21 October 2014

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.

10 February 2015

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

6 March 2015

Kucharski, A, Mills, H, Pinsent, A, Fraser, C, Kerkhove, MV and Riley, S (2015). Data from: Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.2g43n

10 April 2015

Kucharski, A and Edmunds, J (2015). Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks: Simulation and Inference code. [Data Collection]. PLOS Computational Biology. http://doi.org/10.1371/journal.pcbi.1004154.s010

1 June 2015

Kucharski, A, Conlan, AJK and Eames, K (2015). School's Out: Seasonal Variation in the Movement Patterns of School Children. S1 Dataset. Reported individual travel patterns. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0128070.s004

3 November 2015

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.

17 May 2016

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

16 November 2017

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.

12 December 2017

Watson, CH, Coriakula, J, Ngoc, DTT, Flasche, S, Kucharski, AJ, Lau, CL, Thieu, NTV, le Polain de Waroux, O, Rawalai, K, Van, TT, Taufa, M, Baker, S, Nilles, EJ, Kama, M and Edmunds, WJ (2017). Social mixing in Fiji: Who-eats-with-whom contact patterns and the implications of age and ethnic heterogeneity for disease dynamics in the Pacific Islands. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0186911

25 July 2018

Kucharski, AJ, Wenham, C, Brownlee, P, Racon, L, Widmer, N, Eames, KTD and Conlan, AJK (2018). Reported contacts dataset for "Structure and consistency of self-reported social contact networks in British secondary schools". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.1371/journal.pone.0200090.s002

26 July 2018

le Polain de Waroux, O, Flasche, S, Kucharski, AJ, Langendorf, C, Ndazima, D, Mwanga-Amumpaire, J, Grais, RF, Cohuet, S and Edmunds, WJ (2018). Data for: Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections. [Data Collection]. Mendeley Data. https://doi.org/10.17632/rdskdgxrh3.1

14 August 2018

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

29 November 2018

Kucharski, A (2018). scrapR. [Data Collection]. Github. https://github.com/adamkucharski/scrapR/

12 March 2019

Finger, F, Funk, S, White, K, Siddiqui, MR, Edmunds, WJ and Kucharski, AJ (2019). Additional file 2: of 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

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.

31 January 2020

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

19 February 2020

Klepac, P, Kucharski, AJ, Conlan, AJ, Kissler, S, Tang, M, Fry, H and Gog, JR (2020). Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project. [Data Collection]. Medrxiv. https://doi.org/10.1101/2020.02.16.20023754

28 February 2020

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/

3 March 2020

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

18 March 2020

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

22 March 2020

Russell, TW, Hellewell, J, Abbott, S, Jarvis, C, Zandvoort, Kv, Ratnayake, R, CMMID nCov working group, Flasche, S, Eggo, RM, Edmunds, WJ and Kucharski, AJ (2020). thimotei/CFR_calculation. [Data Collection]. Github. https://github.com/thimotei/CFR_calculation

26 March 2020

Russell, TW, Hellewell, J, Jarvis, CI, Van-Zandvoort, K, Abbott, S, Ratnayake, R, Flasche, S, Eggo, RM and Kucharski, AJ (2020). Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship. [Data Collection]. Github. https://github.com/thimotei/cCFRDiamondPrincess

2 April 2020

Davies, NG, Kucharski, AJ, Eggo, RM, Gimma, A, COVID-19 Working Group and Edmunds, WJ (2020). cmmid/covid-uk. [Data Collection]. Github. https://github.com/cmmid/covid-uk

5 April 2020

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

6 April 2020

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

20 May 2020

Gibbs, H, CMMID nCov Working Group, Eggo, RM, Grundy, C and Kucharski, AJ (2020). UK Colocation Dashboard. [Data Collection]. Github. https://cmmid.github.io/colocation_dashboard_cmmid/

7 July 2020

Russell, TW, Wu, JT, Clifford, S, CMMID COVID-19 working group, Edmunds, WJ, Kucharski, AJ and Jit, M (2020). thimotei/covid_travel_restrictions. [Data Collection]. Github. https://github.com/thimotei/covid_travel_restrictions

8 July 2020

Russell, TW, Golding, N, Hellewell, J, Abbott, S, Pearson, CAB, Van zandvoort, K, Jarvis, CI, Gibbs, H, Liu, Y, Eggo, RM, Edmunds, WJ, Kucharski, AJ and CMMID COVID-19 working group (2020). Reconstructing the global dynamics of unreported COVID-19 cases and infections. [Data Collection]. Github. https://github.com/thimotei/covid_underreporting

1 October 2020

Endo, A and Kucharski, AJ (2020). akira-endo/COVID19_backwardtracing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4050267

17 November 2020

Hellewell, J, Russell, TW, The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group, Beale, R, Kelly, G, Houlihan, C, Nastouli, E and Kucharski, AJ (2020). cmmid/pcr-profile. [Data Collection]. Github. https://github.com/cmmid/pcr-profile

11 December 2020

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

14 January 2021

Pearson, CAB, Russell, TW and Kucharski, AJ (2021). cmmid/SA2UK. [Data Collection]. Github. https://github.com/cmmid/SA2UK

18 February 2021

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

25 February 2021

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

24 May 2021

Kucharski, AJ (2021). adamkucharski/covid-import-model. [Data Collection]. Github. https://github.com/adamkucharski/covid-import-model

22 June 2021

Gibbs, H, Waterlow, NR, Cheshire, J, Danon, L, Liu, Y, Grundy, C, Kucharski, AJ and Eggo, RM (2021). Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic - Estimates for Local Authority Districts. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5013619

11 September 2021

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

27 October 2021

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

10 December 2021

Chapman, LAC, Barnard, RC, Russell, TW, Abbott, S, Van Zandvoort, K, Davies, NG and Kucharski, AJ (2021). Unexposed populations and potential COVID-19 burden in European countries as of 21st November 2021. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5772162

16 March 2022

Finch, E and Kucharski, AJ (2022). EmilieFinch/covid-reinfection. [Data Collection]. Github. https://github.com/EmilieFinch/covid-reinfection

1 June 2022

Bacigalupo, S, Ruby Chang, Y, Dixon, L, Gubbins, S, Kucharski, AJ and Drewe, J (2022). The importance of fine-scale predictors of wild boar habitat use in an isolated population. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.4mw6m90cx

6 August 2022

Gibbs, H, Waterlow, NR, Cheshire, J, Danon, L, Liu, Y, Grundy, C, Kucharski, AJ and Eggo, RM (2022). hamishgibbs/facebook_population_2020_2021. [Data Collection]. Github. https://github.com/hamishgibbs/facebook_population_2020_2021

10 August 2022

Pearson, CAB, Russell, TW and Kucharski, AJ (2022). cmmid/SA2UK: CEA submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6979557

23 August 2022

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

15 January 2023

Pung, R, Clapham, HE, Russell, TW, Lee, VJ and Kucharski, AJ (2023). Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7538040

31 March 2023

Pavlich-Mariscal, J, Eggo, RM, Kucharski, AJ, Gruson, H, Russell, TW, Valle Campos, A, Cucunubá, ZM, Santos-Vega, M, Gupte, P, Azam, J, Torres Domínguez, N, Lambert, J, Gomez, G, Umaña, JD, Quevedo-Vega, DS, Gámez López, ME and Carnegie, A (2023). epiverse-trace. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://github.com/epiverse-trace

1 April 2023

Chapman, LA, Aubry, M, Maset, N, Russell, T, Knock, ES, Lees, JA, Mallet, H, Cao-Lormeau, V and Kucharski, AJ (2023). Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7790839

26 April 2023

Lotto Batista, M, Rees, EM, Gómez, A, López, S, Castell, S, Kucharski, AJ, Ghozzi, S, Müller, GV and Lowe, R (2023). Data and R-code to accompany 'Towards an Early Warning System for Leptospirosis in North-Eastern Argentina'. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7865638

29 September 2023

Lambert, J, Gruson, H, Kucharski, AJ, Gupte, P, Salmon, M, Campos, AV and Monticone, P (2023). epiverse-trace/epiparameter. [Data Collection]. Github. https://github.com/epiverse-trace/epiparameter/

29 November 2023

Abbott, S, Russell, TW, Hellewell, J and Kucharski, AJ (2023). thimotei/legacy_ct_modelling: Final version. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10223417

9 January 2024

Lambert, J, Gruson, H, Kucharski, AJ and Tamayo Cuartero, C (2024). epiverse-trace/simulist. [Data Collection]. Github. https://github.com/epiverse-trace/simulist

1 February 2024

Nilles, EJ and Kucharski, AJ (2024). enilles1/immunoepidemiology. [Data Collection]. Github. https://github.com/enilles1/immunoepidemiology

9 April 2024

Gupte, P, Van Leeuwen, E, Kucharski, A, Eggo, RM, Gruson, H, Jombart, T, Valle Campos, A and Lambert, JW (2024). finalsize: Calculate the Final Size of an Epidemic. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=finalsize

12 June 2024

Gupte, PR, Kucharski, AJ, Russell, TW, Lambert, JW, Gruson, H, Taylor, T, Azam, JM, Degoot, AM and Funk, S (2024). cfr: Estimate Disease Severity and Case Ascertainment. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=cfr

18 July 2024

Russell, TW and Kucharski, AJ (2024). thimotei/legacy_nAb_kinetics. [Data Collection]. Github. https://github.com/thimotei/legacy_nAb_kinetics/

4 November 2024

Pung, R, Kucharski, AJ, Firth, J, Russell, TW, Rogers, T and Lee, V (2024). rachaelpung/temporal_networks. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.14032212