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