library.bib

@Manual{EricBrown2020,
  title = {data2019nCoV: Data on the COVID-19 Outbreak},
  author = {Eric Brown},
  year = {2020},
  note = {R package version 0.40.1}
  }

@webpage{WorldHealthOrganization:sitrep,
  author = {{World Health Organization}},
  title = {Coronavirus disease (COVID-2019) situation reports},
  url = {https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports}
}


@Article{NCoVUtils,
  title = {NCoVUtils: Utility functions for the 2019-NCoV outbreak},
  author = {Sam Abbott and Joel Hellewell and James D. Munday and Sebastian Funk},
  journal = {-},
  year = {2020},
  volume = {-},
  number = {-},
  pages = {-},
  doi = {10.5281/zenodo.3635417}
  }
  
@webpage{italydata,
  author = {{Dipartimento della Protezione Civile}},
  title = {Dati COVID-19 Italia},
  url = {https://github.com/pcm-dpc/COVID-19}
}


  @Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2019},
    url = {https://www.R-project.org/},
  }

@Manual{EpiEstim,
    title = {EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves},
    author = {Anne Cori},
    year = {2019},
    note = {R package version 2.2-1},
    url = {https://CRAN.R-project.org/package=EpiEstim}
  }

@article{wallinga2004,
    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},
    volume = {160},
    number = {6},
    pages = {509-516},
    year = {2004},
    month = {09},
    issn = {0002-9262},
    doi = {10.1093/aje/kwh255},
    url = {https://doi.org/10.1093/aje/kwh255},
    eprint = {https://academic.oup.com/aje/article-pdf/160/6/509/179728/kwh255.pdf}
}

@article{cori2013,
    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},
    volume = {178},
    number = {9},
    pages = {1505-1512},
    year = {2013},
    month = {09},
    issn = {0002-9262},
    doi = {10.1093/aje/kwt133},
    url = {https://doi.org/10.1093/aje/kwt133},
    eprint = {https://academic.oup.com/aje/article-pdf/178/9/1505/17341195/kwt133.pdf}
}


@Misc{rstan,
    title = {RStan: the R interface to Stan},
    author = {{Stan Development Team}},
    note = {R package version 2.19.3},
    year = {2020},
    url = {http://mc-stan.org/}
  }
  
@article {Nishiura2020.02.03.20019497,
	author = "Nishiura, Hiroshi and Linton, Natalie M and Akhmetzhanov, Andrei R.",
	title = {Serial interval of novel coronavirus (2019-nCoV) infections},
	elocation-id = {2020.02.03.20019497},
	year = {2020},
	doi = {10.1101/2020.02.03.20019497},
	publisher = {Cold Spring Harbor Laboratory Press},
	URL = {https://www.medrxiv.org/content/early/2020/02/17/2020.02.03.20019497},
	eprint = {https://www.medrxiv.org/content/early/2020/02/17/2020.02.03.20019497.full.pdf},
	journal = {medRxiv}
}

@webpage{Imai:webreport3,
author = "Imai, Natsuki and Cori, Anne and Dorigatti, IIaria and Baguellin, Marc and Donnelly, Christl A and Riley, Steven and Ferguson, Neil M",
title = {Report 3: Transmissibility of 2019-nCoV},
url = {https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-2019-nCoV-transmissibility.pdf}
}


@webpage{kraemer2020epidemiological,
  author = "Xu, Bo and Gutierrez, Bernardo and Hill, Sarah and Scarpino, Samuel and Loskill, Alyssa and Wu, Jessie and Sewalk, Kara and Mekaru, Sumiko and Zarebski, Alexander and Pybus, Oliver and Pigott, David and Kraemer, Moritz",
  title = "Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data",
  url = {http://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337}
}



@article{THOMPSON2019100356,
  title = "Improved inference of time-varying reproduction numbers during infectious disease outbreaks",
  journal = "Epidemics",
  volume = "29",
  pages = "100356",
  year = "2019",
  issn = "1755-4365",
  doi = "https://doi.org/10.1016/j.epidem.2019.100356",
  url = "http://www.sciencedirect.com/science/article/pii/S1755436519300350",
  author = "R.N. Thompson and J.E. Stockwin and R.D. van Gaalen and J.A. Polonsky and Z.N. Kamvar and P.A. Demarsh and E. Dahlqwis and S. Li and E. Miguel and T. Jombart and J. Lessler and S. Cauchemez and A. Cori"
}

@article{Park2019,
title = "A practical generation-interval-based approach to inferring the strength of epidemics from their speed",
journal = "Epidemics",
volume = "27",
pages = "12 - 18",
year = "2019",
issn = "1755-4365",
doi = "https://doi.org/10.1016/j.epidem.2018.12.002",
url = "http://www.sciencedirect.com/science/article/pii/S1755436518300847",
author = "Sang Woo Park and David Champredon and Joshua S. Weitz and Jonathan Dushoff"}


@article{Thompson:2020bc,
  title = "2019-20 Wuhan coronavirus outbreak: Intense surveillance is vital for preventing sustained transmission in new locations",
  author = "R.N. Thompson",
  journal = "bioRxiv",
  year = "2020",
  pages = "1 - 14"
}


@techreport{gehrcke_covid-19_2020,
    address = {Germany},
    type = {Github {Repository}},
    title = {COVID-19 case numbers in Germany by state, over time},
    copyright = {MIT License},
    shorttitle = {{COVID}-19 case numbers in {Germany}},
    url = {https://github.com/jgehrcke/covid-19-germany-gae},
    language = {German},
    author = {Gehrcke, Jan-Philip},
    year = {2020}
}

@techreport{jhu_2019_2020,
    title = {2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository},
    copyright = {Copyright 2020 Johns Hopkins University},
    url = {https://github.com/CSSEGISandData/COVID-19},
    language = {English},
    institution = {Johns Hopkins CSSE},
    year = {2020}
}

@techreport{doughty_visualisation_2020,
    type = {Github Repository},
    title = {Visualisation of COVID-19 official UK case data},
    url = {https://github.com/emmadoughty/Daily_COVID-19/},
    language = {English},
    author = {Doughty, Emma},
    year = {2020}
}

@techreport{ecdc_data,
    title = {Download Today's Data on the Geographic Distribution of COVID-19 Cases Worldwide.},
    url = {www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide},
    language = {English},
    author = {European Centre for Disease Prevention and Control},
    year = {2020}
}

@article{Vehtari2016,
archivePrefix = {arXiv},
arxivId = {arXiv:1507.04544v4},
author = {Vehtari, Aki and Gelman, Andrew and Gabry, Jonah},
doi = {10.1007/s11222-016-9696-4},
eprint = {arXiv:1507.04544v4},
issn = {15731375},
journal = {Stat. Comput.},
number = {September},
pages = {1--20},
title = {Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC},
year = {2016}
}

@article{gneiting_strictly_2007,
	title = {Strictly Proper Scoring Rules, Prediction, and Estimation},
	volume = {102},
	issn = {0162-1459, 1537-274X},
	url = {http://www.tandfonline.com/doi/abs/10.1198/016214506000001437},
	doi = {10.1198/016214506000001437},
	language = {en},
	number = {477},
	urldate = {2020-03-22},
	journal = {Journal of the American Statistical Association},
	author = {Gneiting, Tilmann and Raftery, Adrian E},
	month = mar,
	year = {2007},
	pages = {359--378}
}

@article{NOUVELLET201829,
title = "A simple approach to measure transmissibility and forecast incidence",
journal = "Epidemics",
volume = "22",
pages = "29 - 35",
year = "2018",
note = "The RAPIDD Ebola Forecasting Challenge",
issn = "1755-4365",
doi = "https://doi.org/10.1016/j.epidem.2017.02.012",
url = "http://www.sciencedirect.com/science/article/pii/S1755436517300245",
author = "Pierre Nouvellet and Anne Cori and Tini Garske and Isobel M. Blake and Ilaria Dorigatti and Wes Hinsley and Thibaut Jombart and Harriet L. Mills and Gemma Nedjati-Gilani and Maria D. Van Kerkhove and Christophe Fraser and Christl A. Donnelly and Neil M. Ferguson and Steven Riley"}


@article{jordan_evaluating_2019,
	title = {Evaluating Probabilistic Forecasts with scoringRules},
	volume = {90},
	issn = {1548-7660},
	url = {http://www.jstatsoft.org/v90/i12/},
	doi = {10.18637/jss.v090.i12},
	language = {en},
	number = {12},
	urldate = {2020-03-07},
	journal = {Journal of Statistical Software},
	author = {Jordan, Alexander and Krüger, Fabian and Lerch, Sebastian},
	year = {2019}
}

@article{10.7326/M20-0504,
    author = {Lauer, Stephen A. and Grantz, Kyra H. and Bi, Qifang and Jones, Forrest K. and Zheng, Qulu and Meredith, Hannah R. and Azman, Andrew S. and Reich, Nicholas G. and Lessler, Justin},
    title = "The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application",
    journal = {Annals of Internal Medicine},
    year = {2020},
    month = {03},
    issn = {0003-4819},
    doi = {10.7326/M20-0504},
    url = {https://doi.org/10.7326/M20-0504},
    eprint = {https://annals.org/acp/content\_public/journal/aim/0/aime202005050-m200504.pdf},
}