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Applications and Case Studies

Tracking Epidemics With Google Flu Trends Data and a State-Space SEIR Model

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Pages 1410-1426 | Received 01 Sep 2009, Published online: 21 Dec 2012

REFERENCES

  • American College of Emergency Physicians . 2009 . The National Report Card on the State of Emergency Medicine , Irving, Texas: American College of Emergency Physicians. Available at: http://www.emreportcard.org/uploadedFiles/ACEP-ReportCard-10-22-08.pdf
  • Anderson , R. M. and May , R. M. 1991 . Infectious Diseases of Humans: Dynamics and Control , Oxford : Oxford University Press .
  • Arulampalam , M. , Maskell , S. , Gordon , N. and Clapp , T. 2002 . “A Tutorial on Particle Filters for On-Line Nonlinear/Non-Gaussian Bayesian Tracking,” . IEEE Transactions on Signal Processing , 50 : 174 – 188 .
  • Atkinson , K. E. 1978 . Introduction to Numerical Analysis , New York : Wiley .
  • Cappé , O. , Godsill , S. and Moulines , E. 2007 . “An Overview of Existing Methods and Recent Advances in Sequential Monte Carlo,” . IEEE Proceedings in Signal Processing , 95 : 899 – 924 .
  • Carvalho , C. M. , Johannes , M. , Lopes , H. F. and Polson , N. G. 2010 . “Particle Learning and Smoothing,” . Statistical Science , 25 : 88 – 106 .
  • Cauchemez , S. and Ferguson , N. M. 2008 . “Likelihood-Based Estimation of Continuous-Time Epidemic Models From Time-Series Data: Application to Measles Transmission in London,” . Journal of the Royal Society Interface , 5 : 885 – 897 .
  • Center for Infectious Disease Research & Policy. 2009 . “Novel H1N1 Influenza (swine flu),” . Technical Report, Academic Health Center, University of Minnesota
  • Chowell , G. , Ammon , C. E. , Hengartner , N. W. and Hyman , J. M. 2006 . “Transmission Dynamics of the Great Influenza Pandemic of 1918 in Geneva, Switzerland: Assessing the Effects of Hypothetical Interventions,” . Journal of Theoretical Biology , 241 : 193 – 204 .
  • Chowell , G. , Nishiura , H. and Bettencourt , L. 2007 . “Comparative Estimation of the Reproduction Number for Pandemic Influenza From Daily Case Notification Data,” . Journal of the Royal Society Interface , 4 : 155 – 166 .
  • Cintrón-Arias , A. , Castillo-Chávez , C. , Bettencourt , L. , Lloyd , A. and Banks , H. T. 2009 . “The Estimation of the Effective Reproductive Number From Disease Outbreak Data,” . Mathematical Biosciences and Engineering , 6 : 261 – 282 .
  • Doucet , A. and Johansen , A. 2009 . “A Tutorial on Particle Filtering and Smoothing: Fifteen Years Later,” . In Handbook of Nonlinear Filtering , Oxford : Oxford University Press . , eds. D. Crisan and B. Rozovskii,
  • Elderd , B. , Dukic , V. and Dwyer , G. 2006 . “Uncertainty in Predictions of Disease Spread and Public-Health Responses to Bioterrorism and Emerging Diseases,” . Proceedings of the National Academy of Sciences , 103 : 15693 – 15697 .
  • Eubank , S. , Guclu , H. , Kumar , V. , Marathe , M. , Srinivasan , A. , Toroczkai , Z. and Wang , N. 2004 . “Modelling Disease Outbreaks in Realistic Urban Social Networks,” . Nature , 429 : 180 – 184 .
  • Fearnhead , P. 2002 . “Markov Chain Monte Carlo, Sufficient Statistics, and Particle Filters,” . Journal of Computational and Graphical Statistics , 11 : 848 – 862 .
  • Fearnhead , P. 2008 . “MCMC for Space Models,” . Technical Report, Lancaster University
  • Ferguson , N. M. , Keeling , M. J. , Edmunds , W. J. , Gant , R. , Grenfell , B. T. , Amderson , R. M. and Leach , S. 2003 . “Planning for Smallpox Outbreaks,” . Nature , 425 : 681 – 685 .
  • Fraser , C. , Donnelly , C. A. , Cauchemez , S. , Hanage , W. P. , Van Kerkhove , M. D. , Hollingsworth , T. D. , Griffin , J. , Baggaley , R. F. , Jenkins , H. E. , Lyons , E. J. , Jombart , T. , Hinsley , W. R. , Grassly , N. C. , Balloux , F. , Ghani , A. C. , Ferguson , N. M. , Rambaut , A. , Pybus , O. G. , Lopez-Gatell , H. , Alpuche-Aranda Ietza Bojorquez Chapela , C. M. , Palacios Zavala , E. , Espejo Guevara , D. M. , Checchi , F. , Garcia , E. , Hugonnet , S. , Roth , C. and The WHO Rapid Pandemic Assessment Collaboration . 2009 . “Pandemic Potential of a Strain of Influenza a (H1N1): Early Findings,” . Science , 324 : 1557 – 1561 .
  • Gani , R. , Hughes , H. , Fleming , D. , Griffin , T. , Medlock , J. and Leach , S. 2005 . “Potential Impact of Antiviral Drug Use During Influenza Pandemic,” . Emerging and Infectious Diseases , 11 : 1355 – 1362 .
  • Gani , R. and Leach , S. 2001 . “Transmission Potential of Smallpox in Contemporary Populations,” . Nature , 414 : 748 – 751 .
  • Gilks , W. and Berzuini , C. 2001 . “Following a Moving Target—Monte Carlo Inference for Dynamic Bayesian Models,” . Journal of the Royal Statistical Society, Series B , 63 : 127 – 146 .
  • Ginsberg , J. , Mohebbi , M. , Patel , R. , Brammer , L. , Smolinski , M. and Brilliant , L. 2009 . “Detecting Influenza Epidemics Using Search Engine Query Data,” . Nature , 457 : 1012 – 1014 .
  • He , D. , Ionides , E. L. and King , A. A. 2009 . “Plug-and-Play Inference for Disease Dynamics: Measles in Large and Small Towns as a Case Study,” . Journal of the Royal Society Interface , 7 : 271 – 283 .
  • Hethcote , H. W. 2000 . “The Mathematics of Infectious Diseases,” . SIAM Review , 42 : 599 – 653 .
  • Hindmarsh , A. 1983 . “ODEPACK: A Systematized Collection of ODE Solvers,” . In Scientific Computing , Edited by: Stepleman , R. S. 55 – 64 . Amsterdam : North-Holland .
  • Jègat , C. , Carrat , F. , Lajaunie , C. and Wackernagel , H. 2008 . “ Early Detection and Assessment of Epidemics by Particle Filtering ” . In geoENV VI – Geostatistics for Environmental Applications, Proceedings of the Sixth European Conference on Geostatistics for Environmental Applications , Edited by: Soares , A. , Pereira , M. J. and Dimitrakopoulos , R. Vol. 15 , 23 – 35 . Quantitative Geology and Geostatistics . Available at: http://www.springerlink.com /content /g5h7t3j980304372 /
  • Jewel , C. , Kypraios , T. , Neal , P. and Roberts , G. 2009 . “Bayesian Analysis for Emerging Infectious Diseases,” . Bayesian Analysis , 4 : 465 – 496 .
  • Kantas , N. , Doucet , A. , Singh , S. and Maciejowski , J. 2009 . “An Overview of Sequential Monte Carlo Methods for Parameter Estimation on General State Space Models,” . In IFAC proceedings Volumes (IFAC-Papers Online) , 15, 774–785.
  • Kaplan , E. H. , Craft , D. L. and Wein , L. M. 2002 . “Emergency Response to a Smallpox Attack: The Case for Mass Vaccination,” . Proceedings of the National Academy of Sciences of the United States of America , 99 : 10935 – 10940 .
  • Kermack , W. and McKendrick , A. 1927 . “Contribution to the Mathematical Theory of Epidemics,” . Proceedings of the Royal Society of London, Series A , 115 : 700 – 721 .
  • King , A. A. , Ionides , E. L. , Pascual , M. and Bouma , M. J. 2008 . “Inapparent Infections and Cholera Dynamics,” . Nature , 454 : 877 – 880 .
  • Kitagawa , G. 1998 . “A Self-Organizing State-Space Model,” . Journal of the American Statistical Association , 93 : 1203 – 1215 .
  • Kong , A. , Liu , J. S. and Wong , W. H. 1994 . “Sequential Imputations and Bayesian Missing Data Problems,” . Journal of the American Statistical Association , 89 : 278 – 288 .
  • Leman , S. , Chen , Y. and Lavine , M. 2009 . “The Multiset Sampler,” . Journal of the American Statistical Association , 104 : 1029 – 1041 .
  • Liu , J. and West , M. 2001 . “Combined Parameters and State Estimation in Simulation-Based Filtering,” . In Sequential Monte Carlo Methods in Practice , Edited by: Doucet , A. , de Freitas , N. and Gordon , N. 197 – 223 . New York : Springer-Verlag .
  • Longini , I. , Halloran , M. , Nizam , A. and Yang , Y. 2004 . “Containing Pandemic Influenza With Antiviral Agents,” . American Journal of Epidemiology , 159 : 623 – 633 .
  • Lopes , H. F. , Carvalho , C. M. , Johannes , M. S. and Polson , N. G. 2011 . Particle Learning for Sequential Bayesian Computation,” in Bayesian Statistics 9 , Oxford : Oxford Science Publications . , eds. J. M. Bernardo, M. J. Bayarri, J. O. Berger, A. P. Dawid, D. Heckerman, A. F. M. Smith, and M. West,
  • Lopes , H. F. and Tsay , R. E. 2011 . “Particle Filters and Bayesian Inference in Financial Econometrics,” . Journal of Forecasting , 30 : 168 – 209 .
  • Ludkovski , M. and Niemi , J. 2010 . “Optimal Dynamic Policies for Influenza Management,” . In Statistical Communications in Infectious Diseases , 2, available at http://www.degruyter.com/view/j/scid.2010.2.1/scid.2010.2.1.1020/scid.2010.2.1.1020.xml
  • Meligkotsidou , L. and Fearnhead , P. 2004 . “Exact Filtering for Partially-Observed Continuous-Time Models,” . Journal of the Royal Statistical Society, Series B , 66 : 771 – 789 .
  • Mills , C. E. , Robins , J. M. and Lipsitch , M. 2004 . “Transmissibility of 1918 Pandemic Influenza,” . Nature , 432 : 904 – 906 .
  • Neal , P. J. and Roberts , G. O. 2004 . “Statistical Inference and Model Selection for the 1861 Hagelloch Measles Epidemic,” . Biostatistics , 5 : 249 – 261 .
  • Nishiura , H. 2007 . “Time Variations in the Transmissibility of Pandemic Influenza in Prussia, Germany, From 1918–19,” . Theoretical Biology and Medical Modelling , 4 : 20
  • O’Neill , P. and Roberts , G. O. 1999 . “Bayesian Inference for Partially Observed Stochastic Epidemics,” . Journal of the Royal Statistical Society, Series A , 162 : 121 – 129 .
  • Petzold , L. 1983 . “Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations,” . SIAM Journal on Scientific and Statistical Computing , 4 : 136 – 148 .
  • Pitt , M. and Shephard , N. 1999 . “Filtering via Simulation: Auxiliary Particle Filters,” . Journal of the American Statistical Association , 94 : 590 – 599 .
  • Polson , N. , Stroud , J. and Muller , P. 2008 . “Practical Filtering With Sequential Parameter Learning,” . Journal of the Royal Statistical Society, Series B , 70 : 413 – 428 .
  • Ristic , B. , Arulampalam , S. and Gordon , N. 2004 . Beyond the Kalman Filter: Particle Filters for Tracking Applications , Boston , MA : Artech House .
  • Rodeiro , C. V. and Lawson , A. 2006 . “Online Updating of Space-Time Disease Surveillance Models via Particle Filters,” . Statistical Methods in Medical Research , 15 : 1 – 22 .
  • Storvik , G. 2002 . “Particle Filters in State Space Models With the Presence of Unknown Static Parameters,” . IEEE Transactions on Signal Processing , 50 : 281 – 289 .
  • Tuite , A. R. , Greer , A. L. , Whelan , M. , Winter , A.-L. , Lee , B. , Yan , P. , Wu , J. , Moghadas , S. , Buckeridge , D. , Pourbohloul , B. and Fisman , D. N. 2010 . “Estimated Epidemiological Parameters and Morbidity Associated With Pandemic H1N1 Influenza,” . Canadian Medical Association Journal , 182 : 131 – 136 .
  • U.S. Census Bureau. 2009 . Annual Estimates of the Resident Population for the United States, Regions, States, and Puerto Rico: April 1, 2000 to July 1, 2009 , Washington, DC : Population Division .
  • Vaillant , L. , La Ruche , G. , Tarantola , A. and Barboza , P. 2009 . “Epidemiology of Fatal Cases Associated With Pandemic H1N1 Influenza 2009,” . Eurosurveillance , 14 : 1 – 6 .
  • Vynnycky , E. and Edmunds , W. J. 2008 . “Analyses of the 1957 (Asian) Influenza Pandemic in the United Kingdom and the Impact of School Closures,” . Epidemiology & Infection , 136 : 166 – 179 .
  • Webby , R. J. and Webster , R. G. 2003 . “Are We Ready for Pandemic Influenza?,” . Science , 302 : 1519 – 1522 .
  • West , M. and Harrison , J. 1997 . Bayesian Forecasting and Dynamic Models (2nd ed.) , New York : Springer-Verlag .
  • Yang , Y. , Sugimoto , J. , Halloran , M. , Basta , N. , Chao , D. , Matrajt , L. , Potter , G. , Kenah , E. and Longini , I. 2009 . “The Transmissibility and Control of Pandemic Influenza a (H1N1) Virus,” . Science Express , : 729 – 733 .

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