Objectives
The U.S. Animal Movement Model (USAMM) and Disease Outbreak Simulation (USDOS) were developed through an international collaboration with funding from the United States Department of Agriculture and the Department of Homeland Security.
The United States does not track individual livestock movements, therefore there is a need to characterize livestock shipments at the national scale in the U.S. USAMM provides estimates of the number of cattle or swine shipments between any two counties in the contiguous United States and includes estimates of uncertainty in the predictions. USDOS is a national scale, premises-level simulation model that uses original algorithms to produce outputs very quickly even at large spatial scales. USDOS incorporates both local and long-range transmission together with multiple response options. USDOS has relatively few parameters so that sensitivity of model outputs to changes in parameters can be fully investigated. The model can run using demographic information from any country together with appropriate shipping data and/or local spread transmission. Inquiries about current work on this project may be directed to Lindsay Beck-Johnson at L.Beck-Johnson@colostate.edu
This web site is planned for use by both management and field personnel and disease modelers. This web site contains high-level descriptions of project deliverables, visualization tools, downloadable model predictions that can be ported into users own tools/systems, supporting publications with technical details, freely available downloadable code and user-guides.
Philosophy
Our overall modeling philosophy has three main components:
- Strongly data-based modeling: Increases the relevance of the models to applied questions
- Close working relationship with state and government agencies: Informs model structures and capabilities to handle realistic scenarios
- Parsimonious modeling choices whenever possible: Enhances validation and sensitivity analysis by using fewer, better-informed parameters, optimizes tradeoffs among applied needs, available data and modeling techniques.
People
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Colleen Webb - Title: Vice Provost for Graduate Affairs and Dean of the Graduate School; Professor Affiliations: Graduate School; Department of Biology, Colorado State University Role: Principal Investigator Contact info: colleen.webb@colostate.edu |
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Uno Wennergren - Title: Professor Affiliations: Department of Physics, Chemistry, and Biology / Division of Ecological and Environmental Modeling, Linköping University Role: Principal Investigator Contact info: uno.wennergren@liu.se |
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Michael J. Tildesley - Title: Professor Affiliations: University of Warwick Role: Principal Investigator Contact info: m.j.tildesley@warwick.ac.uk |
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Tom Lindström - Title: Associate Professor Affiliations: Department of Physics, Chemistry, and Biology / Division of Ecological and Environmental Modeling, Linköping University Role: Principal Investigator Contact info: tom.lindstrom@liu.se |
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Lindsay Beck-Johnson - Title: Research Scientist III Affiliations: Colorado State University, Department of Biology Role: Principal Investigator Contact info: l.beck-johnson@colostate.edu |
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Stefan Sellman - Title: Postdoctoral Researcher Affiliations: Department of Physics, Chemistry, and Biology / Division of Ecological and Environmental Modeling, Linköping University and University of Warwick Role: Principal Investigator Contact info: stefan.sellman@liu.se |
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Peter Brommesson - Title: PhD Affiliations: Department of Physics, Chemistry, and Biology / Division of Ecological and Environmental Modeling, Linköping University Role: Senior Personnel Contact info: peter.brommesson@liu.se |
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Jonathan Bertram - Title: Research Associate Affiliations: Colorado State University, Department of Biology Role: Personnel Contact info: jh.bertram@colostate.edu |
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Michael Buhnerkempe - Title: Research Assistant Professor Affiliations: Southern Illinois University School of Medicine Role: Senior Personnel Contact info: mbuhnerkempe66@siumed.edu |
| Dominika Dec Peevey - Title: Affiliations: Colorado State University, Department of Biology Role: Personnel Contact info: Dominika.Peevey@colostate.edu |
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Kendra Gilbertson - Title: PhD Student Affiliations: Colorado State University, Department of Biology Role: Personnel Contact info: Kendra.Gilbertson@colostate.edu |
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Erin Gorsich - Title: Associate Professor Affiliations: University of Warwick, School of Life Sciences Role: Senior Personnel Contact info: https://warwick.ac.uk/fac/sci/lifesci/people/egorsich/ |
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Daniel Grear - Title: Wildlife Disease Ecologist Affiliations: USGS National Wildlife Health Center Role: Senior Personnel Contact info: https://www.usgs.gov/staff-profiles/daniel-a-grear |
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Clayton Hallman - Title: Mathematical Statistician Affiliations: USDA Animal and Plant Health Inspection Service Role: Agency Technical Expert Contact info: clayton.n.hallman@aphis.usda.gov |
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Catherine M. Herzog - Title: Data Scientist Affiliations: CDC Center for Forecasting and Outbreak Analytics, Colorado State University, Department of Biology Role: Personnel Contact info: catherine.herzog@colostate.edu |
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Ryan Miller - Title: Senior Ecologist Affiliations: USDA Animal and Plant Health Inspection Service Role: Agency Lead Contact info: ryan.s.miller@aphis.usda.gov |
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Amanda Minter - Title: Research Fellow Affiliations: Equations of Disease C.I.C. Role: Senior Personnel Contact info: amanda@equationsofdisease.com www.equationsofdisease.com |
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Deedra Murrieta - Title: Biological Science Information Specialist Affiliations: USDA Animal and Plant Health Inspection Service Role: Senior Personnel Contact info: deedra.murrieta@gmail.com |
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Katie Owers Bonner - Title: Public Health Emergency Preparedness Surveillance Program Manager Affiliations: New Hampshire Department of Health and Human Services Role: Senior Personnel Contact info: owersk@gmail.com |
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Katie Portacci - Title: Veterinary Epidemiologist Affiliations: USDA Animal and Plant Health Inspection Service Role: Agency Lead Contact info: Katie.Portacci@aphis.usda.gov |
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Brandon Simony - Title: PhD Candidate Affiliations: Pennsylvania State University, Department of Biology Role: Personnel Contact info: |
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Lauren Smith - Title: Affiliations: USDA Role: Personnel Contact info: Lauren.E.Smith@colostate.edu |
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Sam Smith - Title: Research Associate II Affiliations: Colorado State University, Department of Biology Role: Personnel Contact info: sm.smith@colostate.edu |
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Kim Tsao - Title: Lead Data Scientist for the Chief Data Officer Affiliations: USDA Office of the Chief Information Officer Role: Senior Personnel Contact info: http://www.kimtsao.com |
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Marleen Werkman - Title: Research Associate Affiliations: Imperial College London Role: Senior Personnel Contact info: Personal Website |
Literature
Beck-Johnson, L.M., Gorsich, E.E., Hallman, C., Tildesley, M.J., Miller, R.S., Webb, C.T. 2023. An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case study. Epidemics, 42, 100668
Sellman, S., Beck-Johnson, L.M., Hallman, C., Miller, R.S., Owers Bonner, K.A., Portacci, P., Webb, C.T., Lindström, T. 2022. Modeling Nation-Wide U.S. Swine Movement Networks at the Resolution of the Individual Premises. Epidemics 41 (December)
Sellman, S., Beck-Johnson, L.M., Hallman, C., Miller, R.S., Owers Bonner, K.A., Portacci, P., Webb, C.T., Lindström, T. 2022. Modeling U.S. Cattle Movements until the Cows Come Home: Who Ships to Whom and How Many? Computers and Electronics in Agriculture 203 (December)
Gilbertson, K., Brommesson, P., Minter, A., Hallman, C., Miller, R.S., Portacci, K., Sellman, S., Tildesley, M.J., Webb, C.T., Lindström, T., Beck-Johnson, L.M. 2022. The Importance of Livestock Demography and Infrastructure in Driving Foot and Mouth Disease Dynamics. Life 12 (10)
Brommesson, P., Sellman, S., Beck-Johnson, L.M., Hallman, C., Murrieta, D., Webb, C.T., Miller, R.S., Portacci, K., Lindström, T. 2021. Assessing intrastate shipments from interstate data and expert opinion. Royal Society Open Science, 8(3). 192042
Sellman, S., Tildesley, M.J., Burdett, C.L., Miller, R.S., Hallman, C., Webb, C.T., Wennergren, U., Portacci, K., Lindström, T. 2020. Realistic Assumptions about Spatial Locations and Clustering of Premises Matter for Models of Foot-and-Mouth Disease Spread in the United States. PLOS Computational Biology 16 (2): 1–22
Beck-Johnson, L.M., Hallman, C., Miller, R.S., Portacci, K., Gorsich, E.E., Grear, D.A., Hartmann, K., Webb, C.T., 2019. Estimating and exploring the proportions of inter- and intrastate cattle shipments in the United States. Prev. Vet. Med. 162, 56–66.
Tsao, K., Sellman, S., Beck-Johnson, L., Murrieta, D.J., Hallman, C., Lindström, T., Miller, R.S., Portacci, K., Tildesley, M.J., Webb, C.T. 2019. Effects of regional differences and demography in modelling foot-and-mouth disease in cattle at the national scale. Royal Society Interface Focus, 10(1)
Gorsich, E.E., R.S. Miller, H.S. Mask, C. Hallman, K. Portacci, and C.T. Webb. 2019. Spatio-temporal patterns and characteristics of swine shipments in the U.S. based on Interstate Certificates of Veterinary Inspection. Scientific Reports 9(1), 3915.
Sellman, S., K. Tsao, M.J. Tildesley, P. Brommesson, C.T. Webb, U. Wennergren, M.J. Keeling, and T. Lindström. 2018. Need for speed: An optimized gridding approaches for spatially explicit disease simulations. PloS Computational Biology 14(4)
Gorsich, E. C.D. McKee, D.A. Grear, R.S. Miller, K. Portacci, T. Lindström, C.T. Webb. 2017. Model-guided suggestions for targeted surveillance based on cattle shipments in the U.S.. Preventive Veterinary Medicine, 150 (July 2017): 52-59.
Webb, C.T., M.J. Ferrari, T. Lindström, T. Carpenter, S. Dürr, G. Garner, C. Jewell, M. Stevenson, M.P. Ward, M. Werkman, and M.J. Tildesley. 2017. Ensemble Modeling and Structured Decision Making to Support Emergency Disease Management. Preventive Veterinary Medicine, 138: 124-133.
Brommesson, P., U. Wennergren, and T. Lindström. 2016. Spatiotemporal variation in distance dependent animal movement contacts: one size doesn’t fit all. PLoS ONE 11(10): e0164008
Gorsich, E., A.D. Luis, M.G. Buhnerkempe, D.A. Grear, K. Portacci, R.S. Miller, and C.T. Webb. 2016. Mapping U.S. cattle shipment networks: spatial and temporal patterns of trade communities from 2009 to 2011. Preventive Veterinary Medicine, 134: 82-91.
Probert, W.J.M., K. Shea, C.J. Fonnesbeck, M.C. Runge, C.T. Webb, M.J. Tildesley, and M.J. Ferrari. 2016. Decision-making for foot-and-mouth disease control: objectives matter. Epidemics 15: 10-19.
Werkman, M, M.J. Tildesley, E. Brooks-Pollock, and M.J. Keeling. 2016. Preserving privacy whilst maintaining robust epidemiological predictions. Epidemics (17): 35-41.
Burdett, C.L., B.R. Kraus, S.J. Garza, R.S. Miller, and K.E. Bjork. 2015. Simulating the Distribution of Individual Livestock Farms and Their Populations in the United States: An Example Using Domestic Swine (Sus scrofa domesticus) Farms. Plos One.
Dawson P.M., M. Werkman, E. Brooks-Pollock, M.J. Tildesley. 2015. Epidemic predictions in an imperfect world: modelling disease spread with partial data. Proceedings of the Royal Society B 282(1808).
Lindström, T., Tildesley, M., Webb, C.T. 2015. A Bayesian ensemble approach for epidemiological projections. PLoS Computational Biology.
McKee, C., C. Hallman, C.T. Webb, T. Lindstrom, R.S. Miller, and K. Portacci. 2015. USAMM Shiny Visualization (R package)
Buhnerkempe, M.G., Tildesley, M.J., Lindström, T., Grear, D.A., Portacci, K., Miller, R.S., Lombard, J., Werkman, M., Keeling, M.J., Wennergren, U., Webb, C.T. 2014. The impact of movements and animal density on continental scale cattle disease outbreaks in the United States. PLoS ONE 9(3): e91724
Grear, D.A., J.B. Kaneene, J.J. Averill, and C.T. Webb. 2014. Local cattle movments in response to ongoing bovine tuberculosis zonation and regulations in Michigan, USA. Preventative Veterinary Medicine. 114(3-4):201-12.
Tsao, K., S. Robbe-Austerman, R.S. Miller, K. Portacci, D.A. Grear, and C.T. Webb. 2014. Sources of bovine tuberculosis in the United States. Infection, Genetics and Evolution. 28C:137-143.
Buhnerkempe, M.G., D.A. Grear, K. Portacci, R.S. Miller, J. Lombard, and C.T. Webb. 2013. A national-scale picture of U.S. cattle movements obtained from Interstate Certificate of Veterinary Inspection data. Prev. Vet. Med.112: 318-329
Lindström, T., Grear, D.A., Buhnerkempe, M., Webb, C.T., Miller, R.S., Portacci, K., and U. Wennergren. 2013. A Bayesian approach for modeling cattle movements in the United States: scaling up a partially observed network. PLoS ONE 8(1): e53432
Portacci, K, R.S. Miller, P.D. Riggs, M.G. Buhnerkempe, and L.M. Abrahamsen. 2013. Assessment of paper interstate certificates of veterinary inspection used to support disease tracing in cattle. Journal of the American Veterinary Association 243(4): 555-560.
Lindström T., S. Sternberg Lewerin, and U. Wennergren. 2012. Influence on disease spread dynamics of herd characteristics in a structured livestock industry. Journal of the Royal Society Interface 9(71): 1287-1294.
Lindström T., S. Sternberg Lewerin, and U. Wennergren. 2012. SpecNet: A spatial network algorithm that generates a wide range of specific structures. PLoS ONE.
Tildesley, M.J., G. Smith, and M.J. Keeling. 2012. Modeling the spread and control of foot-and-mouth disease in Pennsylvania following its discovery and options for control. Prev. Vet. Med. 104, 224-239.
Tildesley, M.J. and S.J. Ryan. 2012. Disease prevention versus data privacy: using landcover maps to inform spatial epidemic models. PLoS Computational Biology, 8 (11).
Lindström, T., S.A. Sisson, S.S. Lewerin, and U. Wennergren. 2011. Bayesian analysis of animal movements related to factors at herd and between herd levels: Implications for disease spread modeling. Preventive veterinary medicine 98: 230-242.
Tildesley, M.J., V. Volkova, and M.E.J. Woolhouse. 2011. Potential for Epidemic Take-off from the Primary Outbreak Farm via Livestock Movements. BMC Veterinary Research, 7:76.
Lindström, T, Sisson, S.A., Lewerin, S.S., Wennergren, U. 2010. Estimating Animal Movement Contacts between Holdings of Different Production Types. Preventive Veterinary Medicine 95 (1–2): 23–31
Lindström, T., Sisson, S.A., Nöremark, M., Jonsson, A., Wennergren, U. 2009. Estimation of Distance Related Probability of Animal Movements between Holdings and Implications for Disease Spread Modeling. Preventive Veterinary Medicine 91 (2–4): 85–94
Tildesley, M.J., et al. 2006. Optimal reactive vaccination strategies for a foot-and-mouth outbreak in the UK. Nature, 440(7080): 83-86.
FAQ
To cite this page: Webb, C., U. Wennergren, T. Lindström, M.J. Tildesley, T. Dewey, and C. Leach. 2024. U.S. Animal Movement Model and Disease Outbreak Simulation (On-line). Accessed (date) at https://webblabb.github.io/usammusdos
To cite USDOS: U.S. Disease Outbreak Simulation (USDOS) [Computer Software]. 2022. Accessed (date) at https://webblabb.github.io/usammusdos/usdos.html
To cite USAMM: U.S. Animal Movement Model (USAMM) [Computer Software]. 2022. Accessed (date) at https://webblabb.github.io/usammusdos/usamm.html
Sellman, S., Beck-Johnson, L.M., Hallman, C., Miller, R.S., Owers Bonner, K.A., Portacci, P., Webb, C.T., Lindström, T. 2022. Modeling Nation-Wide U.S. Swine Movement Networks at the Resolution of the Individual Premises. Epidemics 41 (December)
Sellman, S., Beck-Johnson, L.M., Hallman, C., Miller, R.S., Owers Bonner, K.A., Portacci, P., Webb, C.T., Lindström, T. 2022. Modeling U.S. Cattle Movements until the Cows Come Home: Who Ships to Whom and How Many? Computers and Electronics in Agriculture 203 (December)