Simulation code and data for "The effect of linkage disequilibrium on the evolution of resistance to multiple pesticides"

This repository contains the R code and R data files for the manuscript titled 'The effect of linkage disequilibrium on the evolution of resistance to multiple pesticides', which is published in the Journal of Economic Entomology in 2026. Simulation files uses sim_params.Rdata and simulation_function.R to generate all rawdata files as output. For SAR and SGR, rawdata files contain columns: column 1 - ending frequency of allele A, column 2 - ending generation number for allele A, column 3 - ending frequency of allele B, column 4 - ending generation number for allele B. Initial analyses were performed to generate win-loss-draw tables as well as summary matrices, these are provided in this repository too. Further downstream analysis scripts are available. A separate simulation uses sim_params.Rdata and simulation_function_linkage.R to analyse allele linkage under SGR assumptions. Linkage data contains columns: column 1 - Lewontin's D, column 2 - normalised Lewontin's D.