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/

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. http://tbdr.lshtm.ac.uk/

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.

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/

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, Oxford, United Kingdom. https://doi.org/10.1093/bioinformatics/btw758

2017

Luque-Fernandez, MA, Maringe, C and Nelson, P (2017). cvAUROC: Cross-validated Area Under the Curve (AUC). [Data Collection]. GitHub repository. https://github.com/migariane/cvAUROC

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

27 January 2017

Lopez-Bernal, J, Cummins, S and Gasparrini, A (2017). R and STATA code for: "Interrupted time series regression for the evaluation of public health interventions: a tutorial". [Data Collection]. GitHub. http://www.ag-myresearch.com/2017_lopezbernal_ije.html

9 March 2017

Luque, MA (2017). eltmle: Ensemble Learning Targeted Maximum Likelihood Estimation. [Data Collection]. GitHub. https://github.com/migariane/meltmle

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

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

2018

Luque-fernandez, MA, Schomaker, M, Redondo-Sanchez, D, Perez, MJS, Vaidya, A and Schnitzer, ME (2018). Educational Note: Paradoxical Collider Effect in the Analysis of Non-Communicable Disease Epidemiological Data: a reproducible illustration and web application. [Data Collection]. Github. https://github.com/migariane/ColliderApp

17 April 2018

Luque-Fernandez, MA, Schomaker, M, Rachet, B and Schnitzer, ME (2018). Targeted maximum likelihood estimation for a binary treatment: A tutorial. [Data Collection]. Github. https://github.com/migariane/SIM-TMLE-tutorial

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

Luque-fernandez, MA (2019). migariane/EASP_NET_SURV: Tutorial Net Survival. [Data Collection]. Github. https://github.com/migariane/EASP_NET_SURV/tree/v.1

Luque-fernandez, MA and Redondo, D (2019). migariane/hetmor: Effect modification and collapsibility when estimating the effect of public health interventions: A Monte-Carlo Simulation comparing classical multivariable regression adjustment versus the G-Formula based on a cancer epidemiology illustration. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2560819

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

12 July 2019

Cori, A, Kamvar, ZN, Stockwin, J, Jombart, T, Thompson, R and Dahlqwist, E (2019). annecori/EpiEstim: EpiEstim Cran 2.2-1. [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

16 September 2019

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

17 October 2019

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

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

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

18 March 2020

Prem, K, Liu, Y, Russell, TW, Kucharski, AJ, Eggo, RM, Davies, N, 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

2 April 2020

Davies, NG, Kucharski, AJ, Eggo, RM, Gimma, A, COVID-19 Working Group and Edmunds, WJ (2020). Stochastic age-structured model of SARS-nCoV-2 transmission for UK scenario projections. [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 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