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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
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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
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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/