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references.bib
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references.bib
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@Article{rtwebsite,
author = {Abbott, Sam and Hellewell, J and Thompson, RN and Sherratt, K and Gibbs, HP and Bosse, NI and Munday, JD and Meakin, S and Doughty, EL and Chun, JY and Chan, YWD and Finger, F and Campbell, P and Endo, A and Pearson, CAB and Gimma, A and Russell, T and null, null and Flasche, S and Kucharski, AJ and Eggo, RM and Funk, S},
title = {Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts},
journal = {Wellcome Open Research},
volume = {5},
year = {2020},
number = {112},
doi = {10.12688/wellcomeopenres.16006.2}
}
@Manual{epinow2,
title = {EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters},
author = {Sam Abbott and Joel Hellewell and Katharine Sherratt and Katelyn Gostic and Joe Hickson and Hamada S. Badr and Michael DeWitt and Robin Thompson and {EpiForecasts} and Sebastian Funk},
year = {2020},
doi = {10.5281/zenodo.3957489},
}
@article{rt-comparison,
title={Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England},
author={Sherratt, Katharine and Abbott, Sam and Meakin, Sophie R and Hellewell, Joel and Munday, James D and Bosse, Nikos and CMMID Covid-19 working group and Jit, Mark and Funk, Sebastian},
journal={Philosophical Transactions of the Royal Society B},
volume={376},
number={1829},
pages={20200283},
year={2021},
publisher={The Royal Society}
}
@techreport{imperial42,
author = {Volz, E and Mishra, S and Chand, M and Barrett, JC. and Johnson, R and Geidelberg, L and Hinsley, WR and Laydon, DJ and Dabrera, G and O’Toole, A and Amato, R and Manon Ragonnet-Cronin, Harrison, I and Jackson, B and Ariani, CV. and Boyd, O and Loman, N and McCrone, JT and Gonçalves, S and Jorgensen, D and Myers, R and Hill, V and Jackson, DK. and Gaythorpe, K and Groves, N and Sillitoe, J and Kwiatkowski, DP. and {COG-UK} and Flaxman, S and Ratmann, O and Bhatt, S and Hopkins, S and Gandy, A and Rambaut, A and Ferguson, NM},
title = {Transmission of SARS-CoV-2 LineageB.1.1.7 in England: Insights from linkingepidemiological and genetic data},
howpublished = {\url{https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201}},
year = {2020}
}
@article {davies2020,
author = {Davies, Nicholas G. and Barnard, Rosanna C. and Jarvis, Christopher I. and Kucharski, Adam J. and Munday, James and Pearson, Carl A. B. and Russell, Timothy W. and Tully, Damien C. and Abbott, Sam and Gimma, Amy and Waites, William and Wong, Kerry LM and van Zandvoort, Kevin and , and Eggo, Rosalind M. and Funk, Sebastian and Jit, Mark and Atkins, Katherine E. and Edmunds, W. John},
title = {Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England},
elocation-id = {2020.12.24.20248822},
year = {2020},
doi = {10.1101/2020.12.24.20248822},
publisher = {Cold Spring Harbor Laboratory Press},
URL = {https://www.medrxiv.org/content/early/2020/12/26/2020.12.24.20248822},
eprint = {https://www.medrxiv.org/content/early/2020/12/26/2020.12.24.20248822.full.pdf},
journal = {medRxiv}
}
@article {ferretti,
author = {Ferretti, Luca and Ledda, Alice and Wymant, Chris and Zhao, Lele and Ledda, Virginia and Abeler-Dorner, Lucie and Kendall, Michelle and Nurtay, Anel and Cheng, Hao-Yuan and Ng, Ta-Chou and Lin, Hsien-Ho and Hinch, Rob and Masel, Joanna and Kilpatrick, A. Marm and Fraser, Christophe},
title = {The timing of COVID-19 transmission},
elocation-id = {2020.09.04.20188516},
year = {2020},
doi = {10.1101/2020.09.04.20188516},
publisher = {Cold Spring Harbor Laboratory Press},
URL = {https://www.medrxiv.org/content/early/2020/09/16/2020.09.04.20188516},
eprint = {https://www.medrxiv.org/content/early/2020/09/16/2020.09.04.20188516.full.pdf},
journal = {medRxiv}
}
@article {ganyani,
author = "Ganyani, Tapiwa and Kremer, Cécile and Chen, Dongxuan and Torneri, Andrea and Faes, Christel and Wallinga, Jacco and Hens, Niel",
title = "Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020",
journal = "Eurosurveillance",
year = "2020",
volume = "25",
number = "17",
eid = 2000257,
pages = "",
url = "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.17.2000257",
doi = "10.2807/1560-7917.ES.2020.25.17.2000257"
}
@Article{brms,
title = {Advanced {Bayesian} Multilevel Modeling with the {R} Package {brms}},
author = {Paul-Christian Bürkner},
journal = {The R Journal},
year = {2018},
volume = {10},
number = {1},
pages = {395--411},
doi = {10.32614/RJ-2018-017},
encoding = {UTF-8},
}
@misc{ukgov,
title = {Coronavirus (Covid-19) in the UK},
howpublished = {\url{https://coronavirus.data.gov.uk/details/healthcare}},
year = 2021,
}
@misc{google,
title = {Covid-19 Community Mobility Reports},
howpublished = {\url{https://www.google.com/covid19/mobility/}},
year = 2021,
}
@misc{tiers1,
author = {Hamish Gibbs and Christopher I Jarvis and Rosalind M Eggo},
title = {UK Tier Data},
year = 2021,
publisher = {Zenodo},
version = {0.0.2},
doi = {10.5281/zenodo.4421649}
}
@misc{tiers2,
title = {Covid 19 local restriction tiers by area},
howpublished = {\url{https://github.com/ONSgeo/Covid19_Tiers}},
year = 2021,
}
@misc{phe,
author = {{Public Health England}},
title = {Investigation of novel SARS-CoV-2 variant: Variant of Concern 202012/01.},
year = 2020,
howpublished = {\url{https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201}},
}
@Article{brms,
title = {Advanced {Bayesian} Multilevel Modeling with the {R} Package {brms}},
author = {Paul-Christian Bürkner},
journal = {The R Journal},
year = {2018},
volume = {10},
number = {1},
pages = {395--411},
doi = {10.32614/RJ-2018-017},
encoding = {UTF-8},
}
@Manual{covidnhsdata,
title = {NHS trust level Covid-19 data aggregated to a range of spatial scales},
author = {Sophie Meakin and Sam Abbott and Sebastian Funk},
year = {2021},
doi = {10.5281/zenodo.4447465},
}
@misc{phe2,
author = {Public Health England},
title = {Variant Of Concern 202012/01: Technical Briefing 2. Investigation of novel SARS-CoV-2 variant},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/949639/Technical_Briefing_VOC202012-2_Briefing_2_FINAL.pdf}},
}
@misc{phe3,
author = {Public Health England},
title = {Variant Of Concern 202012/01: Technical Briefing 3.},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/954978/s1014-phe-voc-202012-01-technical-briefing-3.pdf}},
}
@misc{nervtag,
author = {Peter Horby, Catherine Huntley, Nick Davies, John Edmunds, Neil Ferguson, Graham Medley, Andrew Hayward, Muge Cevik, Calum Semple},
title = {NERVTAG note on B.1.1.7 severity},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/955239/NERVTAG_paper_on_variant_of_concern__VOC__B.1.1.7.pdf}},
}
@misc{imperial,
author = {Ferguson, N.},
title = {Non-parametric analysis of fatal outcomes associated with B1.1.7.},
year = 2021,
howpublished = {unpublished analysis},
}
@misc{lshtm-davies,
author = {Davies, N. , Diaz-Ordaz, K., Keogh, R},
title = {Relative fatality hazard in Pillar 2 tested individuals with VOC.},
year = 2021,
howpublished = {unpublished analysis},
}
@misc{cocin,
author = {Docherty A., Harrison, E., Semple, C.},
title = {Hospital case fatality and emergence of variant of concern B.1.1.7},
year = 2021,
howpublished = {unpublished analysis},
}
@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/}
}
@misc{keeling2021,
author = {Matt Keeling},
title = {Estimating the Transmission Advantage for B.1.617.2},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/993156/S1269_WARWICKTransmission_Advantage.pdf}},
}
@misc{ferguson2021,
author = {Neil Ferguson},
title = {B.1.617.2 transmission in England: risk factors and transmission advantage},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/993159/S1270_IMPERIAL_B.1.617.2.pdf}},
}
@misc{kucharski2021,
author = {Adam Kucharski, Nicholas Davies, Rosalind Eggo, Sebastian Funk, CMMID Working Group},
title = {Dynamics of B.1.617.2 in England NHS regions from importations, traveller-linked and non-traveller-linked transmission},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/993232/S1272_LSHTM_Modelling_Paper_B.1.617.2.pdf}},
}
@misc{phe14,
author = {{Public Health England}},
title = {SARS-CoV-2 variants of concern and variants under investigation in England. Technical briefing 14},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/991343/Variants_of_Concern_VOC_Technical_Briefing_14.pdf}},
}
@article {park2021,
author = {Sang Woo Park, Benjamin M. Bolker, Sebastian Funk, C. Jessica E. Metcalf, Joshua S. Weitz, Bryan T. Grenfell, Jonathan Dushoff},
title = {Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants
},
year = {2021},
doi = {10.1101/2021.05.03.21256545},
publisher = {Cold Spring Harbor Laboratory Press},
URL = {https://doi.org/10.1101/2021.05.03.21256545},
journal = {medRxiv}
}
@misc{abbott2021,
author = {Sam Abbott, Sebastian Funk, CMMID Working Group},
title = {Local area reproduction numbers and S-gene positivity},
year = 2021,
howpublished = {\url{https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/993228/S1271_Local_area_reproduction_numbers_and_S-gene_positivity.pdf}},
}
@article{Davies3055,
author = {Davies, Nicholas G. and Abbott, Sam and Barnard, Rosanna C. and Jarvis, Christopher I. and Kucharski, Adam J. and Munday, James D. and Pearson, Carl A. B. and Russell, Timothy W. and Tully, Damien C. and Washburne, Alex D. and Wenseleers, Tom and Gimma, Amy and Waites, William and Wong, Kerry L. M. and van Zandvoort, Kevin and Silverman, Justin D. and CMMID COVID-19 Working Group and COVID-19 Genomics UK (COG-UK) Consortium and Diaz-Ordaz, Karla and Keogh, Ruth and Eggo, Rosalind M. and Funk, Sebastian and Jit, Mark and Atkins, Katherine E. and Edmunds, W. John},
doi = {10.1126/science.abg3055},
elocation-id = {eabg3055},
eprint = {https://science.sciencemag.org/content/372/6538/eabg3055.full.pdf},
issn = {0036-8075},
journal = {Science},
number = {6538},
publisher = {American Association for the Advancement of Science},
title = {Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England},
url = {https://science.sciencemag.org/content/372/6538/eabg3055},
volume = {372},
year = {2021},
Bdsk-Url-1 = {https://science.sciencemag.org/content/372/6538/eabg3055},
Bdsk-Url-2 = {https://doi.org/10.1126/science.abg3055}
}
@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/},
}
@webpage{wikicoviduk,
author = {{Wikipedia}},
title = {{COVID-19 pandemic in the United Kingdom}},
url = {https://en.wikipedia.org/wiki/COVID-19_pandemic_in_the_United_Kingdom}
}
@webpage{Abbott:pr,
author = {Abbott, Sam and Funk, Sebastian},
title = {{covid19.sgene.utla.rt: Recast to a non-linear model}},
url = {https://github.com/epiforecasts/covid19.sgene.utla.rt/pull/42}
}
@Article{covidregionaldata,
title = {covidregionaldata: Subnational data for COVID-19 epidemiology},
author = {Joseph Palmer and Katharine Sherratt and Richard Martin-Nielsen and Jonnie Bevan and Hamish Gibbs and Sebastian Funk and Sam Abbott},
journal = {Journal of Open Source Software},
year = {2021},
volume = {6},
number = {62},
pages = {3290},
doi = {10.5281/zenodo.3957539},
}