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 25:621633. http://dx.doi.org/10.1890/14-0417.1


Supplement

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

Copyright


Authors
File list (downloads)
Description


Author(s)

Suzanne M. O'Regan
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: smoregan@uga.edu

Krisztian Magori
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Current address:
Department of Biology
Eastern Washington University
Cheney, Washington 99004
Email: kmagori@ewu.edu

J. Tomlin Pulliam
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: tomlinp@uga.edu

Marcus A. Zokan
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: mzokan@yahoo.com

RajReni B. Kaul
Odum School of Ecology
University of Georgia
Athens, Georgia 30602
Email: reni@uga.edu

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: hdbarton@gcc.edu

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: jdrake@uga.edu


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

Literature Cited

Maher, S. P., A. M. Kramer, J. T. Pulliam, M. A. Zokan, S. E. Bowden, H. D. Barton, and J. M. Drake. 2012. Spread of white-nose syndrome on a network regulated by geography and climate. Nature Communications 3:1306. doi:10.1038/ncomms2301