Raw data and code

Data and code from our experiment examining the transmission of native Drosophila viruses, between and across species, and costs in terms of lifespan and offspring production to Drosophila melanogaster.
Description of the data and file structureFor the figures in the main text, use the details below (files to load are also detailed in code comments) to re-run analyses and re-make figures;
Fig. 1 - load exp_exp_transmission_vial_data.csv, and exp_exper_exposure_infected_dat.csv and run the code in transmission_prevalence.R
Fig. 2 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in mortality_w_viral_infection.R
Fig. 3 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in lifespan_models_and_plots.R (code also makes table S4, and Fig. S4, S5 and S8)
Fig. 4 - load EE_virus_w_fec_overtime_and_male_off_analysis.csv, and run the code in lifetime_offspring_production_models_and_plots.R (code also makes table S5, S6, and S9, and Fig. S1, S7, S9, and S15)
Code/SoftwareThe included R files can be used to re-run all models in the paper, and re-make all figures (including supplementary figures and tables). The script section outlines allow you to jump to particular figures or tables if needed. All analyses were run in R version 4.3.2, with all packages needed listed at the top of each script.
If you'd prefer not to re-run models or want to inspect our run outputs, load the Rdata files into the scripts to look at the exact model runs desribed in the paper.
The shell script included is for the analysis of public datasets downloaded from the SRA. To re-run this analysis you will need to download these datasets (which we provide details of in the supplementary methods), and re-run the script in a linux environment. We provide the output from this script (mapped reads across host genes and viruses) to make the heatmap produced in the paper (in the SRA_transmission_mapping_analyses.R file).