Item Type Date Title No Grouping

superspreading: Understand Individual-Level Variation in Infectious Disease Transmission. (2025) Lambert, Joshua W., Kucharski, Adam J., Adam, Dillon C., Funk, Sebastian, Gupte, Pratik, Gruson, Hugo, Azam, James M., Hartgerink, Chris

kingaa/pomp. (2025) King, Aaron A, O'Dea, Eamon, Asfaw, Kidus, Wheeler, Jesse, Breto, Carles, Ionides, Edward, Akinshin, Andrey, Voipio, Timo, Funk, Sebastian

simulist: Simulate Disease Outbreak Line List and Contacts Data. (2025) Lambert, Joshua W., Tamayo, Carmen, Gruson, Hugo, Gupte, Pratik R., Kucharski, Adam J., Hartgerink, Chris, Funk, Sebastian

epiforecasts/eval-by-method. (2025) Sherratt, Katharine, Funk, Sebastian

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

epichains: Simulating and Analysing Transmission Chain Statistics Using Branching Process Models. (2024) Azam, James M., Funk, Sebastian, Finger, Flavio, Kamvar, Zhian N., Gruson, Hugo, Mané, Karim, Gupte, Pratik, Lambert, Joshua W.

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

cfr: Estimate Disease Severity and Case Ascertainment. (2024) Gupte, Pratik R., Kucharski, Adam J., Russell, Timothy W., Lambert, Joshua W., Gruson, Hugo, Taylor, Tim, Azam, James M., Degoot, Abdoelnaser M., Funk, Sebastian

epiforecasts/multi-model-information: Publication release. (2024) Sherratt, Katharine, Funk, Sebastian

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

Weekly CoMix contact matrices for UKHSA COVID-19 dashboard and ONS COVID-19 infection survey age-groups. (2022) Munday, James D., Jarvis, Christopher I., Gimma, Amy, Wong, Kerry LM, Van Zandvoort, Kevin, Funk, Sebastian, Edmunds, W John

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

akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. (2022) Endo, Akira, Uchida, Mitsuo, Liu, Yang, Atkins, Katherine E., Kucharski, Adam J., Funk, Sebastian

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

covid19-forecast-hub-europe/euro-hub-ensemble: Zenodo release. (2022) Sherratt, Katharine, 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

epiforecasts/ons_severity_estimates. (2022) Funk, Sebastian

Supplementary Material: Climate-sensitive disease outbreaks in the aftermath of extreme climatic events: a scoping review. (2022) Alcayna, Tilly, Fletcher, Isabel, Gibb, Rory, Tremblay, Léo, Funk, Sebastian, Rao, Bhargavi, Lowe, Rachel

Mean contacts by age and date. (2022) Gimma, Amy, Munday, James D., Wong, Kerry L. M., Coletti, Pietro, Van Zandvoort, Kevin, Prem, Kiesha, Klepac, Petra, Rubin, G. James, Funk, Sebastian, Edmunds, W. John, Jarvis, Christopher I.

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

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

akira-endo/schooldynamics_FluMatsumoto14-15: Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. (2021) Endo, Akira, Uchida, Mitsuo, Hayashi, Naoki, Liu, Yang, Atkins, Katherine E., Kucharski, Adam J., Funk, Sebastian

o2geosocial: Reconstruction of Transmission Chains from Surveillance Data. (2021) Robert, Alexis, Funk, Sebastian, Kucharski, Adam J., Jombart, Thibaut

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

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

Supplementary material from "Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study". (2021) Lovell-Read, Francesca A., Funk, Sebastian, Obolski, Uri, Donnelly, Christl A., Thompson, Robin N.

CoMix - Age structured contact matrices for 9 key periods of the COVID-19 epidemic in England. (2021) Munday, James D, Jarvis, Christopher I., Gimma, Amy, Wong, Kerry L, van Zandvoort, Kevin, Funk, Sebastian, Edmunds, W. John

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

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

o2geosocial. (2020) Robert, Alexis, Funk, Sebastian, Kucharski, Adam J.

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

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

COVID19 settings of transmission - collected reports database. (2020) Leclerc, Quentin J., Fuller, Naomi M., Knight, Lisa E., Funk, Sebastian, Knight, Gwenan M.

sbfnk/rbi.helpers. (2020) Funk, Sebastian, Finger, Flavio

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

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

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

yangclaraliu/2019nCoV_proportion_asym: WOR Submission. (2020) Liu, Yang, Funk, Sebastian, Flasche, Stefan

Social Contact Rates (SOCRATES) Data Tool. (2020) Willem, Lander, Hoang, Van Thang, Funk, Sebastian, Coletti, Pietro, Beutels, Philippe, Hens, Niel

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

Probability of a large 2019-nCoV outbreak following introduction of cases. (2020) Kucharski, Adam J., Russell, Timothy W., Diamond, Charlie, CMMID nCoV working group, Funk, Sebastian, Eggo, Rosalind M.

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

Social Contacts Data. (2019) Funk, Sebastian, White, Richard, Edmunds, W. John

sbfnk/epimixr. (2019) Funk, Sebastian

Additional file 2: of Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. (2019) Finger, Flavio, Funk, Sebastian, White, Kate, Siddiqui, M. Ruby, Edmunds, W. John, Kucharski, Adam J.

Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. (2019) Finger, Flavio, Funk, Sebastian, White, Kate, Siddiqui, M. Ruby, Edmunds, W. John, Kucharski, Adam J.

R Code accompanying the manuscript "Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15". (2019) Funk, Sebastian

adamkucharski/fiji-denv3-2014. (2018) Kucharski, Adam J, Kama, Mike, Watson, Conall H, Aubry, Maite, Funk, Sebastian, Henderson, Alasdair D, Brady, Oliver J, Vanhomwegen, Jessica, Manuguerra, Jean-Claude, Lau, Colleen L, Edmunds, W John, Aaskov, John, Nilles, Eric James, Cao-Lormeau, Van-Mai, Hue, Stephane, Hibberd, Martin L

Follow up time from The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. (2018) Knight, Gwenan M., Zimic, Mirko, Funk, Sebastian, Gilman, Robert H., Friedland, Jon S., Grandjean, Louis

Socialmixr: Social Mixing Matrices for Infectious Disease Modelling. (2018) Funk, Sebastian

Ebola Dataset for "Learning Clinical Epidemiology with R" tutorial. (2017) Marks, Michael, Camacho, Anton, Kucharski, Adam, Funk, Sebastian, Edmunds, John, Piot, Peter description

R files for: Mathematical Modeling of Programmatic Requirements for Yaws Eradication. (2017) Marks, Michael, Mitja, Oriol, Fitzpatrick, Christopher, Asiedu, Kingsley, Solomon, Anthony W., Mabey, David, Funk, Sebastian description

rbi: R Interface to LibBi. (2017) Jacob, Pierre E., Lee, Anthony, Murray, Lawrence, Funk, Sebastian

S1 Dataset for "Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013–14 French Polynesia Outbreak". (2016) Kucharski, Adam J., Funk, Sebastian, Eggo, Rosalind M., Mallet, Henri-Pierre, Edmunds, W. John, Nilles, Eric J. description

Ebola virus disease in the Democratic Republic of the Congo, 1976-2014: Figures and Data. (2015) Rosello, Alicia, Mossoko, Mathias, Flasche, Stefan, Vanhoek, Albert, Mbala, Placide, Camacho, Anton, Funk, Sebastian, Kucharski, Adam, Ilunga, Benoit Kebela, Edmunds, John, Piot, Peter, Baguelin, Marc, Tamfum, Jean-Jacques Muyembe description

Bed capacity for Ebola patients in Sierra Leone. (2015) Camacho, Anton, Kucharski, Adam J., Aki-Sawyerr, Y, White, M A, Flasche, Stefan, Baguelin, Marc, Pollington, T M, Carney, J, Glover, Rebecca, Smout, E, Tiffany, A, Edmunds, W. John, Funk, Sebastian

Potential for large outbreaks of Ebola virus disease: Supplementary Data. (2014) Camacho, Anton, Kucharski, Adam, Funk, Sebastian, Breman, J, Piot, Peter, Edmunds, John