Item Type Date Title No Grouping

Dataset

epinowcast/baselinenowcast-paper. (2025) Johnson, Kaitlyn E.; Abbott, Sam; Bracher, Johannes

epinowcast/epidist. (2025) Abbott, Sam; Howes, Adam; Park, Sang Woo; Funk, Sebastian; Bayer, Damon; DeWitt, Michael

EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters. (2024) Abbott, Sam; Hellewell, Joel; Sherratt, Katharine; Gostic, Katelyn; Hickson, Joe; Badr, Hamada S.; DeWitt, Michael; Azam, James M.; EpiForecasts; Funk, Sebastian

Improving modelling for epidemic responses: reflections. (2023) Sherratt, Katharine; Abbott, Sam; Carnegie, Anna; Liu, Yang

thimotei/legacy_ct_modelling: Final version. (2023) Abbott, Sam; Russell, Timothy W.; Hellewell, Joel; Kucharski, Adam J.

epiforecasts/ringbp. (2023) Abbott, Sam; Hellewell, Joel; Lucas, Tim; Funk, Sebastian; Gimma, Amy

epiforecasts/transformation-forecast-evaluation. (2023) Bosse, Nikos; Bracher, Johannes; Abbott, Sam; Funk, Sebastian

Data for "Human judgement forecasting of COVID-19 in the UK" by Bosse et. al (2023). (2023) Bosse, Nikos I.; Abbott, Sam; Bracher, Johannes; Van leeuwen, Edwin; Cori, Anne; Funk, Sebastian

seabbs/badtobetter: Initial release. (2023) Abbott, Sam

epiforecasts/covid.german.forecasts. (2022) Bosse, Nikos; Abbott, Sam; Funk, Sebastian

epiforecasts/simplified-forecaster-evaluation. (2022) Abbott, Sam; Bosse, Nikos

seabbs/ecdc-weekly-growth-forecasts. (2022) Abbott, Sam; Sherratt, Katharine

akira-endo/monkeypox_heavytail: Heavy-tailed sexual contact networks and the epidemiology of monkeypox outbreak in non-endemic regions. (2022) Endo, Akira; Murayama, Hiroaki; Abbott, Sam; Ratnayake, Ruwan; Pearson, Carl A. B.; Edmunds, W. John; Fearon, Elizabeth; Funk, Sebastian

epiforecasts/scoringutils. (2022) Bosse, Nikos; Abbott, Sam; Reich, Nicholas G; Funk, Sebastian

covid19-forecast-hub-europe/covid19-forecast-hub-europe. (2022) actions-user; Sherratt, Katharine; Gruson, Hugo; Funk, Sebastian; Bracher, Johannes; BIOCOM-SC; Walraven, Robert; miraanto; h-veronika; Rodiah, Isti; gr3gr3; Kraus, David; hgurung-iem; epiforecasts-bot; Xu, Frost Tianjian; Heyder, Stefan; aniruddhadiga; Abbott, Sam; Sun, Tao; Mingio, Marco; Deuschel, Jannik; pmontman; janezz25; neele-itwm; Gibson, Graham; EpiGraph; Tarantino, Barbara; Karlen, Dean; Bhatia, Sangeeta; borjarv

dchodge/hero-study: Version submitted with WOR reviewers comments. (2022) Hodgson, David; Abbott, Sam

epiforecasts/covid19-hospital-activity. (2022) Meakin, Sophie; Abbott, Sam

Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy. (2021) Abbott, Sam; Sherratt, Katharine; Funk, Sebastian

epiforecasts/forecast.vocs. (2021) Abbott, Sam; Bracher, Johannes

Unexposed populations and potential COVID-19 burden in European countries as of 21st November 2021. (2021) Chapman, Lloyd A C; Barnard, Rosanna C; Russell, Timothy W; Abbott, Sam; Van Zandvoort, Kevin; Davies, Nicholas G; Kucharski, Adam J

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Test Results. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

epiforecasts/epinowcast. (2021) Abbott, Sam; Monticone, Pietro

rmjlros/COVID19_care_home_NPIs. (2021) Rosello, Alicia; Abbott, Sam; Barnard, Rosanna C.

Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Canada Based on Test Results. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

epiforecasts/covid19.sgene.utla.rt. (2021) Abbott, Sam; Funk, Sebastian

Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

fsera/COVIDWeather. (2021) Sera, Francesco; Abbott, Sam; Roye, Dominic

reichlab/covidHubUtils. (2021) Wang, Serena Yijin; Stark, Ariane; Evan Ray; Bosse, Nikos; Reich, Nicholas G; Sherratt, Katharine; Shah, Apurv; Wattanachit, Nutcha; Khoale1096; Huang, Yuxin David; Gerding, Aaron; Gruson, Hugo; Cramer, Estee; Shandross, Li; Abbott, Sam; Funk, Sebastian

epiforecasts/EpiNow2. (2021) Abbott, Sam; Hickson, Joe; Badr, Hamada S.; Funk, Sebastian; Monticone, Pietro; Ellis, Peter; Munday, James D.; Allen, Jamie; Pearson, Carl A. B.; DeWitt, Michael; Bosse, Nikos; Meakin, Sophie

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Colombia Based on Test Results. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

KITmetricslab/covid19-forecast-hub-de. (2021) Bracher, J.; Wolffram, D.; Deuschel, J.; Görgen, K.; Ketterer, J.L.; Ullrich, A.; Abbott, Sam; Barbarossa, M.V.; Bertsimas, D.; Bhatia, S.; Bodych, M.; Bosse, Nikos I.; Burgard, J.P.; Castro, L.; Fairchild, G.; Fuhrmann, J.; Funk, Sebastian; Gogolewski, K.; Gu, Q.; Heyder, S.; Hotz, T.; Kheifetz, Y.; Kirsten, H.; Krueger, T.; Krymova, E.; Li, M.L.; Meinke, J.H.; Michaud, I.J.; Niedzielewski, K.; Ożański, T.; Rakowski, F.; Scholz, M.; Soni, S.; Srivastava, A.; Zieliński, J.; Zou, D.; Gneiting, T.; Schienle, M.

Continent Summary Reproduction Number (R) Based on Reported Cases. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Belgium Based on Test Results. (2021) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

Data and R code accompanying the manuscript "The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia". (2021) Pavelka, Martin; van Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; Jarcuska, Pavel; Krajci, Marek; Flasche, Stefan; Funk, Sebastian

Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". (2021) Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C.; Jarvis, Christopher I.; Kucharski, Adam J.; Munday, James; Pearson, Carl A. B.; Russell, Timothy W.; Tully, Damien C.; Washburne, Alex D.; Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D.; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M.; Funk, Sebastian; Jit, Mark; Atkins, Katherine E.; Edmunds, W. John

Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 Variant of Concern 202012/01 in England". (2021) Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C.; Jarvis, Christopher I.; Kucharski, Adam J.; Munday, James; Pearson, Carl A. B.; Russell, Timothy W.; Tully, Damien C.; Washburne, Alex D.; Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D.; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M.; Funk, Sebastian; Jit, Mark; Atkins, Katherine E.; Edmunds, W. John

martyn1fyles/HouseholdContactTracing. (2021) Abbott, Sam; Fyles, Martyn

epiforecasts/covid19.nhs.data: Initial release. (2021) Abbott, Sam; Meakin, Sophie

covidregionaldata: Subnational data for COVID-19 epidemiology. (2021) Palmer, Joseph; Sherratt, Katharine; Martin-Nielsen, Richard; Bevan, Jonnie; Gibbs, Hamish; CMMID COVID-19 Working Group; Funk, Sebastian; Abbott, Sam

Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

Collated Results of the National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Tests, Hospital Admissions and Deaths. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

timcdlucas/ringbp: Code as used in the paper "Engagement and adherence trade-offs for SARS-CoV-2 contact tracing". (2020) Hellewell, Joel; Lucas, Tim; Davis, Emma; Abbott, Sam; Gimma, Amy; Thompson, Robin

Continent Summary Reproduction Number (R) Based on Reported Deaths. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National Reproduction Number (R) Based on Reported Cases. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National Reproduction Number (R) Estimates Based on Reported Deaths. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results. (2020) Abbott, Sam; Bennett, Christopher; Hickson, Joe; Allen, Jamie; Sherratt, Katharine; Funk, Sebastian

RtD3. (2020) Gibbs, Hamish; Abbott, Sam; Funk, Sebastian

Reconstructing the global dynamics of unreported COVID-19 cases and infections. (2020) Russell, Timothy W.; Golding, Nick; Hellewell, Joel; Abbott, Sam; Pearson, Carl A B; Van zandvoort, Kevin; Jarvis, Christopher I; Gibbs, Hamish; Liu, Yang; Eggo, Rosalind M.; Edmunds, W. John; Kucharski, Adam J.; CMMID COVID-19 working group

idmodelr: Infectious Disease Model Library and Utilities. (2020) Abbott, Sam; Endo, Akira

seabbs/getTBinR. (2020) Abbott, Sam; Bekker-Nielsen Dunbar, Maria; Smith, Arfon

epiforecasts/covid: Submission release. (2020) Abbott, Sam; Sherratt, Katharine; Funk, Sebastian; Hellewell, Joel

epiforecasts/EpiSoon. (2020) Abbott, Sam; Bosse, Nikos; DeWitt, Michael; Rau, Andrea; Chateigner, Aurelien; Mareschal, Sylvain; Hellewell, Joel

epiforecasts/NCoVUtils. (2020) Abbott, Sam; Sherratt, Katharine; Gibbs, Hamish; Finger, Flavio; Campbell, Paul; Hellewell, Joel; Barks, Patrick; Meakin, Sophie; Lee, Haze

qleclerc/nhs_pathways_report. (2020) Leclerc, Quentin J.; Nightingale, Emily; Abbott, Sam

akira-endo/COVID19_clustersize: Estimating the amount of superspreading using outbreak sizes of COVID-19 outside China. (2020) Endo, Akira; Abbott, Sam; Kucharski, Adam J.; Funk, Sebastian

Extended data: Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. (2020) Endo, Akira; Abbott, Sam; Kucharski, Adam J.; Funk, Sebastian

Inferring COVID-19 cases from recent death. (2020) Jombart, Thibaut; Abbott, Sam; Gimma, Amy; Van zandvoort, Kevin; Jarvis, Christopher

seabbs/CovidInterventionReview: CC0 license. (2020) Abbott, Sam; Gaythorpe, Katy A.M.; Imai, Natsuko; Liu, Yang

Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship. (2020) Russell, Timothy W.; Hellewell, Joel; Jarvis, Christopher I.; Van-Zandvoort, Kevin; Abbott, Sam; Ratnayake, Ruwan; Flasche, Stefan; Eggo, Rosalind M; Kucharski, Adam J.

thimotei/CFR_calculation. (2020) Russell, Timothy W.; Hellewell, Joel; Abbott, Sam; Jarvis, Christopher; Zandvoort, Kevin van; Ratnayake, Ruwan; CMMID nCov working group; Flasche, Stefan; Eggo, Rosalind M.; Edmunds, W. John; Kucharski, Adam J.

Age-structured SEIR model for COVID-19 outbreak in Wuhan, China. (2020) Prem, Kiesha; Liu, Yang; Russell, Timothy W; Kucharski, Adam J; Eggo, Rosalind M; Davies, Nicholas G; Jit, Mark; Klepac, Petra; Flasche, Stefan; Clifford, Samuel; Pearson, Carl A B; Munday, James D; Abbott, Sam; Gibbs, Hamish; Rosello, Alicia; Quilty, Billy J; Jombart, Thibaut; Sun, Fiona; Diamond, Charlie; Gimma, Amy; Van zandvoort, Kevin; Funk, Sebastian; Jarvis, Christopher I; Edmunds, W John; Bosse, Nikos I; Hellewell, Joel

Inferring COVID-19 cases from deaths of confirmed cases. (2020) Jombart, Thibaut; Abbott, Sam; Gimma, Amy; Zandvoort, Kevin; Clifford, Samuel; Jarvis, Christopher; Russell, Timothy; Funk, Sebastian; Gibbs, Hamish; Eggo, Rosalind M.; Kucharski, Adam J.; CMMID COVID-19 Working Group; Edmunds, W. John

Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. (2020) Hellewell, Joel; Abbott, Sam; Gimma, Amy; Bosse, Nikos; Jarvis, Christopher; Russell, Timothy; Munday, James; Kucharski, Adam; Edmunds, W John; Funk, Sebastian; Eggo, Rosalind; Sun, Fiona; Flasche, Stefan; Quilty, Billy; Davies, Nicholas; Liu, Yang; Clifford, Samuel; Klepac, Petra; Jit, Mark; Diamond, Charlie; Gibbs, Hamish; Van Zandvoort, Kevin

epiforecasts/WuhanSeedingVsTransmission: Resubmission to Wellcome Open Research. (2020) Abbott, Sam; Funk, Sebastian; Munday, James D.; Hellewell, Joel

Wuhan Seeding Vs Transmission. (2020) Abbott, Sam; Funk, Sebastian; Munday, James D.; Hellewell, Joel

Pathways to Low Fertility. (2020) Abbott, Sam; Funk, Sebastian; Munday, James D.; Hellewell, Joel

seabbs/AssessBCGPolicyChange. (2019) Abbott, Sam

seabbs/SpeedyMarkov. (2019) Abbott, Sam

seabbs/EstZoonoticTB. (2019) Abbott, Sam

seabbs/ModelTBBCGEngland. (2019) Abbott, Sam