Sherratt, K and Funk, S (2024). epiforecasts/multi-model-information: Publication release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10891376

Abbott, S, Hellewell, J, Lucas, T, Funk, S and Gimma, A (2023). epiforecasts/ringbp. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3749529

Bosse, N, Bracher, J, Abbott, S and Funk, S (2023). epiforecasts/transformation-forecast-evaluation. [Data Collection]. Github. https://github.com/epiforecasts/transformation-forecast-evaluation

Bosse, NI, Abbott, S, Bracher, J, Van leeuwen, E, Cori, A and Funk, S (2023). Data for "Human judgement forecasting of COVID-19 in the UK" by Bosse et. al (2023). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7897288

Munday, JD, Jarvis, CI, Gimma, A, Wong, KL, Van Zandvoort, K, Funk, S and Edmunds, WJ (2022). Weekly CoMix contact matrices for UKHSA COVID-19 dashboard and ONS COVID-19 infection survey age-groups. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7351950

Bosse, N, Abbott, S and Funk, S (2022). epiforecasts/covid.german.forecasts. [Data Collection]. Github. https://github.com/epiforecasts/covid.german.forecasts

Endo, A, Uchida, M, Liu, Y, Atkins, KE, Kucharski, AJ and Funk, S (2022). akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5604502

Endo, A, Murayama, H, Abbott, S, Ratnayake, R, Pearson, CAB, Edmunds, WJ, Fearon, E and Funk, S (2022). akira-endo/monkeypox_heavytail: Heavy-tailed sexual contact networks and the epidemiology of monkeypox outbreak in non-endemic regions. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6984337

Sherratt, K and Funk, S (2022). covid19-forecast-hub-europe/euro-hub-ensemble: Zenodo release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6895699

Bosse, N, Abbott, S, Reich, NG and Funk, S (2022). epiforecasts/scoringutils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4618017

actions-user, Sherratt, K, Gruson, H, Funk, S, Bracher, J, BIOCOM-SC, Walraven, R, miraanto, h-veronika, Rodiah, I, gr3gr3, Kraus, D, hgurung-iem, epiforecasts-bot, Xu, FT, Heyder, S, aniruddhadiga, Abbott, S, Sun, T, Mingio, M, Deuschel, J, pmontman, janezz25, neele-itwm, Gibson, G, EpiGraph, Tarantino, B, Karlen, D, Bhatia, S and borjarv (2022). covid19-forecast-hub-europe/covid19-forecast-hub-europe. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6401421

Funk, S (2022). epiforecasts/ons_severity_estimates. [Data Collection]. Github. https://github.com/epiforecasts/ons_severity_estimates

Alcayna, T, Fletcher, I, Gibb, R, Tremblay, L, Funk, S, Rao, B and Lowe, R (2022). Supplementary Material: Climate-sensitive disease outbreaks in the aftermath of extreme climatic events: a scoping review. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6376135

Gimma, A, Munday, JD, Wong, KLM, Coletti, P, Van Zandvoort, K, Prem, K, Klepac, P, Rubin, GJ, Funk, S, Edmunds, WJ and Jarvis, CI (2022). Mean contacts by age and date. [Data Collection]. PLOS Medicine. https://doi.org/10.1371/journal.pmed.1003907.s015

Abbott, S, Sherratt, K and Funk, S (2021). Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5799135

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/17XS9I

Endo, A, Uchida, M, Hayashi, N, Liu, Y, Atkins, KE, Kucharski, AJ and Funk, S (2021). akira-endo/schooldynamics_FluMatsumoto14-15: Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5604502

Robert, A, Funk, S, Kucharski, AJ and Jombart, T (2021). o2geosocial: Reconstruction of Transmission Chains from Surveillance Data. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=o2geosocial

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/UIM3MB

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Canada Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/2CNKZJ

Abbott, S and Funk, S (2021). epiforecasts/covid19.sgene.utla.rt. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5236661

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/0NYGXE

Wang, SY, Stark, A, Evan Ray, Bosse, N, Reich, NG, Sherratt, K, Shah, A, Wattanachit, N, Khoale1096, Huang, YD, Gerding, A, Gruson, H, Cramer, E, Shandross, L, Abbott, S and Funk, S (2021). reichlab/covidHubUtils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5207939

Abbott, S, Hickson, J, Badr, HS, Funk, S, Monticone, P, Ellis, P, Munday, JD, Allen, J, Pearson, CAB, DeWitt, M, Bosse, N and Meakin, S (2021). epiforecasts/EpiNow2. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957489

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Colombia Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/GI8EVP

Bracher, J, Wolffram, D, Deuschel, J, Görgen, K, Ketterer, J, Ullrich, A, Abbott, S, Barbarossa, M, Bertsimas, D, Bhatia, S, Bodych, M, Bosse, NI, Burgard, J, Castro, L, Fairchild, G, Fuhrmann, J, Funk, S, Gogolewski, K, Gu, Q, Heyder, S, Hotz, T, Kheifetz, Y, Kirsten, H, Krueger, T, Krymova, E, Li, M, Meinke, J, Michaud, I, Niedzielewski, K, Ożański, T, Rakowski, F, Scholz, M, Soni, S, Srivastava, A, Zieliński, J, Zou, D, Gneiting, T and Schienle, M (2021). KITmetricslab/covid19-forecast-hub-de. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4439666

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Continent Summary Reproduction Number (R) Based on Reported Cases. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/F9HVNL

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Belgium Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/NALGQJ

Lovell-Read, FA, Funk, S, Obolski, U, Donnelly, CA and Thompson, RN (2021). Supplementary material from "Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study". [Data Collection]. The Royal Society. https://doi.org/10.6084/m9.figshare.c.5416023.v1

Munday, JD, Jarvis, CI, Gimma, A, Wong, KL, van Zandvoort, K, Funk, S and Edmunds, WJ (2021). CoMix - Age structured contact matrices for 9 key periods of the COVID-19 epidemic in England. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.4677018

Pavelka, M, van Zandvoort, K, Abbott, S, Sherratt, K, Majdan, M, Jarcuska, P, Krajci, M, Flasche, S and Funk, S (2021). Data and R code accompanying the manuscript "The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4570938

Davies, NG, Abbott, S, Barnard, RC, Jarvis, CI, Kucharski, AJ, Munday, J, Pearson, CAB, Russell, TW, Tully, DC, Washburne, AD, Wenseleers, T, Gimma, A, Waites, W, Wong, KL, van Zandvoort, K, Silverman, JD, Diaz-Ordaz, K, Keogh, R, Eggo, RM, Funk, S, Jit, M, Atkins, KE and Edmunds, WJ (2021). Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.4562961

Davies, NG, Abbott, S, Barnard, RC, Jarvis, CI, Kucharski, AJ, Munday, J, Pearson, CAB, Russell, TW, Tully, DC, Washburne, AD, Wenseleers, T, Gimma, A, Waites, W, Wong, KL, van Zandvoort, K, Silverman, JD, Diaz-Ordaz, K, Keogh, R, Eggo, RM, Funk, S, Jit, M, Atkins, KE and Edmunds, WJ (2021). Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 Variant of Concern 202012/01 in England". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4549674

Palmer, J, Sherratt, K, Martin-Nielsen, R, Bevan, J, Gibbs, H, CMMID COVID-19 Working Group, Funk, S and Abbott, S (2021). covidregionaldata: Subnational data for COVID-19 epidemiology. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957539

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/ISLFJB

Robert, A, Funk, S and Kucharski, AJ (2020). o2geosocial. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4317439

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). 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. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/4L3OKY

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). Continent Summary Reproduction Number (R) Based on Reported Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/A12ADQ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National Reproduction Number (R) Based on Reported Cases. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/TTLQRN

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National Reproduction Number (R) Estimates Based on Reported Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/RBZVJE

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/METDW2

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/LNMJYJ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/PRP6CY

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/8DUSHZ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/QVWUJ5

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/CCE4XT

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/S07EZB

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/BZ7FPH

Gibbs, H, Abbott, S and Funk, S (2020). RtD3. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4011841

Leclerc, QJ, Fuller, NM, Knight, LE, Funk, S and Knight, GM (2020). COVID19 settings of transmission - collected reports database. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12173343.v5

Funk, S and Finger, F (2020). sbfnk/rbi.helpers. [Data Collection]. Github. https://github.com/sbfnk/rbi.helpers

Abbott, S, Sherratt, K, Funk, S and Hellewell, J (2020). epiforecasts/covid: Submission release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746396

Endo, A, Abbott, S, Kucharski, AJ and Funk, S (2020). akira-endo/COVID19_clustersize: Estimating the amount of superspreading using outbreak sizes of COVID-19 outside China. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3741744

Endo, A, Abbott, S, Kucharski, AJ and Funk, S (2020). Extended data: Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3740348

Prem, K, Liu, Y, Russell, TW, Kucharski, AJ, Eggo, RM, Davies, NG, Jit, M, Klepac, P, Flasche, S, Clifford, S, Pearson, CAB, Munday, JD, Abbott, S, Gibbs, H, Rosello, A, Quilty, BJ, Jombart, T, Sun, F, Diamond, C, Gimma, A, Van zandvoort, K, Funk, S, Jarvis, CI, Edmunds, WJ, Bosse, NI and Hellewell, J (2020). Age-structured SEIR model for COVID-19 outbreak in Wuhan, China. [Data Collection]. Github. https://github.com/kieshaprem/covid19-agestructureSEIR-wuhan-social-distancing

Liu, Y, Funk, S and Flasche, S (2020). yangclaraliu/2019nCoV_proportion_asym: WOR Submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3709941

Willem, L, Hoang, VT, Funk, S, Coletti, P, Beutels, P and Hens, N (2020). Social Contact Rates (SOCRATES) Data Tool. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3706787

Jombart, T, Abbott, S, Gimma, A, Zandvoort, K, Clifford, S, Jarvis, C, Russell, T, Funk, S, Gibbs, H, Eggo, RM, Kucharski, AJ, CMMID COVID-19 Working Group and Edmunds, WJ (2020). Inferring COVID-19 cases from deaths of confirmed cases. [Data Collection]. CMMID Repository. https://cmmid.github.io/visualisations/inferring-covid19-cases-from-deaths

Hellewell, J, Abbott, S, Gimma, A, Bosse, N, Jarvis, C, Russell, T, Munday, J, Kucharski, A, Edmunds, WJ, Funk, S, Eggo, R, Sun, F, Flasche, S, Quilty, B, Davies, N, Liu, Y, Clifford, S, Klepac, P, Jit, M, Diamond, C, Gibbs, H and Van Zandvoort, K (2020). Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. [Data Collection]. Github. https://github.com/cmmid/ringbp/

Kucharski, AJ, Russell, TW, Diamond, C, CMMID nCoV working group, Funk, S and Eggo, RM (2020). Probability of a large 2019-nCoV outbreak following introduction of cases. [Data Collection]. Github. https://cmmid.github.io/visualisations/new-outbreak-probability

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). epiforecasts/WuhanSeedingVsTransmission: Resubmission to Wellcome Open Research. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3630424

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). Wuhan Seeding Vs Transmission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3630424

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). Pathways to Low Fertility. [Data Collection]. Zenodo, London, United Kingdom. http://doi.org/10.5281/zenodo.3627833

Funk, S, White, R and Edmunds, WJ (2019). Social Contacts Data. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://www.socialcontactdata.org/

Funk, S (2019). sbfnk/epimixr. [Data Collection]. Github. https://github.com/sbfnk/epimixr

Finger, F, Funk, S, White, K, Siddiqui, MR, Edmunds, WJ and Kucharski, AJ (2019). Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.7829816.v1.

Funk, S, Camacho, A, Kucharski, AJ, Lowe, R, Eggo, RM and Edmunds, WJ (2019). 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". [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.2547701

Kucharski, AJ, Kama, M, Watson, CH, Aubry, M, Funk, S, Henderson, AD, Brady, OJ, Vanhomwegen, J, Manuguerra, J, Lau, CL, Edmunds, WJ, Aaskov, J, Nilles, EJ, Cao-Lormeau, V, Hue, S and Hibberd, ML (2018). adamkucharski/fiji-denv3-2014. [Data Collection]. Github. https://github.com/adamkucharski/fiji-denv3-2014

Knight, GM, Zimic, M, Funk, S, Gilman, RH, Friedland, JS and Grandjean, L (2018). Follow up time from The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6480617.v1

Funk, S (2018). Socialmixr: Social Mixing Matrices for Infectious Disease Modelling. [Data Collection]. The Comprehensive R Archive Network. https://CRAN.R-project.org/package=socialmixr https://github.com/sbfnk/socialmixr

Marks, M, Camacho, A, Kucharski, A, Funk, S, Edmunds, J and Piot, P (2017). Ebola Dataset for "Learning Clinical Epidemiology with R" tutorial. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000608.

Marks, M, Mitja, O, Fitzpatrick, C, Asiedu, K, Solomon, AW, Mabey, D and Funk, S (2017). R files for: Mathematical Modeling of Programmatic Requirements for Yaws Eradication. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.266.

Jacob, PE, Lee, A, Murray, L and Funk, S (2017). rbi: R Interface to LibBi. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=rbi

Kucharski, AJ, Funk, S, Eggo, RM, Mallet, H, Edmunds, WJ and Nilles, EJ (2016). S1 Dataset for "Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013–14 French Polynesia Outbreak". [Data Collection]. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0004726.s016

Rosello, A, Mossoko, M, Flasche, S, Vanhoek, A, Mbala, P, Camacho, A, Funk, S, Kucharski, A, Ilunga, BK, Edmunds, J, Piot, P, Baguelin, M and Tamfum, JM (2015). Ebola virus disease in the Democratic Republic of the Congo, 1976-2014: Figures and Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.30.

Camacho, A, Kucharski, AJ, Aki-Sawyerr, Y, White, MA, Flasche, S, Baguelin, M, Pollington, TM, Carney, J, Glover, R, Smout, E, Tiffany, A, Edmunds, WJ and Funk, S (2015). Bed capacity for Ebola patients in Sierra Leone. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1304889.v1

Camacho, A, Kucharski, A, Funk, S, Breman, J, Piot, P and Edmunds, J (2014). Potential for large outbreaks of Ebola virus disease: Supplementary Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.27.