2009

Carver, T, Thomson, N, Bleasby, A, Berriman, M and Parkhill, J (2009). DNAPlotter: circular and linear interactive genome visualization. [Data Collection]. Github. http://sanger-pathogens.github.io/Artemis/DNAPlotter/

2012

Preston, MD, Manske, M, Horner, N, Assefa, S, Campino, S, Auburn, S, Zongo, I, Ouedraogo, J, Nosten, F, Anderson, T and Clark, T (2012). VCF Viewer (VARB). [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://pathogenseq.lshtm.ac.uk/

1 November 2013

De barra, M (2013). Infectious disease and disgust sensitivity in Bangladesh. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.839646

May 2014

Coll, F, Preston, M, Guerra-Assunção, JA, Hill-Cawthorn, G, Harris, D, Perdigão, J, Viveiros, M, Portugal, I, Drobniewski, F, Gagneux, S, Glynn, JR, Pain, A, Parkhill, J, McNerney, R, Martin, N and Clark, T (2014). PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://pathogenseq.lshtm.ac.uk/#tuberculosis

8 September 2014

Pigott, DM, Golding, N, Mylne, A, Huang, Z, Henry, AJ, Weiss, DJ, Brady, OJ, Kraemer, MU, Smith, DL, Moyes, CL, Bhatt, S, Gething, PW, Horby, PW, Bogoch, II, Brownstein, JS, Mekaru, SR, Tatem, AJ, Khan, K and Hay, SI (2014). Source code for analysis of the zoonotic niche of Ebolavirus. [Data Collection]. GitHub, Inc.. https://doi.org/10.7554/eLife.04395.

2015

Coll, F, Mcnerney, R, Preston, MD, Guerra-assunção, JA, Warry, A, Hill-Cawthorne, G, Mallard, K, Nair, M, Miranda, A, Alves, A, Perdigão, J, Viveiros, M, Portugal, I, Hasan, Z, Hasan, R, Glynn, J, Martin, N, Pain, A and Clark, T (2015). TB Profiler. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom.

26 March 2015

Benavente, E, Coll, F, Furnham, N, Mcnerney, R, Glynn, J, Campino, S, Pain, A, Mohareb, FR and Clark, T (2015). PhyloTrack. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.82.

1 June 2015

Jennings, S and McNicholl, R (2015). EPrints Geographic Location plugin. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.262.

29 July 2015

Davey, C, Aiken, A, Hayes, R and Hargreaves, J (2015). Replication and re-analysis of a Kenyan stepped-wedge trial – Analysis files. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.8.

22 October 2015

Chapman, LAC, Dyson, L, Courtenay, O, Chowdhury, R, Bern, C, Medley, G and Hollingsworth, TD (2015). Additional file 2: of Quantification of the natural history of visceral leishmaniasis and consequences for control. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.3610364_D1.v1

2016

Limburg, H, Meester, W, Kuper, H and Polack, S (2016). RAAB - Rapid Assessment of Avoidable Blindness. [Data Collection]. Community Eye Health Journal. https://www.cehjournal.org/resources/raab/

January 2016

Sadique, Z, Lopman, B, Cooper, BS and Edmunds, J (2016). Cost-effectiveness of Ward Closure to Control Outbreaks of Norovirus Infection in UK National Health Service Hospitals: Epidemic simulation model. [Data Collection]. Oxford University Press. https://doi.org/10.1093/infdis/jiv410

20 October 2016

Reid, A (2016). MESH subjects file for Eprints. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000267.

22 December 2016

Chen, F, Wang, S, Jiang, X, Ding, S, Lu, Y, Kim, J, Sahinalp, SC, Shimizu, C, Burns, JC, Wright, VJ, Png, E, Hibberd, ML, Lloyd, DD, Yang, H, Telenti, A, Bloss, CS, Fox, D, Lauter, K and Ohno-Machado, L (2016). PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS. [Data Collection]. Bioinformatics. https://doi.org/10.1093/bioinformatics/btw758

15 January 2017

Tobías, A, Armstrong, B and Gasparrini, A (2017). R Code and Data for: "Investigating Uncertainty in the Minimum Mortality Temperature: Methods and Application to 52 Spanish Cities". [Data Collection]. Github. https://github.com/gasparrini/2017_tobias_Epidem_Rcodedata

Gasparrini, A (2017). R Code for: "Modelling lagged associations in environmental time series data: a simulation study". [Data Collection]. Github. https://github.com/gasparrini/2016_gasparrini_Epidem_Rcode

Armstrong, BG, Gasparrini, A and Tobias, A (2017). R and STATA code for: "Conditional Poisson models: a flexible alternative to conditional logistic case cross-over analysis". [Data Collection]. Github. https://github.com/gasparrini/2014_armstrong_BMCmrm_Codedata

Vicedo-cabrera, AM, Forsberg, B, Tobias, A, Zanobetti, A, Schwartz, J, Armstrong, B and Gasparrini, A (2017). R code and data for: "Associations of Inter- and Intraday Temperature Change With Mortality". [Data Collection]. Github. https://github.com/gasparrini/2016_vicedo-cabrera_AJE_Rcodedata

Gasparrini, A, Armstrong, B and Kenward, MG (2017). R code for: "Distributed lag non-linear models". [Data Collection]. Github. https://github.com/gasparrini/2010_gasparrini_StatMed_Rcode

Gasparrini, A (2017). R code for: "Modeling exposure–lag–response associations with distributed lag non-linear models". [Data Collection]. Github. https://github.com/gasparrini/2014_gasparrini_StatMed_Rcodedata

Gasparrini, A and Armstrong, B (2017). R code for: "The impact of heat waves on mortality". [Data Collection]. Github. https://github.com/gasparrini/2011_gasparrini_Epidem_Rcode

Bhaskaran, K, Gasparrini, A, Hajat, S, Smeeth, L and Armstrong, B (2017). R code, Stata code and data for: "Time series regression studies in environmental epidemiology". [Data Collection]. Github. https://github.com/gasparrini/2013_bhaskaran_IJE_Codedata

Gasparrini, A (2017). Tutorial code for "Distributed Lag Linear and Non-Linear Models in R: The Package dlnm". [Data Collection]. Github. https://github.com/gasparrini/2011_gasparrini_JSS_Rcode

16 January 2017

Gasparrini, A, Armstrong, B and Scheipl, F (2017). dlnm: Distributed Lag Non-Linear Models. [Data Collection]. The Comprehensive R Archive Network. https://CRAN.R-project.org/package=dlnm

9 March 2017

Luque, MA (2017). migariane/meltmle: Ensemble Learning Targeted Maximum Likelihood Estimation for Stata users. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560827

3 June 2017

Bartlett, J and Keogh, R (2017). smcfcs: Multiple Imputation of Covariates by Substantive Model Compatible Fully Conditional Specification. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=smcfcs

20 June 2017

Kabudula, C and Rentsch, C (2017). Point-of-contact Interactive Record Linkage (PIRL). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.998867

22 September 2017

Roberts, C (2017). Open Data Kit PDF Report Creator. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://github.com/chrissyhroberts/ODK_PDF_Reports

2 November 2017

van Kleef, E, Luangasanatip, N, Bonten, MJ and Cooper, BS (2017). R code: why sensitive bacteria are resistant to hospital infection control. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1045530

5 December 2017

Gasparrini, A, Armstrong, B and Kenward, MG (2017). R code and data for: "Multivariate meta-analysis for non-linear and other multi-parameter associations". [Data Collection]. Github. https://github.com/gasparrini/2012_gasparrini_StatMed_Rcodedata

Gasparrini, A and Armstrong, B (2017). R code and data for: "Reducing and meta-analysing estimates from distributed lag non-linear models". [Data Collection]. Github. https://github.com/gasparrini/2013_gasparrini_BMCmrm_Rcodedata

Gasparrini, A, Guo, Y, Hashizume, M, Kinney, PL, Petkova, EP, Lavigne, E, Zanobetti, A, Schwartz, JD, Tobias, A, Leone, M, Tong, S, Honda, Y, Kim, H and Armstrong, BG (2017). R code and data for: "Temporal Variation in Heat–Mortality Associations: A Multicountry Study". [Data Collection]. Github. https://github.com/gasparrini/2015_gasparrini_EHP_Rcodedata

17 April 2018

Fernandez, MAL, Schomaker, M, Rachet, B and Schnitzer, ME (2018). Targeted maximum likelihood estimation for a binary treatment: A tutorial. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560802

14 May 2018

Jombart, T, Kendall, M, Almagro-Garcia, J and Colijn, C (2018). treespace: exploration of landscapes of phylogenetic trees. [Data Collection]. Github. https://thibautjombart.github.io/treespace/

18 June 2018

Keogh, R (2018). MI-CC. [Data Collection]. Github. https://github.com/ruthkeogh/MI-CC

19 June 2018

Keogh, R (2018). MI-TVE. [Data Collection]. Github. https://github.com/ruthkeogh/MI-TVE

17 September 2018

Keogh, R (2018). Landmark_CF. [Data Collection]. Github. https://github.com/ruthkeogh/landmark_CF

21 September 2018

MacPherson, P, Khundi, M, Nliwasa, M, Choko, AT, Phiri, VK, Webb, EL, Dodd, PJ, Cohen, T, Harris, R and Corbett, EL (2018). BlantyreTBEpi. [Data Collection]. Github. https://github.com/petermacp/BlantyreTBEpi

29 November 2018

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

30 November 2018

Jombart, T, Campbell, F and Fitzjohn, R (2018). outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. [Data Collection]. The Comprehensive R Archive Network. https://CRAN.R-project.org/package=outbreaker2

11 December 2018

Chandna, A, White, L, Pongvongsa, T, Mayxay, M, Newton, P, Day, N and Lubell, Y (2018). YLubell/SEA-CTN: surveillance-poct. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.2206940

2019

Dyble, M, Thorley, J, Page, AE, Smith, D and Migliano, AB (2019). Engagement in agricultural work is associated with reduced leisure time among Agta hunter-gatherers. [Data Collection]. Nature Human Behaviour. https://doi.org/10.1038/s41562-019-0614-6

19 January 2019

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

9 February 2019

Fernandez, MAL, Schomaker, M, Redondo-Sanchez, D, Perez, MJS, Vaidya, A and Schnitzer, ME (2019). migariane/ColliderApp: ColliderAppLuque. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560807

Fernandez, MAL (2019). migariane/EASP_NET_SURV: Tutorial Net Survival. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.2560811

14 March 2019

Fernandez, MAL and Redondo, D (2019). migariane/HETMOR-Causal-Inference: Effect Modification and Collapsibility in Evaluations of Public Health Interventions. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560819

Fernandez, MAL (2019). migariane/cvAUROC: Cross-validated AUC for Stata users. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560816

22 May 2019

Leurent, B, Gomes, M, Cro, S, Wiles, N and Carpenter, JR (2019). CEmimix Stata do-file - First version. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.8168021.v1

29 June 2019

Thompson, J (2019). SWPERMUTE: Stata module to compute Permutation tests for Stepped-Wedge Cluster-Randomised Trials. [Data Collection]. Statistical Software Components S458426, Boston College Department of Economics. https://ideas.repec.org/c/boc/bocode/s458426.html

12 July 2019

Cori, A, Kamvar, ZN, Stockwin, J, Jombart, T, Thompson, R and Dahlqwist, E (2019). mrc-ide/EpiEstim: 2.2-3. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3333653

22 July 2019

Keogh, R and Bartlett, J (2019). Measurement error correction methods applied to NHANES data. [Data Collection]. Github. https://github.com/ruthkeogh/meas_error_handbook

29 July 2019

Stockwin, J, Thompson, R, Cori, A, Jombart, T, Kamvar, ZN and FitzJohn, R (2019). jstockwin/EpiEstimApp: v1.0.0. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3275999

8 August 2019

Abbott, S (2019). seabbs/ModelTBBCGEngland. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3360668

16 September 2019

Knight, G (2019). gwenknight/empiricprescribing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3418998

26 September 2019

Abbott, S (2019). seabbs/EstZoonoticTB. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3462381

7 October 2019

Gasparrini, A (2019). gasparrini/2019_armstrong_EHP_Rcodedata. [Data Collection]. Github. https://github.com/gasparrini/2019_armstrong_EHP_Rcodedata

17 October 2019

Flasche, S (2019). Denvaxia-in-Phillippines. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3496819

11 November 2019

Gasparrini, A (2019). gasparrini/2019_sera_StatMed_Rcode. [Data Collection]. Github. https://github.com/gasparrini/2019_sera_StatMed_Rcode

28 November 2019

Abbott, S (2019). seabbs/SpeedyMarkov. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3556670

29 November 2019

Timaeus, I (2019). convertCMC: Convert century month codes to Stata dates. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3557306

12 December 2019

Pearson, C, Abbas, KM, Clifford, S, Flasche, S and Hladish, TJ (2019). denvax: Simple Dengue Test and Vaccinate Cost Thresholds. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/web/packages/denvax/index.html

19 December 2019

Brady, OJ and Bastos, L (2019). Code for simulating release of Wolbachia mosquitoes in Indonesia and assessing their cost effectiveness in different places over time. [Data Collection]. Github. https://github.com/obrady/Wolbachia_CE/

27 January 2020

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

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

6 February 2020

Paradis, E, Kamvar, ZN, Jombart, T, Brian, K and Frederic, M (2020). pegas: Population and Evolutionary Genetics Analysis System. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3647668

12 February 2020

Keogh, R, Seaman, SR, Gran, JM and Vansteelandt, S (2020). Causal Sim code. [Data Collection]. Github. https://github.com/ruthkeogh/causal_sim

Willem, L, Xiao, L, Antillon, M, Bilcke, J, Jit, M and Beutels, P (2020). Multi-Country Model Application for RSV Cost-Effectiveness Policy (McMarcel). [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3663447

13 February 2020

Parker, E (2020). Covid 2019 tracker. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://vac-lshtm.shinyapps.io/ncov_tracker/

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

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

11 March 2020

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

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

30 March 2020

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

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

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

9 April 2020

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

20 April 2020

Flasche, S (2020). StefanFlasche/Pneumo_Trans_Inf. [Data Collection]. Github. https://github.com/StefanFlasche/Pneumo_Trans_Inf

22 April 2020

Shaver, J, Power, EA, Purzycki, BG, Shenk, MK, Bulbulia, JA, Sear, R, Sosis, R and Watts, J (2020). Religion, Cooperation, Fertility, and Child Outcomes. [Data Collection]. OSF. https://osf.io/4mt9y/

19 May 2020

Abbott, S, Bosse, N, DeWitt, M, Rau, A, Chateigner, A, Mareschal, S and Hellewell, J (2020). epiforecasts/EpiSoon. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746394

Abbott, S, Sherratt, K, Gibbs, H, Finger, F, Campbell, P, Hellewell, J, Barks, P, Meakin, S and Lee, H (2020). epiforecasts/NCoVUtils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3635417

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/

Jombart, T, Kamvar, ZN, Collins, C, Luštrik, R, Beugin, M, Knaus, BJ, Solymos, P, Mikryukov, V, Schliep, K, Maié, T, Morkovsky, L, Ahmed, I, Cori, A, Calboli, F, Ewing, R, Michaud, F, DeCamp, R and Courtiol, A (2020). adegenet: Exploratory Analysis of Genetic and Genomic Data. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/web/packages/adegenet/

24 May 2020

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

25 May 2020

Quaife, M (2020). mquaife/kenya_mixing. [Data Collection]. Github. https://github.com/mquaife/kenya_mixing

10 June 2020

Jombart, T and Schumacher, D (2020). trendbreaker 0.1.0: Detect Changes in Temporal Trends. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3888493

11 June 2020

Abbott, S and Endo, A (2020). idmodelr: Infectious Disease Model Library and Utilities. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=idmodelr

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

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

24 July 2020

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

28 July 2020

Scortichini, M, Schneider dos santos, R, De' Donato, De Sario, M, Michelozzi, P, Davoli, M, Masselot, P, Sera, F and Gasparrini, A (2020). gasparrini/ItalyCOVIDdeath. [Data Collection]. Github. https://github.com/gasparrini/ItalyCOVIDdeath

30 July 2020

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

10 August 2020

Sumner, T (2020). tomsumner/Latency_Model_Comparison_Public. [Data Collection]. Github. https://github.com/tomsumner/Latency_Model_Comparison_Public

12 August 2020

Herrett, E (2020). emilyherrett/qrisk_cprd_gold: QRISK bundle version 2.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3981237

19 August 2020

Greener, R (2020). Machine learning methods to investigate segments of the British consumer food market and to predict weight status: Source code. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3992349

20 August 2020

Holt, KE (2020). Kleborate. [Data Collection]. Github. https://github.com/katholt/Kleborate

2 September 2020

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

7 September 2020

Liu, Y, Gong, W, Clifford, S, Sundaram, ME, CMMID COVID-19 Working Group, Jit, M, Flasche, S and Klepac, P (2020). yangclaraliu/covid_surveillance_strategy: WOR Submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4017353

11 September 2020

Lopez-Bernal, J, Cummins, S and Gasparrini, A (2020). gasparrini/2017_lopezbernal_IJE_codedata. [Data Collection]. GitHub. http://www.ag-myresearch.com/2017_lopezbernal_ije.html

21 September 2020

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

24 September 2020

Nash, S, Thompson, J and Leurent, B (2020). CLAN: Stata module to perform cluster-level analysis of cluster randomised trials. [Data Collection]. Statistical Software Components S458844, Boston College Department of Economics. https://ideas.repec.org/c/boc/bocode/s458844.html

Chapman, LAC (2020). LloydChapman/VLSpatiotemporalModelling. [Data Collection]. Github. https://github.com/LloydChapman/VLSpatiotemporalModelling

25 September 2020

Thompson, J (2020). Comparison of small-sample standard-error corrections for generalised estimating equations in stepped wedge cluster randomised trials with a binary outcome: A simulation study. [Data Collection]. Zenodo. https://zenodo.org/10.5281/zenodo.4049828

16 October 2020

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

28 October 2020

Checchi, F (2020). francescochecchi/aden_covid. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://github.com/francescochecchi/aden_covid

29 October 2020

Clifford, S and Quilty, B (2020). cmmid/pcr_test_trace. [Data Collection]. Github. https://github.com/cmmid/pcr_test_trace

2 November 2020

Page, AE, Emmott, EH and Myers, S (2020). Testing the buffering hypothesis: breastfeeding problems, cessation and social support. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/74ERF

3 November 2020

Hellewell, J, Lucas, T, Davis, E, Abbott, S, Gimma, A and Thompson, R (2020). timcdlucas/ringbp: Code as used in the paper "Engagement and adherence trade-offs for SARS-CoV-2 contact tracing". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4221774

9 November 2020

Holt, KE, Lam, M and Wick, R (2020). Kleborate v2.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4923014

16 November 2020

Gasparrini, A (2020). gasparrini/2019_vicedo-cabrera_Epidem_Rcodedata. [Data Collection]. Github. https://github.com/gasparrini/2019_vicedo-cabrera_Epidem_Rcodedata

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

27 November 2020

Tazare, J (2020). johntaz/COVID-Collateral. [Data Collection]. Github. https://github.com/johntaz/COVID-Collateral

3 December 2020

Besançon, L, Deforet, M, Leyrat, C, Segalas, C, Jiang, H and Masuzzo, P (2020). Open Science during the pandemic. [Data Collection]. OSF. https://osf.io/renxy/

11 December 2020

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

15 December 2020

Fernandez, MAL, Zivich, P and Smith, MJ (2020). migariane/TutorialCausalInferenceEstimators: Computational Causal Inference for Applied Researchers. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4424912

6 January 2021

Gibbs, H, Jarvis, CI and Eggo, RM (2021). uk_tier_data. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4421648

14 January 2021

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

15 January 2021

Bhaskaran, K and Inglesby, P (2021). opensafely/covid-vs-noncovid-deaths-research. [Data Collection]. Github. https://github.com/opensafely/covid-vs-noncovid-deaths-research

19 January 2021

Powell-Jackson, T, Kovacs, R and Borghi, J (2021). Code for: "Socioeconomic inequalities in the quality of primary care under Brazil’s national pay-for-performance programme: a longitudinal study of family health teams". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002016.

2 February 2021

Jarvis, C (2021). jarvisc1/comix_uk_covid_restrictions. [Data Collection]. Github. https://github.com/jarvisc1/comix_uk_covid_restrictions

17 February 2021

Chapman, LAC (2021). LloydChapman/COVID_homeless_modelling. [Data Collection]. Github. https://github.com/LloydChapman/COVID_homeless_modelling

18 February 2021

Munday, JD and Jarvis, CI (2021). jdmunday/CoMix_schools_reopening. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5172069

19 February 2021

Munday, JD (2021). jdmunday/SchoolHouseholdNetworksCOVID: Initial release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4552421

21 February 2021

Liu, Y, Sandmann, F, Barnard, RC, Pearson, CAB, LSHTM CMMID COVID-19 Working Group, Davies, NG and Jit, M (2021). Country Level COVID-19 Vaccination Prioritisation Decision Support Tool for WHO EUR. [Data Collection]. ShinyApps.io. https://cmmid-lshtm.shinyapps.io/demo/

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

1 March 2021

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

4 March 2021

Alexander, N, Carabali, M and Lim, JK (2021). Data for: "Estimating force of infection from serologic surveys with imperfect tests". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002252.

Davies, NG, Jarvis, CI, CMMID COVID-19 Working Group, Edmunds, WJ, Jewell, NP, Diaz-Ordaz, K and Keogh, RH (2021). Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4579856

12 March 2021

Quilty, BJ, Hellewell, J, Clifford, S and CMMID COVID-19 working group (2021). R code for: "Confirmatory testing with a second lateral flow test may mitigate false positives at low levels of SARS-CoV-2 prevalence in English schools". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002074.

17 March 2021

Holt, KE, Hawkey, J and Paranagama, K (2021). katholt/sonneityping: v20210201. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4609812

18 March 2021

Rees, E (2021). erees/seasonalHCoV. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4618261

30 March 2021

McCreesh, N (2021). NickyMcC/WithinClinics. [Data Collection]. Github. https://github.com/NickyMcC/WithinClinics

Kessler, NJ (2021). knowah/bssnper2. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4647012

1 April 2021

Brand, S and Ojal, J (2021). ojal/KenyaSerology. [Data Collection]. Github. https://github.com/ojal/KenyaSerology

2 April 2021

Quilty, B (2021). cmmid/quar_test_contact_tracing. [Data Collection]. Github. https://github.com/cmmid/quar_test_contact_tracing

19 April 2021

Burke, R (2021). rachaelmburke/tbcovidblantyre. [Data Collection]. Github. https://github.com/rachaelmburke/tbcovidblantyre

20 April 2021

Lee, SA (2021). Data and R code to accompany 'Spatial connectivity in mosquito-borne disease models: a systematic review of methods and assumptions'. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4706865

27 April 2021

Krauer, F and Schmid, BV (2021). Datasets and code for "Mapping the plague through natural language processing". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4724015

28 April 2021

Pearson, CAB (2021). cmmid/covidTestVac. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4725814

1 May 2021

Gibbs, H (2021). cmmid/uk_movement_communities_covid. [Data Collection]. Github. https://github.com/cmmid/uk_movement_communities_covid

5 May 2021

Banterle, M, Zhao, Z, Bottolo, L, Richardson, S, Leoncio, W, Lewin, A, Zucknick, M and Zhao, Z (2021). BayesSUR: Bayesian Seemingly Unrelated Regression. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=BayesSUR

Pung, R (2021). rachaelpung/covid_missed_infections. [Data Collection]. Github. https://github.com/rachaelpung/covid_missed_infections

6 May 2021

Colón-González, FJ, Soares Bastos, L, Hofmann, B, Hopkin, A, Harpham, Q, Crocker, T, Amato, R, Ferrario, I, Moschini, F, James, S, Malde, S, Ainscoe, E, Sinh Nam, V, Quang Tan, D, Duc Khoa, N, Harrison, M, Tsarouchi, G, Lumbroso, D, Brady, OJ and Lowe, R (2021). R code for the paper "Probabilistic seasonal dengue forecasting in Vietnam: A modelling study using superensembles". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4740093

12 May 2021

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

31 May 2021

Vicedo-Cabrera, AM, Gasparrini, A and Royé, D (2021). anavica/mcc_ccattr_NCC. [Data Collection]. Github. https://github.com/anavica/mcc_ccattr_NCC

1 June 2021

Timaeus, I (2021). BugBunny/oRphanhood. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4889479

Prem, K (2021). kieshaprem/nsum: Release of NSUM codes version 1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4889457

Prem, K (2021). kieshaprem/synthetic-contact-matrices. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4889499

6 June 2021

Tackney, MS, Cook, DG, Stahl, D, Ismail, K, Williamson, E and Carpenter, J (2021). Additional file 1 of A framework for handling missing accelerometer outcome data in trials. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14738652.v1

7 June 2021

Pollington, TM, Tildesley, MJ, Hollingsworth, TD and Chapman, LAC (2021). t-pollington/developments_tau_statistic. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4906403

9 June 2021

Leclerc, QJ (2021). qleclerc/COVID_bed_occupancy. [Data Collection]. Github. https://github.com/qleclerc/COVID_bed_occupancy

10 June 2021

Quilty, B (2021). cmmid/covid_quar_test_import_risk. [Data Collection]. Github. https://github.com/cmmid/covid_quar_test_import_risk

16 June 2021

Bosse, N (2021). nikosbosse/mirmeth: Alpha version. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4968864

17 June 2021

Castaneda-Guzman, M, Mantilla-Saltos, G, Murray, KA, Settlage, R and Escobar, LE (2021). Methods and Code. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.13708642.v4

9 July 2021

Courtin, E, Greener, R, Weiss, J, Ware, EB, Dowd, JB and Rehkopf, D (2021). Analysis for: The changing relationship between genetic risk and cognitive decline across birth cohorts. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4982053

10 July 2021

Charvat, H and Belot, A (2021). mexhaz: Mixed Effect Excess Hazard Models. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=mexhaz

20 July 2021

Davies, NG (2021). nicholasdavies/amr-competition-diversity: Full release for publication. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5116443

21 July 2021

Yakob, L (2021). lwyakob/COVIDquarantine. [Data Collection]. Github. https://github.com/lwyakob/COVIDquarantine

27 July 2021

Greener, R, Lewis, D, Reades, J, Miles, S and Cummins, S (2021). Software and results for: An agent-based model for simulating the impact of social norms on active commuting interventions. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4916753

28 July 2021

De Figueiredo, A (2021). Global intent to accept COVID-19 vaccines. [Data Collection]. OSF. https://osf.io/8vezs

Sumner, T (2021). tomsumner/CORTIS_HR_CE. [Data Collection]. Github. https://github.com/tomsumner/CORTIS_HR_CE

12 August 2021

Simons, D (2021). DidDrog11/smoking_covid_bayes. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4002046

16 August 2021

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

18 August 2021

Sera, F, Abbott, S and Roye, D (2021). fsera/COVIDWeather. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.5215841

22 August 2021

Pung, R (2021). rachaelpung/serial_interval_covid_b.1.617.2. [Data Collection]. Github. https://github.com/rachaelpung/serial_interval_covid_b.1.617.2

23 August 2021

Millington, J, Okpako, O and Herrick, C (2021). Analysis of non-communicable disease reports contributing to UN high-level meeting process (2000-2020). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5236552

25 August 2021

Oliveira, MD, Dimitrovová, K, Angelis, A, Kanavos, P and Bana e Costa, C (2021). Results of the Web-Delphi process to YLV stakeholders (three rounds). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5257424

27 August 2021

Oliveira, MD, Dimitrovová, K, Angelis, A, Kanavos, P and Bana e Costa, C (2021). Results of the Web-Delphi process to INAMI stakeholders (three rounds). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5257297

6 September 2021

Waterlow, NR, Van Leeuwen, E, Davies, N, Flasche, S and Eggo, RM (2021). cmmid/coronavirus_immunity. [Data Collection]. Github. https://github.com/cmmid/coronavirus_immunity

14 September 2021

Mayerová, D and Abbas, KM (2021). d-mayerova/Vaccine_confidence_Albania. [Data Collection]. Github. https://github.com/d-mayerova/Vaccine_confidence_Albania

21 September 2021

Gruson, H, Grenié, M, actions-user and Henry, L (2021). Bisaloo/fundiversity: fundiversity. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.4761754

Landau, W, Landau, W, Bond-Lamberty, B, Strasiotto, M, McBain, M, Müller, K, Mahr, T, Hughes, E, Ross, N, Bell, K, Ingerson, S, Aden-Buie, G, Gomolka, M, Knoblauch, N, Albers, S, brendanf, evalparse, Denney, B, Muir, C, Barrett, M, Krug, RM, Kehayas, V, Schratz, P, Zhao, B, Hlynur, Gruson, H, Jasper, Ooms, J, Walthert, L and Dray, M (2021). ropensci/drake. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1160696

22 September 2021

Checchi, F, Testa, A, Gimma, A, Koum-Besson, E and Warsame, A (2021). francescochecchi/mortality_small_area_estimation. [Data Collection]. Github. https://github.com/francescochecchi/mortality_small_area_estimation

28 September 2021

Koltai, M (2021). mbkoltai/covid_lmic_model: Model fitting excess mortality data in Mogadishu v1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5534762

1 October 2021

Fu, H and Abbas, KM (2021). lshtm-vimc/dynamice. [Data Collection]. Github. https://github.com/lshtm-vimc/dynamice

6 October 2021

Williams, J, Naylor, N and Briggs, A (2021). Decision Modelling for Health Economic Evaluation R Code. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5552710

21 October 2021

Mee, P, Alexander, N and Colón-González, FJ (2021). Paul-Mee/clic_brazil. [Data Collection]. Github. https://github.com/Paul-Mee/clic_brazil

1 November 2021

Strongman, H and Carreira, H (2021). STATA Do files for "Factors associated with excess mortality in the first wave of COVID-19 pandemic in the UK: a cohort analysis using the Clinical Practice Research Databank". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002560.

6 December 2021

Hesselbarth, M, actions-user, Sciaini, M, Hereñú, D, Gruson, H and Etherington, T (2021). r-spatialecology/shar. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5761582

9 December 2021

Lindsey, BB, Villabona-Arenas, CJ, Atkins, KE and Campbell, F (2021). Chjulian/sheffield_HT: Characterising within-hospital SARS-CoV-2 transmission events. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5769865

20 December 2021

Harris, RC, Quaife, M, Weerasuriya, CK, Gomez, GB, Sumner, T, Bozzani, F and White, RG (2021). lshtm-tbmg/natcomms-m72sa: Nat Comms - code. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5793302

5 January 2022

Davidson, J, Herrett, E, Strongman, H and Gadd, S (2022). emilyherrett/qrisk_cprd_aurum: QRISK Aurum bundle version 2.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5822520

25 January 2022

Weerasuriya, CK (2022). weerasuriya/tbconvax-pcb. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5902656

19 April 2022

Messenger, LA and Pelloquin, B (2022). Code for analysis of mosquito microbiota data. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4548775