A

Abbas, KM (2020). vaccine-impact/epi_covid. [Data Collection]. Github. https://github.com/vaccine-impact/epi_covid

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). 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

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 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, Gaythorpe, KA, Imai, N and Liu, Y (2020). seabbs/CovidInterventionReview: CC0 license. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3728162

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

C

Clifford, S, Quilty, BJ, Russell, TW, Liu, Y, Chan, YD, Pearson, CAB, Eggo, RM, Endo, A, CMMID COVID-19 Working Group, Flasche, S and Edmunds, WJ (2020). cmmid/travel_screening_strategies. [Data Collection]. Github. https://github.com/cmmid/travel_screening_strategies

Clifford, S, Quilty, B, CMMID nCoV working group, Pearson, C, Flasche, S and Eggo, RM (2020). Effectiveness of airport-based interventions at detecting travellers and delaying an outbreak of COVID-19 (formerly 2019-nCoV). [Data Collection]. Github. https://github.com/cmmid/screening_outbreak_delay

Coletti, P, Wambua, J, Gimma, A, Willem, L, Vercruysse, S, Vanhoutte, B, Jarvis, CI, Van Zandvoort, K, Edmunds, J, Beutels, P and Hens, N (2020). Social contact data from CoMix survey (Belgium). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4035001

D

Dawa, J, Emukule, GO, Barasa, E, Widdowson, MA, Anzala, O, Van Leeuwen, E, Baguelin, M, Chaves, SS and Eggo, RM (2020). Additional file 3 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12831246.v1

Dawa, J, Emukule, GO, Barasa, E, Widdowson, MA, Anzala, O, Van leeuwen, E, Baguelin, M, Chaves, SS and Eggo, RM (2020). Additional file 1 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12831240.v1

E

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

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

G

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

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/

H

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

J

Jarvis, C, Van zandvoort, K, Gimma, A, Prem, K, CMMID, Cwg, Klepac, P, Rubin, GJ and Edmunds, WJ (2020). Contact survey during COVID-19. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3741391

Jombart, T, Abbott, S, Gimma, A, Van zandvoort, K and Jarvis, C (2020). Inferring COVID-19 cases from recent death. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3733046

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

Jombart, T, Clifford, S, Pearson, Carl A. B. Pearson, Rees, E, Nightingale, E, Procter, S and Knight, G (2020). thibautjombart/covid19_bed_occupancy: Second major release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746662

Jombart, T, Nouvellet, P, Bhatia, S, Kamvar, ZN, Taylor, T and Ghozzi, S (2020). projections: Project Future Case Incidence. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=projections

K

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

L

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

Leng, T and Flasche, S (2020). tsleng93/SocialBubble: Social Bubble (including density dependence). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3982789

N

Nightingale, E, Waterlow, N, Clifford, S and Rees, E (2020). COVID-19 length of hospital stay. [Data Collection]. Github. https://github.com/esnightingale/los_review

P

Pearson, CAB, Van zandvoort, K, Jarvis, CI, Davies, NG, Thompson, S, Checchi, F, Jit, M, Eggo, RM and LSHTM CMMID COVID-19 Working Group (2020). Projections of COVID-19 epidemics in LMIC countries. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001564.

R

Ratnayake, R (2020). ruwanepi/Detection-analysis. [Data Collection]. Github. https://github.com/ruwanepi/Detection-analysis

Robert, A (2020). geosocial-outbreaker: Integrating geographical and social contact data to reconstruct transmission chains. [Data Collection]. Github. https://github.com/alxsrobert/o2geosocial

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

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

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

S

Sherratt, K (2020). epiforecasts/rt-comparison-uk-public: v1.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4029074

Y

Yakob, L and Nightingale, E (2020). lwyakob/COVIDsaturates. [Data Collection]. Github. https://github.com/lwyakob/COVIDsaturates