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Number of items: 261.

Thompson, JA, Leyrat, C, Fielding, KL and Hayes, RJ (2022). Additional file 2 of Cluster randomised trials with a binary outcome and a small number of clusters: comparison of individual and cluster level analysis method. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20484843.v1

Endo, A, Van leeuwen, E and Jomaba, M (2022). akira-endo/Intro-PMCMC. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6984353

Endo, A, Murayama, H, Abbott, S, Ratnayake, R, Pearson, CAB, Edmunds, WJ, Fearon, E and Funk, S (2022). akira-endo/monkeypox_heavytail: Heavy-tailed sexual contact networks and the epidemiology of monkeypox outbreak in non-endemic regions. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6984337

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

Greener, R (2022). ragreener1/deliveroo-scraper. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6961922

Greener, R (2022). ragreener1/justeat-scraper. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6962017

Greener, R (2022). ragreener1/ubereats-scraper. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6962078

Koltai, M and Krauer, F (2022). mbkoltai/RSV-resurgence-model. [Data Collection]. Github. https://github.com/mbkoltai/RSV-resurgence-model

Sherratt, K and Funk, S (2022). covid19-forecast-hub-europe/euro-hub-ensemble: Zenodo release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6895699

Checchi, F, Frison, S and Warsame, A (2022). francescochecchi/acute_malnutrition_predictive_models. [Data Collection]. Github. https://github.com/francescochecchi/acute_malnutrition_predictive_models

Barnard, RC (2022). rosannaclairebarnard/covidm-mtd-Omi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6806636

Huang, S and Libiseller-Rgger, J (2022). ShujiaHuang/qmplot. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6776156

Vallat, R, Appelhoff, S, Spaak, E, JElfner, systole-docs, Tan, G, Paulino, A, Dominic C., Leicas, Nárai, Ádám, Wallan, S, Barthélemy, Q, Weixin, J, Singaravelan, K, Crabtree, KN, Punčochář, M, Legrand, N, Jolly, E, Cederstrand, E, To, I, Hale, J, Kahle, M, Mathot, S, Wase, V, Filipec, V, gedeck, Libiseller-Egger, J and xfz329 (2022). raphaelvallat/pingouin. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1491783

Thindwa, D, Jambo, KC, Ojal, J, MacPherson, P, Dennis Phiri, M, Pinsent, A, Khundi, M, Chiume, L, Gallagher, KE, Heyderman, RS, Corbett, EL, French, N and Flasche, S (2022). deusthindwa/social.contact.rates.estimation.hiv.malawi. [Data Collection]. Github. https://github.com/deusthindwa/social.contact.rates.estimation.hiv.malawi

O'Reilly, KM (2022). kath-o-reilly/wbe_prevalence_england_python. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6674384

Roberts, C (2022). chrissyhroberts/OMR_LSHTM. [Data Collection]. Github. https://github.com/chrissyhroberts/OMR_LSHTM

Madaniyazi, L, Tobias, A, Kim, Y, Chung, Y, Armstrong, B and Hashizume, M (2022). LinaMadaniyazi/Assessing-seasonality-and-the-role-of-its-potential-drivers-in-environmental-epidemiology-a-tutorial. [Data Collection]. Github. https://github.com/LinaMadaniyazi/Assessing-seasonality-and-the-role-of-its-potential-drivers-in-environmental-epidemiology-a-tutorial

Colelli, FP, Emmerling, J, Mistry, M, Marangoni, G and De Cian, E (2022). Additional Data and Code from "Increased energy use for adaptation significantly impacts mitigation pathways". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6603718

Wick, R, kelwyres and Holt, KE (2022). katholt/Kaptive. [Data Collection]. Github. https://github.com/katholt/Kaptive

Clark, R, Mukandavire, C, Weerasuriya, C, Bakker, R and White, RG (2022). TBVAX Model. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6421372

Dyson, ZA (2022). zadyson/SNV_Stats_Generator. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6581275

Bosse, N, Abbott, S, Reich, NG and Funk, S (2022). epiforecasts/scoringutils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4618017

Jombart, T (2022). epiverse-trace/linelist. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6532786

Allel, K (2022). kasimallel/Modelling-analysing-GN-ABR-for-transmission-in-a-Chilean-semi-rural-community. [Data Collection]. Github. https://github.com/kasimallel/Modelling-analysing-GN-ABR-for-transmission-in-a-Chilean-semi-rural-community

Eletti, A, Marra, G, Quaresma, M, Radice, R and Rubio, FJ (2022). FJRubio67/LBANS/. [Data Collection]. Github. https://github.com/FJRubio67/LBANS/

Morris, TP, Walker, AS, Williamson, EJ and White, IR (2022). Additional file 1 of Planning a method for covariate adjustment in individually randomised trials: a practical guide. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19613608.v1

Morris, TP, Walker, AS, Williamson, EJ and White, IR (2022). Additional file 2 of Planning a method for covariate adjustment in individually randomised trials: a practical guide. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19613611.v1

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

Gasparrini, A (2022). gasparrini/Extended2stage. [Data Collection]. Github. https://github.com/gasparrini/Extended2stage

d-j-e, Holt, KE and Wyres, KL (2022). katholt/RedDog. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6460229

Endo, A (2022). akira-endo/reanalysis_Fukumoto2021: 'Not finding causal effect' is not 'finding no causal effect' of school closure on COVID-19. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6457915

Liu, Y (2022). yangclaraliu/COVID_Vac_Delay. [Data Collection]. Github. https://github.com/yangclaraliu/COVID_Vac_Delay

actions-user, Sherratt, K, Gruson, H, Funk, S, Bracher, J, BIOCOM-SC, Walraven, R, miraanto, h-veronika, Rodiah, I, gr3gr3, Kraus, D, hgurung-iem, epiforecasts-bot, Xu, FT, Heyder, S, aniruddhadiga, Abbott, S, Sun, T, Mingio, M, Deuschel, J, pmontman, janezz25, neele-itwm, Gibson, G, EpiGraph, Tarantino, B, Karlen, D, Bhatia, S and borjarv (2022). covid19-forecast-hub-europe/covid19-forecast-hub-europe. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6401421

Leclerc, QJ (2022). qleclerc/mrsa_phage_dynamics. [Data Collection]. Github. https://github.com/qleclerc/mrsa_phage_dynamics

Martin, JL, Messenger, LA, Mosha, FW, Lukole, E, Mosha, JF, Kulkarni, M, Churcher, TS, Sherrard-Smith, E, Manjurano, A, Protopopoff, N and Rowland, M (2022). Supporting files for: "Durability of three types of dual active ingredient long-lasting insecticidal net compared to a pyrethroid-only LLIN in Tanzania: methodology for a prospective cohort study nested in a cluster randomized controlled trial". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002833.

Kiniry, SJ and Judge, C (2022). skiniry/Trips-Viz. [Data Collection]. Github. https://github.com/skiniry/Trips-Viz

Hodgson, D and Abbott, S (2022). dchodge/hero-study: Version submitted with WOR reviewers comments. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5215671

Melendez-Torres, GJ, Warren, E, Ukoumunne, OC, Viner, R and Bonell, C (2022). Additional file 1 of Locating and testing the healthy context paradox: examples from the INCLUSIVE trial. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19246465.v1

Sweeney, S (2022). Stata Do Files for pooling and analysis. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/9XZBGE

Foster, N, Nguyen, HV, Nguyen, NV, Nguyen, HB, Cobelens, F, Tiemersma, EW, Quaife, M and Houben, R (2022). Viet Nam tuberculosis prevalence survey: equity analysis code. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002373.

Williams, J (2022). jackrdwilliams/CRASH-Mild-Model. [Data Collection]. Github. https://github.com/jackrdwilliams/CRASH-Mild-Model

Greener, R, Lewis, D, Reades, J, Miles, S and Cummins, S (2022). Software and results for: Incorporating social norms into a configurable agent-based model of commuting behaviour. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4916753

Mulick, A (2022). amulick/MCEE-u5mort2019. [Data Collection]. Github. https://github.com/amulick/MCEE-u5mort2019

Coll, F (2022). francesccoll/powerbacgwas. [Data Collection]. Github. https://github.com/francesccoll/powerbacgwas/

Schwarzer, G, Carpenter, JR and Rücker, G (2022). metasens: Statistical Methods for Sensitivity Analysis in Meta-Analysis. [Data Collection]. The Comprehensive R Archive Network.

Knight, G and Baede, VO (2022). gwenknight/strain_growth. [Data Collection]. Github. https://github.com/gwenknight/strain_growth

Meakin, S and Abbott, S (2022). epiforecasts/covid19-hospital-activity. [Data Collection]. Github. https://github.com/epiforecasts/covid19-hospital-activity

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

Nightingale, E (2022). esnightingale/covid_deaths_spatial. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5763663

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

Silver, M (2021). SoCFourier. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5801479

Abbott, S, Sherratt, K and Funk, S (2021). Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5799135

Rubio, FJ, Alvares, D, Redondo-Sanchez, D and Luque-fernandez, MA (2021). migariane/BayesVarImpComorbiCancer. [Data Collection]. Github. https://github.com/migariane/BayesVarImpComorbiCancer

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

Lin, LY (2021). liang-yu12/vd_covid. [Data Collection]. Github. https://github.com/liang-yu12/vd_covid

Jarvis, CI and Jombart, T (2021). jarvisc1/2020-reporting. [Data Collection]. Github. https://github.com/jarvisc1/2020-reporting

Abbott, S and Bracher, J (2021). epiforecasts/forecast.vocs. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5559016

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

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

Abbott, S and Monticone, P (2021). epiforecasts/epinowcast. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5637165

Rosello, A, Abbott, S and Barnard, RC (2021). rmjlros/COVID19_care_home_NPIs. [Data Collection]. Github. https://github.com/rmjlros/COVID19_care_home_NPIs

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.

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

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

Clements, AJ and Fadai, NT (2021). nfadai/Clements2021. [Data Collection]. GitHub. https://github.com/nfadai/Clements2021

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

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

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

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

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

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

Dodd, PJ (2021). petedodd/NotTB. [Data Collection]. Github. https://github.com/petedodd/NotTB

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

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

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

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

Pishgar, F, Greifer, N, Leyrat, C and Stuart, E (2021). MatchThem: Matching and Weighting Multiply Imputed Datasets. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=MatchThem

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

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

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

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

Roberts, C and Stott, C (2021). LSHTM-ORK/ODK_Biometrics. [Data Collection]. Github. https://github.com/LSHTM-ORK/ODK_Biometrics

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

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

Tanner, KT, Sharples, LD, Daniel, RM and Keogh, RH (2021). KamTan/MediationSimulation. [Data Collection]. GitHub. https://github.com/KamTan/MediationSimulation

Knight, G (2021). gwenknight/hai_first_wave. [Data Collection]. Github. https://github.com/gwenknight/hai_first_wave

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

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

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

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

Liu, Y, Sandmann, FG, Barnard, RC, Pearson, CA, CMMID Working-19 Working Group, Pastore, R, Pebody, R, Flasche, S and Jit, M (2021). Optimising health and economic impacts of COVID-19 vaccine rollout strategies in the WHO European Region. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4964148

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

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

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

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

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

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

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

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

Auzenbergs, M, Fountain, H, Macklin, G, Lyons, H and O'reilly, KM (2021). mauzenbergs/polio_vdpv. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4769689

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

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

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

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

Tazare, J (2021). johntaz/HDPS-Diagnostics. [Data Collection]. Github. https://github.com/johntaz/HDPS-Diagnostics/tree/master/code

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

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

Dyson, ZA and Holt, KE (2021). katholt/genotyphi: GenoTyphi v1.9.1. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4707613

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

Brand, S and Ojal, J (2021). ojal/KenyaSerology. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4705243

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

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

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

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

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

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.

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

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

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

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/

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

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

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

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

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.

Abbott, S and Meakin, S (2021). epiforecasts/covid19.nhs.data: Initial release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4447465

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

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

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

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

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

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/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, 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

Funk, S and Finger, F (2020). sbfnk/rbi.helpers. [Data Collection]. Github. https://github.com/sbfnk/rbi.helpers

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

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

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

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

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/

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

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/

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

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

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

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

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

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

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

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/

Hellewell, J (2020). cmmid/ringbp. [Data Collection]. Github. https://github.com/cmmid/ringbp

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

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

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

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

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/

Brady, OJ and Bastos, L (2019). obrady/Wolbachia_CE. [Data Collection]. Github. https://github.com/obrady/Wolbachia_CE/

Abbott, S (2019). seabbs/AssessBCGPolicyChange. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2635687

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

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

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

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

Funk, S (2019). sbfnk/epimixr. [Data Collection]. Github. https://github.com/sbfnk/epimixr

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

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

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

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

Lytras, T, Gasparrini, A and Wang, S (2019). FluMoDL: Influenza-Attributable Mortality with Distributed-Lag Models. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=FluMoDL

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

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

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

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

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

Roberts, C and LSHTM Global Health Analytics Group (2019). LSHTM-ORK/OBD. [Data Collection]. Github. https://github.com/LSHTM-ORK/OBD

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

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

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

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

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

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

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

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

Brady, OJ (2018). obrady/Brazil_microcepahly_analysis_public. [Data Collection]. Github. https://github.com/obrady/Brazil_microcepahly_analysis_public

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

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

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

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

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/

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

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

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

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

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

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

Choi, YH, Campbell, H, Amirthalingam, G, Van Hoek, AJ and Miller, E (2017). Additional file 3: of Investigating the pertussis resurgence in England and Wales, and options for future control. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.3614585_D1.v1

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

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

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

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

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.

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

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/

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

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.

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.

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.

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/

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.

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

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

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/

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/

This list was generated on Tue Sep 6 02:55:30 2022 BST.