Genotype and sex-based host variation in behaviour and susceptibility drives population disease dynamics

Simulation of disease on contact networks derived from empirical Drosophila data infected with Drosophila C Virus (DCV) for White LA, Siva-Jothy JA, Craft ME, Vale PF. 2020 Genotype and sex-based host variation in behaviour and susceptibility drives population disease dynamics. Proc. R. Soc. B 20201653. http://dx.doi.org/10.1098/rspb.2020.1653

Raw Experimental Data

• Dmel DCV Load and Shed.csv- experimental measurements of viral load detection for experimentally infected flies
• Dmel Fixed Radius Social Aggregation.csv- experimental measurements of social aggregation within 10 mm, 15 mm, and 20 mm
• Dmel Infection Duration and Lethal Load.csv- experimental measurements of duration of infection (time till death post-infection)

Basic Functions

• Exp1functions.R - Experiment 1 functions needed to run in parallel on supercomputer
• Exp2functions.R - Experiment 2 functions needed to run in parallel on supercomputer
• Exp3functions.R - Experiment 2 functions needed to run in parallel on supercomputer

Supercomputer

• Exp1Parallel.R- Run Experiment 1 in parallel via clusters

• Exp2Parallel.R- Run Experiment 2 in parallel via clusters

• Exp3Parallel.R- Run Experiment 3 in parallel via clusters

• Exp1Parallel.txt- bash script for submitting Exp1Parallel.R

• Exp2Parallel.txt- bash script for submitting Exp2Parallel.R

• Exp3Parallel.txt- bash script for submitting Exp3Parallel.R

Random Forest Analysis

• DrosophilaRF.R - Random forest analysis for Drosophila simulations: Experiment 1
• DrosophilaRF2.R - Random forest analysis for Drosophila simulations: Experiment 2
• DrosophilaRF3.R - Random forest analysis for Drosophila simulations: Experiment 3

Plotting

• DrosophilaMSIFileCleaning.R- cleans and combines raw data outputed from the supercomputer
• DrosophilaAnalysis.R - creates heatmap plots for Experiments #1, 2 & 3
• PlotRF.R - code for plotting variable importance results from random forest analysis for Experiments #1, 2 & 3

Results

• Experiment1Summary.csv - compiled simulation data for Experiment 1

• Experiment2Summary.csv - compiled simulation data for Experiment 2

• Experiment3Summary.csv - compiled simulation data for Experiment 3

• Exp#beta...tiff - Heat map results for each experiment with different parameter combinations

• Exp#RF_R0...csv- Random forest results (variable importance scores) for R0

• Exp#RF_dur...csv- Random forest results (variable importance scores) for epidemic duration

• Exp#RF_logit...csv- Random forest results (variable importance scores) for whether or not outbreak spread beyond initially infected individual

• Exp#RF_maxI...csv- Random forest results (variable importance scores) for maximum number of infected individuals