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@Article{funk2018real,
author = {Funk, Sebastian and Camacho, Anton and Kucharski, Adam J.
and Eggo, Rosalind M. and Edmunds, W. John},
title = {Real-time forecasting of infectious disease dynamics with a
stochastic semi-mechanistic model},
journal = {Epidemics},
year = 2018,
volume = 22,
month = mar,
pages = {56–61},
issn = {1755-4365},
doi = {10.1016/j.epidem.2016.11.003},
url = {http://dx.doi.org/10.1016/j.epidem.2016.11.003},
publisher = {Elsevier BV}
}
@Article{czado2009,
author = {Czado, Claudia and Gneiting, Tilmann and Held, Leonhard},
title = {Predictive Model Assessment for Count Data},
journal = {Biometrics},
year = 2009,
volume = 65,
number = 4,
month = nov,
pages = {1254–1261},
issn = {1541-0420},
doi = {10.1111/j.1541-0420.2009.01191.x},
url = {http://dx.doi.org/10.1111/j.1541-0420.2009.01191.x},
publisher = {Oxford University Press (OUP)}
}
@Article{gneiting2007,
author = {Gneiting, Tilmann and Raftery, Adrian E},
title = {Strictly Proper Scoring Rules, Prediction, and Estimation},
journal = {Journal of the American Statistical Association},
year = 2007,
volume = 102,
number = 477,
month = mar,
pages = {359–378},
issn = {1537-274X},
doi = {10.1198/016214506000001437},
url = {http://dx.doi.org/10.1198/016214506000001437},
publisher = {Informa UK Limited},
note = {PDF available at https://sites.stat.washington.edu/raftery/Research/PDF/Gneiting2007jasa.pdf}
}
@Article{bosse2023scorin,
author = {Bosse, Nikos I. and Abbott, Sam and Cori, Anne and van
Leeuwen, Edwin and Bracher, Johannes and Funk, Sebastian},
title = {Scoring epidemiological forecasts on transformed scales},
journal = {PLOS Computational Biology},
year = 2023,
editor = {McCaw, James M},
volume = 19,
number = 8,
month = aug,
pages = {e1011393},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1011393},
url = {http://dx.doi.org/10.1371/journal.pcbi.1011393},
publisher = {Public Library of Science (PLoS)}
}
@Article{czado2009,
author = {Czado, Claudia and Gneiting, Tilmann and Held, Leonhard},
title = {Predictive Model Assessment for Count Data},
journal = {Biometrics},
year = 2009,
volume = 65,
number = 4,
month = nov,
pages = {1254–1261},
issn = {1541-0420},
doi = {10.1111/j.1541-0420.2009.01191.x},
url = {http://dx.doi.org/10.1111/j.1541-0420.2009.01191.x},
publisher = {Oxford University Press (OUP)}
}
@Article{Reich2022-jo,
title = "Collaborative hubs: Making the most of predictive epidemic
modeling",
author = "Reich, Nicholas G and Lessler, Justin and Funk, Sebastian and
Viboud, Cecile and Vespignani, Alessandro and Tibshirani, Ryan J
and Shea, Katriona and Schienle, Melanie and Runge, Michael C and
Rosenfeld, Roni and Ray, Evan L and Niehus, Rene and Johnson,
Helen C and Johansson, Michael A and Hochheiser, Harry and
Gardner, Lauren and Bracher, Johannes and Borchering, Rebecca K
and Biggerstaff, Matthew",
journal = "Am. J. Public Health",
publisher = "American Public Health Association",
pages = "e1--e4",
month = apr,
year = 2022,
doi = "10.2105/ajph.2022.306831",
issn = "0090-0036,1541-0048",
language = "en"
}
@misc{abbottEpiNow2EstimateRealtime2025,
title = {{{EpiNow2}}: {{Estimate}} Real-Time Case Counts and Time-Varying Epidemiological Parameters},
author = {Abbott, Sam and Hellewell, Joel and Sherratt, Katharine and Gostic, Katelyn and Hickson, Joe and Badr, Hamada S. and DeWitt, Michael and Azam, James M. and {EpiForecasts} and Funk, Sebastian},
year = {2025}
}
@article{amaralPostprocessingWeightedCombination2025,
title = {Post-Processing and Weighted Combination of Infectious Disease Nowcasts},
author = {Amaral, Andr{\'e} Victor Ribeiro and Wolffram, Daniel and Moraga, Paula and Bracher, Johannes},
year = {2025},
month = mar,
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012836},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1012836},
pmcid = {PMC11902281},
pmid = {40029911}
}
@article{asherForecastingEbolaRegression2018,
title = {Forecasting {{Ebola}} with a Regression Transmission Model},
author = {Asher, Jason},
year = {2018},
month = mar,
journal = {Epidemics},
volume = {22},
pages = {50--55},
issn = {1878-0067},
doi = {10.1016/j.epidem.2017.02.009},
pmid = {28342787}
}
@misc{bhattSemiMechanisticBayesianModeling2020,
title = {Semi-{{Mechanistic Bayesian Modeling}} of {{COVID-19}} with {{Renewal Processes}}},
author = {Bhatt, Samir and Ferguson, Neil and Flaxman, Seth and Gandy, Axel and Mishra, Swapnil and Scott, James A.},
year = {2020},
month = dec,
number = {arXiv:2012.00394},
eprint = {2012.00394},
primaryclass = {stat},
publisher = {arXiv},
doi = {10.48550/arXiv.2012.00394},
archiveprefix = {arXiv}
}
@article{bosseScoringEpidemiologicalForecasts2023,
title = {Scoring Epidemiological Forecasts on Transformed Scales},
author = {Bosse, Nikos I. and Abbott, Sam and Cori, Anne and van Leeuwen, Edwin and Bracher, Johannes and Funk, Sebastian},
year = {2023},
month = aug,
journal = {PLOS Computational Biology},
volume = {19},
number = {8},
pages = {e1011393},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1011393}
}
@article{bracherEvaluatingEpidemicForecasts2021,
title = {Evaluating Epidemic Forecasts in an Interval Format},
author = {Bracher, Johannes and Ray, Evan L. and Gneiting, Tilmann and Reich, Nicholas G.},
year = {2021},
month = feb,
journal = {PLOS Computational Biology},
volume = {17},
number = {2},
pages = {e1008618},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1008618}
}
@article{brockhausWhyAreDifferent2023,
title = {Why Are Different Estimates of the Effective Reproductive Number so Different? {{A}} Case Study on {{COVID-19}} in {{Germany}}},
author = {Brockhaus, Elisabeth K. and Wolffram, Daniel and Stadler, Tanja and Osthege, Michael and Mitra, Tanmay and Littek, Jonas M. and Krymova, Ekaterina and Klesen, Anna J. and Huisman, Jana S. and Heyder, Stefan and Helleckes, Laura M. and an der Heiden, Matthias and Funk, Sebastian and Abbott, Sam and Bracher, Johannes},
year = {2023},
month = nov,
journal = {PLOS Computational Biology},
volume = {19},
number = {11},
pages = {e1011653},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1011653}
}
@article{burknerBrmsPackageBayesian2017,
title = {Brms: {{An R Package}} for {{Bayesian Multilevel Models Using Stan}}},
author = {B{\"u}rkner, Paul-Christian},
year = {2017},
month = aug,
journal = {Journal of Statistical Software},
volume = {80},
pages = {1--28},
issn = {1548-7660},
doi = {10.18637/jss.v080.i01},
copyright = {Copyright (c) 2017 Paul-Christian B{\"u}rkner}
}
@misc{CDCgovWastewaterinformedcovidforecasting2025,
title = {{{CDCgov}}/Wastewater-Informed-Covid-Forecasting},
year = {2025},
month = jun,
copyright = {Apache-2.0},
howpublished = {Centers for Disease Control and Prevention}
}
@article{charnigaBestPracticesEstimating2024,
title = {Best Practices for Estimating and Reporting Epidemiological Delay Distributions of Infectious Diseases},
author = {Charniga, Kelly and Park, Sang Woo and Akhmetzhanov, Andrei R. and Cori, Anne and Dushoff, Jonathan and Funk, Sebastian and Gostic, Katelyn M. and Linton, Natalie M. and Lison, Adrian and Overton, Christopher E. and Pulliam, Juliet R. C. and Ward, Thomas and Cauchemez, Simon and Abbott, Sam},
year = {2024},
month = oct,
journal = {PLOS Computational Biology},
volume = {20},
number = {10},
pages = {e1012520},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1012520}
}
@article{coriNewFrameworkSoftware2013,
title = {A {{New Framework}} and {{Software}} to {{Estimate Time-Varying Reproduction Numbers During Epidemics}}},
author = {Cori, Anne and Ferguson, Neil M. and Fraser, Christophe and Cauchemez, Simon},
year = {2013},
month = nov,
journal = {American Journal of Epidemiology},
volume = {178},
number = {9},
pages = {1505--1512},
issn = {0002-9262},
doi = {10.1093/aje/kwt133}
}
@article{czadoPredictiveModelAssessment2009,
title = {Predictive {{Model Assessment}} for {{Count Data}}},
author = {Czado, Claudia and Gneiting, Tilmann and Held, Leonhard},
year = {2009},
month = dec,
journal = {Biometrics},
volume = {65},
number = {4},
pages = {1254--1261},
issn = {0006-341X},
doi = {10.1111/j.1541-0420.2009.01191.x}
}
@article{delignette-mullerFitdistrplusPackageFitting2015,
title = {Fitdistrplus: {{An R Package}} for {{Fitting Distributions}}},
author = {{Delignette-Muller}, Marie Laure and Dutang, Christophe},
year = {2015},
month = mar,
journal = {Journal of Statistical Software},
volume = {64},
pages = {1--34},
issn = {1548-7660},
doi = {10.18637/jss.v064.i04},
copyright = {Copyright (c) 2013 Marie Laure Delignette-Muller, Christophe Dutang}
}
@article{funkAssessingPerformanceRealtime2019,
title = {Assessing the Performance of Real-Time Epidemic Forecasts: {{A}} Case Study of {{Ebola}} in the {{Western Area}} Region of {{Sierra Leone}}, 2014-15},
author = {Funk, Sebastian and Camacho, Anton and Kucharski, Adam J. and Lowe, Rachel and Eggo, Rosalind M. and Edmunds, W. John},
year = {2019},
month = feb,
journal = {PLOS Computational Biology},
volume = {15},
number = {2},
pages = {e1006785},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1006785}
}
@article{funkRealtimeForecastingInfectious2018,
title = {Real-Time Forecasting of Infectious Disease Dynamics with a Stochastic Semi-Mechanistic Model},
author = {Funk, Sebastian and Camacho, Anton and Kucharski, Adam J. and Eggo, Rosalind M. and Edmunds, W. John},
year = {2018},
month = mar,
journal = {Epidemics},
series = {The {{RAPIDD Ebola Forecasting Challenge}}},
volume = {22},
pages = {56--61},
issn = {1755-4365},
doi = {10.1016/j.epidem.2016.11.003}
}
@article{gneitingStrictlyProperScoring2007,
title = {Strictly {{Proper Scoring Rules}}, {{Prediction}}, and {{Estimation}}},
author = {Gneiting, Tilmann and Raftery, Adrian E},
year = {2007},
month = mar,
journal = {Journal of the American Statistical Association},
volume = {102},
number = {477},
pages = {359--378},
issn = {0162-1459, 1537-274X},
doi = {10.1198/016214506000001437}
}
@article{gosticPracticalConsiderationsMeasuring2020,
title = {Practical Considerations for Measuring the Effective Reproductive Number, {{Rt}}},
author = {Gostic, Katelyn M. and McGough, Lauren and Baskerville, Edward B. and Abbott, Sam and Joshi, Keya and Tedijanto, Christine and Kahn, Rebecca and Niehus, Rene and Hay, James A. and Salazar, Pablo M. De and Hellewell, Joel and Meakin, Sophie and Munday, James D. and Bosse, Nikos I. and Sherrat, Katharine and Thompson, Robin N. and White, Laura F. and Huisman, Jana S. and Scire, J{\'e}r{\'e}mie and Bonhoeffer, Sebastian and Stadler, Tanja and Wallinga, Jacco and Funk, Sebastian and Lipsitch, Marc and Cobey, Sarah},
year = {2020},
month = dec,
journal = {PLOS Computational Biology},
volume = {16},
number = {12},
pages = {e1008409},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1008409}
}
@misc{hadleyVisualPreferencesCommunicating2025,
title = {Visual Preferences for Communicating Modelling: A Global Analysis of {{COVID-19}} Policy and Decision Makers},
author = {Hadley, Liza and Rich, Caylyn and Tasker, Alex and Restif, Olivier and Funk, Sebastian},
year = {2025},
month = jan,
pages = {2024.11.05.24316774},
publisher = {medRxiv},
doi = {10.1101/2024.11.05.24316774},
archiveprefix = {medRxiv},
copyright = {{\copyright} 2025, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}
}
@article{heldProbabilisticForecastingInfectious2017,
title = {Probabilistic Forecasting in Infectious Disease Epidemiology: The 13th {{Armitage}} Lecture},
author = {Held, Leonhard and Meyer, Sebastian and Bracher, Johannes},
year = {2017},
journal = {Statistics in Medicine},
volume = {36},
number = {22},
pages = {3443--3460},
issn = {1097-0258},
doi = {10.1002/sim.7363},
copyright = {Copyright {\copyright} 2017 John Wiley \& Sons, Ltd.}
}
@article{howertonContextdependentRepresentationBetweenmodel2023,
title = {Context-Dependent Representation of within- and between-Model Uncertainty: Aggregating Probabilistic Predictions in Infectious Disease Epidemiology},
author = {Howerton, Emily and Runge, Michael C. and Bogich, Tiffany L. and Borchering, Rebecca K. and Inamine, Hidetoshi and Lessler, Justin and Mullany, Luke C. and Probert, William J. M. and Smith, Claire P. and Truelove, Shaun and Viboud, C{\'e}cile and Shea, Katriona},
year = {2023},
month = jan,
journal = {Journal of The Royal Society Interface},
volume = {20},
number = {198},
pages = {20220659},
publisher = {Royal Society},
doi = {10.1098/rsif.2022.0659}
}
@book{hyndmanForecastingPrinciplesPractice2021,
title = {Forecasting: {{Principles}} and {{Practice}}},
author = {Hyndman, Rob J and Athanasopoulos, George},
year = {2021},
edition = {3},
publisher = {OTexts},
address = {Melbourne, Australia}
}
@article{lisonGenerativeBayesianModeling2024,
title = {Generative {{Bayesian}} Modeling to Nowcast the Effective Reproduction Number from Line List Data with Missing Symptom Onset Dates},
author = {Lison, Adrian and Abbott, Sam and Huisman, Jana and Stadler, Tanja},
year = {2024},
month = apr,
journal = {PLOS Computational Biology},
volume = {20},
number = {4},
pages = {e1012021},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1012021}
}
@article{lopezChallengesCOVID19Case2024,
title = {Challenges of {{COVID-19 Case Forecasting}} in the {{US}}, 2020--2021},
author = {Lopez, Velma K. and Cramer, Estee Y. and Pagano, Robert and Drake, John M. and O'Dea, Eamon B. and Adee, Madeline and Ayer, Turgay and Chhatwal, Jagpreet and Dalgic, Ozden O. and Ladd, Mary A. and Linas, Benjamin P. and Mueller, Peter P. and Xiao, Jade and Bracher, Johannes and Rivadeneira, Alvaro J. Castro and Gerding, Aaron and Gneiting, Tilmann and Huang, Yuxin and Jayawardena, Dasuni and Kanji, Abdul H. and Le, Khoa and M{\"u}hlemann, Anja and Niemi, Jarad and Ray, Evan L. and Stark, Ariane and Wang, Yijin and Wattanachit, Nutcha and Zorn, Martha W. and Pei, Sen and Shaman, Jeffrey and Yamana, Teresa K. and Tarasewicz, Samuel R. and Wilson, Daniel J. and Baccam, Sid and Gurung, Heidi and Stage, Steve and Suchoski, Brad and Gao, Lei and Gu, Zhiling and Kim, Myungjin and Li, Xinyi and Wang, Guannan and Wang, Lily and Wang, Yueying and Yu, Shan and Gardner, Lauren and Jindal, Sonia and Marshall, Maximilian and Nixon, Kristen and Dent, Juan and Hill, Alison L. and Kaminsky, Joshua and Lee, Elizabeth C. and Lemaitre, Joseph C. and Lessler, Justin and Smith, Claire P. and Truelove, Shaun and Kinsey, Matt and Mullany, Luke C. and {Rainwater-Lovett}, Kaitlin and Shin, Lauren and Tallaksen, Katharine and Wilson, Shelby and Karlen, Dean and Castro, Lauren and Fairchild, Geoffrey and Michaud, Isaac and Osthus, Dave and Bian, Jiang and Cao, Wei and Gao, Zhifeng and Ferres, Juan Lavista and Li, Chaozhuo and Liu, Tie-Yan and Xie, Xing and Zhang, Shun and Zheng, Shun and Chinazzi, Matteo and Davis, Jessica T. and Mu, Kunpeng and y Piontti, Ana Pastore and Vespignani, Alessandro and Xiong, Xinyue and Walraven, Robert and Chen, Jinghui and Gu, Quanquan and Wang, Lingxiao and Xu, Pan and Zhang, Weitong and Zou, Difan and Gibson, Graham Casey and Sheldon, Daniel and Srivastava, Ajitesh and Adiga, Aniruddha and Hurt, Benjamin and Kaur, Gursharn and Lewis, Bryan and Marathe, Madhav and Peddireddy, Akhil Sai and Porebski, Przemyslaw and Venkatramanan, Srinivasan and Wang, Lijing and Prasad, Pragati V. and Walker, Jo W. and Webber, Alexander E. and Slayton, Rachel B. and Biggerstaff, Matthew and Reich, Nicholas G. and Johansson, Michael A.},
year = {2024},
month = may,
journal = {PLOS Computational Biology},
volume = {20},
number = {5},
pages = {e1011200},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1011200}
}
@misc{parkEstimatingEpidemiologicalDelay2024,
title = {Estimating Epidemiological Delay Distributions for Infectious Diseases},
author = {Park, Sang Woo and Akhmetzhanov, Andrei R. and Charniga, Kelly and Cori, Anne and Davies, Nicholas G. and Dushoff, Jonathan and Funk, Sebastian and Gostic, Katie and Grenfell, Bryan and Linton, Natalie M. and Lipsitch, Marc and Lison, Adrian and Overton, Christopher E. and Ward, Thomas and Abbott, Sam},
year = {2024},
month = jan,
pages = {2024.01.12.24301247},
publisher = {medRxiv},
doi = {10.1101/2024.01.12.24301247},
archiveprefix = {medRxiv},
copyright = {{\copyright} 2024, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}
}
@article{reichCollaborativeHubsMaking2022,
title = {Collaborative {{Hubs}}: {{Making}} the {{Most}} of {{Predictive Epidemic Modeling}}},
author = {Reich, Nicholas G. and Lessler, Justin and Funk, Sebastian and Viboud, Cecile and Vespignani, Alessandro and Tibshirani, Ryan J. and Shea, Katriona and Schienle, Melanie and Runge, Michael C. and Rosenfeld, Roni and Ray, Evan L. and Niehus, Rene and Johnson, Helen C. and Johansson, Michael A. and Hochheiser, Harry and Gardner, Lauren and Bracher, Johannes and Borchering, Rebecca K. and Biggerstaff, Matthew},
year = {2022},
month = jun,
journal = {American Journal of Public Health},
volume = {112},
number = {6},
pages = {839--842},
publisher = {American Public Health Association},
issn = {0090-0036},
doi = {10.2105/AJPH.2022.306831}
}
@misc{samabbottEpinowcastEpidistTemporary2024,
title = {Epinowcast/Epidist: {{Temporary}} Development Release},
author = {{Sam Abbott} and {Adam Howes} and {Sang Woo Park} and {Damon Bayer} and {Michael DeWitt}},
year = {2024},
month = nov,
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