Supplement 1. Data, R source code, and script files to perform analysis and simulation of multi-scale models.

File List CountyDurationsScript.R (MD5: 11c986e429c95939119dfba189c36f31) frag_runner.r (MD5: 2f7485ebe2d2ad6f87c731dc1409124f) GammaDistributedCountyDurationsScript.R (MD5: 564c893438c156880dbf7c72bf01f9de) GLMModelFitCaveData.R (MD5: f184fb5e3fae0854c0be7c537548a551) NYPA_caves_infections.csv (MD5: 8e48980a329d637d317af5211ba5e3b4) si_dur.Rdata (MD5: 91473c25d66a90f099d3564e5a87f443) us_data.csv (MD5: 37d75dbf0e9966f305c7fc4ef562abde) us_data_dur.csv (MD5: 6d6e2fea108b8d4ac05b86ff31a54959) WNS-GT-Duration.R (MD5: 688935e135f35abddcb4ff6321a3e7c4) Description CountyDurationsScript.R - R script to calculate county infection durrations assuming exponentialy distributed hibernaculum infection times. frag_runner.r - R script to simulate SIR and SI epidimics GammaDistributedCountyDurationsScript.R - R script to calculate county infection durrations assuming gamma distributed hibernaculum infection times GLMModelFitCaveData.R - R script to parameterize the county model by fitting a GLM to incidence data from New York and Pennsylvania NYPA_caves_infections.csv - Incidence data from Ney Yourk and Pennsylvania used to parameterize the county model si_dur.Rdata - Calculated county infection durration data assuming an SI county model us_data.csv - Data table of cave counts and WNS incidence from Maher et al. us_data_dur.csv - Copy of us_data.csv with added county infection durration column WNS-GT-Duration.R - R function definitions to simulate epidimics