mkdir build
cd build
cmake -S ../src -B .
make

Run

./MalariaPopSim

Configuration

1. In fitness_values.csv: Adjust fitness of wildtype clones according to assumed length of transmission cycle
2. In simulator.cpp: starting clones and starting clone frequencies
3. In settings.h: everything else (demography, genetics map, recombination, treatment)