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