Data Collection

Abbott, S, Hellewell, J, Funk, S and Clifford, S (2020). epiforecasts/EpiNow: Forecasting. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746392

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

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

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

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/

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

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

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

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. http://doi.org/10.5281/zenodo.3631830

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

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

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

Sumner, T (2018). Mathematical model projections for: "Application of provincial data in mathematical modelling to inform sub-national tuberculosis program decision-making in South Africa". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000950.

Witmer, K, Sherrard-Smith, E, Straschil, U, Tunnicliff, M, Baum, J and Delves, M (2018). MOESM1 of An inexpensive open source 3D-printed membrane feeder for human malaria transmission studies. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6933695.v1

Witmer, K, Sherrard-Smith, E, Straschil, U, Tunnicliff, M, Baum, J and Delves, M (2018). MOESM2 of An inexpensive open source 3D-printed membrane feeder for human malaria transmission studies. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6933704.v1

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

Eggo, RM (2018). Computer code of the coinfection model. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1006770.s004.

Langham, S, Wright, A, Kenworthy, J, Grieve, R and Dunlop, WC (2018). Cost-Effectiveness of Take-Home Naloxone for the Prevention of Overdose Fatalities among Heroin Users in the United Kingdom: Supplemental Materials. [Data Collection]. Value in Health. https://doi.org/10.1016/j.jval.2017.07.014

Rentsch, CT, Kabudula, CW, Catlett, J, Beckles, D, Machemba, R, Mtenga, B, Masilela, N, Michael, D, Natalis, R, Urassa, M, Todd, J, Zaba, B and Reniers, G (2018). Point-of-contact Interactive Record Linkage (PIRL): A software tool to prospectively link demographic surveillance and health facility data. [Data Collection]. Gates Open Research. https://doi.org/10.12688/gatesopenres.12751.2 https://github.com/LSHTM-ALPHAnetwork/PIRL_RecordLinkageSoftware

van Kleef, E, Luangasanatip, N, Bonten, MJ and Cooper, BS (2017). R code: why sensitive bacteria are resistant to hospital infection control. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.1045530

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.

Rossell, D and Rubio, FJ (2017). Tractable Bayesian variable selection: beyond normality. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.5410747.v1

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

Le Rutte, EA, Chapman, LA, Coffeng, LE, Jervis, S, Hasker, EC, Dwivedi, S, Karthick, M, Das, A, Mahapatra, T, Chaudhuri, I, Boelaert, MC, Medley, GF, Srikantiah, S, Hollingsworth, TD and de Vlas, SJ (2017). Elimination of visceral leishmaniasis in the Indian subcontinent: a comparison of predictions from three transmission models. [Data Collection]. Epidemics. http://doi.org/10.1016/j.epidem.2017.01.002

Kessy, A, Lewin, A and Strimmer, K (2017). Optimal Whitening and Decorrelation. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.4568002.v1

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

Marks, M and Roberts, C (2017). Poisson Regression Dataset for "Learning Clinical Epidemiology with R" tutorial. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom.

Choi, YH, Campbell, H, Amirthalingam, G, Van Hoek, AJ and Miller, E (2016). Investigating the pertussis resurgence in England and Wales, and options for future control. [Data Collection]. BMC Medicine. https://doi.org/10.1186/s12916-016-0665-8.

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

Diaz-ordaz, K, Kenward, M, Gomes, M and Grieve, R (2016). Multiple imputation methods for bivariate outcomes in cluster randomised trials: Supporting Information. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.99.

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. http://jid.oxfordjournals.org/content/213/suppl_1/S19/suppl/DC1

Jeandron, A, Saidi, JM, Kapama, A, Burhole, M, Birembano, F, Vandevelde, T, Gasparrini, A, Armstrong, B, Cairncross, S and Ensink, J (2015). Water Supply Interruptions and Suspected Cholera Incidence: A Time-Series Regression in the Democratic Republic of the Congo. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pmed.1001893.

Kucharski, A and Edmunds, J (2015). Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks: Simulation and Inference code. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.1371/journal.pcbi.1004154.s010.

Phillips, A, Cambiano, V, Nakagawa, F, Magubu, T, Miners, A, Ford, D, Pillay, D, De Luca, A, Lundgren, J and Revill, P (2014). Cost-Effectiveness of HIV Drug Resistance Testing to Inform Switching to Second Line Antiretroviral Therapy in Low Income Settings: Supporting material. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1155223 https://doi.org/10.6084/m9.figshare.1155221

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.

Okumu, F (2012). Combining insecticide treated bed nets and indoor residual spraying for malaria vector control in Africa. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.39.

Pocock, S, Bennett, M, Mccormack, V, Gueyffier, F, Boutitie, F, Fagard, RH and Boissel, J (2006). Cardiovascular Risk Score Calculator. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://riskscore.lshtm.ac.uk/