Ecological Archives A025-033-S1

Suzanne M. O'Regan, Krisztian Magori, J. Tomlin Pulliam, Marcus A. Zokan, Rajreni B. Kaul, Heather D. Barton, and John M. Drake. 2015. Multi-scale model of epidemic fade-out: Will local extirpation events inhibit the spread of white-nose syndrome? Ecological Applications 25:621–633. http://dx.doi.org/10.1890/14-0417.1

Data, R source code, and script files to perform analysis and simulation of multi-scale models.
Ecological Archives A025-033-S1.

Suzanne M. O'Regan
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: [email protected]

Krisztian Magori
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Current address:
Department of Biology
Eastern Washington University
Cheney, Washington 99004
Email: [email protected]

J. Tomlin Pulliam
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: [email protected]

Marcus A. Zokan
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: [email protected]

RajReni B. Kaul
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: [email protected]

Heather D. Barton
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Current address:
Department of Biology
Grove City College
Grove City, Pennsylvania 16127
Email: [email protected]

John M. Drake
Odum School of Ecology
University of Georgia
Athens, Georgia 30602, USA
Department of Zoology
University of Oxford
South Parks Road, Oxford OX1 3PS, UK
Email: [email protected]

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)

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