bibliography.bib

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@Article{Ma-Earn:2006,
  Title                    = {Generality of the Final Size Formula for an Epidemic of a Newly Invading Infectious Disease},
  Author                   = {Ma, Junling and Earn, DavidJ.D.},
  Journal                  = {Bull. Math. Biol.},
  Year                     = {2006},
  Number                   = {3},
  Pages                    = {679-702--},
  Volume                   = {68},
  Booktitle                = {Bulletin of Mathematical Biology},
  ISSN                     = {0092-8240},
  Keywords                 = {Epidemic models, Final size, Arbitrary stage durations, Integro-differential equations 1991 MSC:92D30},
  Publisher                = {Springer-Verlag},
  Url                      = {http://dx.doi.org/10.1007/s11538-005-9047-7}
}

@Article{Miller:2012,
  author  = {Miller, Joel C.},
  title   = {A Note on the Derivation of Epidemic Final Sizes},
  journal = {Bull. Math. Biol.},
  year    = {2012},
  volume  = {74},
  number  = {9},
  pages   = {2125--2141},
  month   = sep,
  issn    = {1522-9602},
  url     = {https://doi.org/10.1007/s11538-012-9749-6},
}

@Article{Orbann-etal:2017,
  author   = {Orbann, Carolyn and Sattenspiel, Lisa and Miller, Erin and Dimka, Jessica},
  title    = {Defining epidemics in computer simulation models: How do definitions influence conclusions?},
  journal  = {Epidemics},
  year     = {2017},
  volume   = {19},
  pages    = {24--32},
  month    = jun,
  issn     = {1755-4365},
  keywords = {Infectious disease modeling, Agent-based simulation, Infectious disease history, Epidemic criteria},
  url      = {http://www.sciencedirect.com/science/article/pii/S1755436516300627},
}

@Article{Vega-etal:2015,
  author        = {Vega, Tomás and Lozano, José E. and Meerhoff, Tamara and Snacken, René and Beauté, Julien and Jorgensen, Pernille and Ortiz de Lejarazu, Raúl and Domegan, Lisa and Mossong, Joël and Nielsen, Jens},
  title         = {Influenza surveillance in Europe: comparing intensity levels calculated using the moving epidemic method},
  journal       = {Influenza and Other Respiratory Viruses},
  year          = {2015},
  volume        = {9},
  number        = {5},
  pages         = {234--246},
  issn          = {1750-2659},
  publisher     = {Wiley Online Library},
}

@Article{Vega-etal:2013,
  author        = {Vega, Tomás and Lozano, Jose Eugenio and Meerhoff, Tamara and Snacken, René and Mott, Joshua and Ortiz de Lejarazu, Raul and Nunes, Baltazar},
  title         = {Influenza surveillance in Europe: establishing epidemic thresholds by the moving epidemic method},
  journal       = {Influenza and Other Respiratory Viruses},
  year          = {2013},
  volume        = {7},
  number        = {4},
  pages         = {546--558},
  issn          = {1750-2659},
  publisher     = {Wiley Online Library},
}

@Article{Groendyke-Welch:2018,
  author        = {Groendyke, Chris and Welch, David},
  title         = {epinet: An R Package to Analyze Epidemics Spread Across Contact Networks},
  journal       = {J. Stat. Softw.},
  year          = {2018},
  volume        = {83},
  number        = {11},
  pages         = {1--22},
  issn          = {1548-7660},
  publisher     = {JOURNAL STATISTICAL SOFTWARE UCLA DEPT STATISTICS, 8130 MATH SCIENCES BLDG, BOX 951554, LOS ANGELES, CA 90095-1554 USA},
}

@Article{Obadia-etal:2012,
  author  = {Obadia, Thomas and Haneef, Romana and Boelle, Pierre-Yves},
  title   = {The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks},
  journal = {BMC Med. Inform. Decis. Mak.},
  year    = {2012},
  volume  = {12},
  number  = {1},
  pages   = {147--},
  issn    = {1472-6947},
  url     = {http://www.biomedcentral.com/1472-6947/12/147},
}

@Article{Mossong-etal:2008,
  author    = {Mossong, Joël and Hens, Niel and Jit, Mark and Beutels, Philippe and Auranen, Kari and Mikolajczyk, Rafael and Massari, Marco and Salmaso, Stefania and Tomba, Gianpaolo Scalia and Wallinga, Jacco and Heijne, Janneke and Sadkowska-Todys, Malgorzata and Rosinska, Magdalena and Edmunds, W. John},
  title     = {Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases},
  journal   = {PLoS Med},
  year      = {2008},
  volume    = {5},
  number    = {3},
  pages     = {e74--},
  month     = mar,
  doi       = {10.1371/journal.pmed.0050074},
  publisher = {Public Library of Science},
  url       = {http://dx.doi.org/10.1371%2Fjournal.pmed.0050074},
}

@Article{Squires-etal:2012,
  author    = {Squires, R. Burke and Noronha, Jyothi and Hunt, Victoria and García-Sastre, Adolfo and Macken, Catherine and Baumgarth, Nicole and Suarez, David and Pickett, Brett E. and Zhang, Yun and Larsen, Christopher N. and Ramsey, Alvin and Zhou, Liwei and Zaremba, Sam and Kumar, Sanjeev and Deitrich, Jon and Klem, Edward and Scheuermann, Richard H.},
  title     = {Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance},
  journal   = {Influenza and Other Respiratory Viruses},
  year      = {2012},
  volume    = {6},
  number    = {6},
  pages     = {404--416},
  month     = nov,
  issn      = {1750-2659},
  keywords  = {Bioinformatics, epitope, influenza virus, integrated, surveillance},
  publisher = {Blackwell Publishing Ltd},
  url       = {http://dx.doi.org/10.1111/j.1750-2659.2011.00331.x},
}

@Article{Panhuis-etal:2013,
  author    = {van Panhuis, Willem G. and Grefenstette, John and Jung, Su Yon and Chok, Nian Shong and Cross, Anne and Eng, Heather and Lee, Bruce Y. and Zadorozhny, Vladimir and Brown, Shawn and Cummings, Derek and Burke, Donald S.},
  title     = {Contagious Diseases in the United States from 1888 to the Present},
  journal   = {New England Journal of Medicine},
  year      = {2013},
  volume    = {369},
  number    = {22},
  pages     = {2152--2158},
  month     = nov,
  issn      = {0028-4793},
  booktitle = {New England Journal of Medicine},
  comment   = {doi: 10.1056/NEJMms1215400},
  doi       = {10.1056/NEJMms1215400},
  publisher = {Massachusetts Medical Society},
  url       = {http://dx.doi.org/10.1056/NEJMms1215400},
}

@Article{Lazer-etal:2014,
  author    = {Lazer, David and Kennedy, Ryan and King, Gary and Vespignani, Alessandro},
  title     = {The Parable of Google Flu: Traps in Big Data Analysis},
  journal   = {Science},
  year      = {2014},
  volume    = {343},
  number    = {6176},
  pages     = {1203--1205},
  month     = mar,
  comment   = {10.1126/science.1248506},
  url       = {http://www.sciencemag.org/content/343/6176/1203.short},
}

@Article{Ginsberg-etal:2009,
  author    = {Ginsberg, Jeremy and Mohebbi, Matthew H. and Patel, Rajan S. and Brammer, Lynnette and Smolinski, Mark S. and Brilliant, Larry},
  title     = {Detecting influenza epidemics using search engine query data},
  journal   = {Nature},
  year      = {2009},
  volume    = {457},
  number    = {7232},
  pages     = {1012--1014},
  month     = feb,
  issn      = {0028-0836},
  comment   = {10.1038/nature07634},
  publisher = {Macmillan Publishers Limited. All rights reserved},
  url       = {http://dx.doi.org/10.1038/nature07634},
}

@Article{Butler:2013,
  author    = {Declan Butler},
  title     = {When Google got flu wrong},
  journal   = {Nature},
  year      = {2013},
  volume    = {494},
  number    = {7436},
  pages     = {155--156},
  month     = {February 13},
  url       = {http://www.nature.com/news/when-google-got-flu-wrong-1.12413},
}

@Article{Freifeld-etal:2008,
  author  = {Freifeld, Clark C. and Mandl, Kenneth D. and Reis, Ben Y. and Brownstein, John S.},
  title   = {HealthMap: Global Infectious Disease Monitoring through Automated Classification and Visualization of Internet Media Reports},
  journal = {Journal of the American Medical Informatics Association},
  year    = {2008},
  volume  = {15},
  number  = {2},
  pages   = {150--157},
  month   = mar,
  url     = {http://jamia.oxfordjournals.org/content/15/2/150.abstract},
}

@Article{Wallinga-Teunis:2004,
  author  = {Wallinga, Jacco and Teunis, Peter},
  title   = {Different Epidemic Curves for Severe Acute Respiratory Syndrome Reveal Similar Impacts of Control Measures},
  journal = {American Journal of Epidemiology},
  year    = {2004},
  volume  = {160},
  number  = {6},
  pages   = {509--516},
  month   = sep,
  comment = {10.1093/aje/kwh255},
  url     = {http://aje.oxfordjournals.org/content/160/6/509.abstract},
}

@Book{Porta:2014,
  title         = {A dictionary of epidemiology},
  publisher     = {Oxford university press},
  year          = {2014},
  author        = {Porta, Miquel},
  issn          = {0199390053},
}

@Article{Mishra-etal:2010,
  author  = {Mishra, Sharmistha and Fisman, David N. and Boily, Marie-Claude},
  title   = {The ABC of terms used in mathematical models of infectious diseases},
  journal = {Journal of Epidemiology and Community Health},
  year    = {2010},
  month   = oct,
  comment = {10.1136/jech.2009.097113},
  url     = {http://jech.bmj.com/content/early/2010/10/21/jech.2009.097113.abstract},
}

@Article{Milwid-etal:2016,
  author  = {Milwid, Rachael and Steriu, Andreea and Arino, Julien and Heffernan, Jane and Hyder, Ayaz and Schanzer, Dena and Gardner, Emma and Haworth-Brockman, Margaret and Isfeld-Kiely, Harpa and Langley, Joanne M. and Moghadas, Seyed M.},
  title   = {Toward Standardizing a Lexicon of Infectious Disease Modeling Terms},
  journal = {Frontiers in Public Health},
  year    = {2016},
  volume  = {4},
  pages   = {213},
  issn    = {2296-2565},
  url     = {http://journal.frontiersin.org/article/10.3389/fpubh.2016.00213},
}

@Article{Fraser:2007,
  author    = {Fraser, Christophe},
  title     = {Estimating Individual and Household Reproduction Numbers in an Emerging Epidemic},
  journal   = {PLoS ONE},
  year      = {2007},
  volume    = {2},
  number    = {8},
  pages     = {e758--},
  month     = aug,
  doi       = {10.1371/journal.pone.0000758},
  publisher = {Public Library of Science},
  url       = {http://dx.plos.org/10.1371/journal.pone.0000758},
}

@Article{Fine:2003,
  author  = {Fine, Paul E. M.},
  title   = {The Interval between Successive Cases of an Infectious Disease},
  journal = {American Journal of Epidemiology},
  year    = {2003},
  volume  = {158},
  number  = {11},
  pages   = {1039--1047},
  month   = dec,
  comment = {10.1093/aje/kwg251},
  url     = {http://aje.oxfordjournals.org/content/158/11/1039.abstract},
}

@Article{Cori-etal:2013,
  author  = {Cori, Anne and Ferguson, Neil M. and Fraser, Christophe and Cauchemez, Simon},
  title   = {A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics},
  journal = {American Journal of Epidemiology},
  year    = {2013},
  volume  = {178},
  number  = {9},
  pages   = {1505--1512},
  month   = nov,
  comment = {10.1093/aje/kwt133},
  url     = {http://aje.oxfordjournals.org/content/178/9/1505.abstract},
}

@Article{Cauchemez-etal:2006,
  author    = {Cauchemez, Simon and Boëlle, Pierre-Yves and Donnelly, Christl A. and Ferguson, Neil M. and Thomas, Guy and Leung, Gabriel M. and Hedley, Anthony J. and Anderson, Roy M. and Valleron, Alain-Jacques},
  title     = {Real-time Estimates in Early Detection of SARS},
  journal   = {Emerging Infectious Diseases},
  year      = {2006},
  volume    = {12},
  number    = {1},
  pages     = {110},
  issn      = {1080-6059},
  booktitle = {Emerging Infectious Disease journal},
  keywords  = {communicable diseases, disease outbreaks, emerging, epidemiologic methods, Hong Kong, population surveillance, reproduction number, research, Severe acute respiratory syndrome},
  url       = {http://wwwnc.cdc.gov/eid/article/12/1/05-0593},
}

@Article{Altman-etal:2005,
  author        = {Altman, Douglas G. and Armitage, P. and Colton, T.},
  title         = {Encyclopedia of biostatistics},
  journal       = {Encyclopedia of biostatistics},
  year          = {2005},
  publisher     = {John Wiley Chichester},
}

@Article{Finkenstaedt-Grenfell:2000,
  author    = {Finkenstädt, B. F. and Grenfell, B. T.},
  title     = {Time series modelling of childhood diseases: a dynamical systems approach},
  journal   = {Journal of the Royal Statistical Society: Series C (Applied Statistics)},
  year      = {2000},
  volume    = {49},
  number    = {2},
  pages     = {187--205},
  month     = jan,
  issn      = {1467-9876},
  keywords  = {Cyclicity and seasonality in measles populations, Dynamical models in epidemics, England and Wales measles data, Population dynamics of childhood diseases, Susceptible-exposed-infected-recovered model},
  publisher = {Blackwell Publishers Ltd.},
  url       = {http://dx.doi.org/10.1111/1467-9876.00187},
}

@Book{Keeling-Rohani:2008,
  title         = {Modeling infectious diseases in humans and animals},
  publisher     = {Princeton University Press},
  year          = {2008},
  author        = {Keeling, Matt J. and Rohani, Pejman},
  issn          = {0691116172},
}

@Manual{ECDC:2012,
  title     = {Field Epidemiology Manual},
  author    = {{European Centre for Disease Prevention and Control (ECDC)}},
  year      = {2012},
  owner     = {Tony Tsai},
  timestamp = {2021.03.05},
  url       = {https://wiki.ecdc.europa.eu/fem/Pages/Incubation\%20period,\%20Latent\%20period\%20and\%20Generation\%20time..aspx},
}

@Comment{jabref-meta: databaseType:bibtex;}