Item Type Title No Grouping

Dataset

SoCFourier. (2021) Silver, Matt description

Real-time estimation of the time-varying transmission advantage of Omicron in England using S-Gene Target Status as a Proxy. (2021) Abbott, Sam; Sherratt, Katharine; Funk, Sebastian

migariane/BayesVarImpComorbiCancer. (2021) Rubio, Francisco Javier; Alvares, Danilo; Redondo-Sanchez, Daniel; Luque-fernandez, Miguel Angel

lshtm-tbmg/natcomms-m72sa: Nat Comms - code. (2021) Harris, Rebecca C; Quaife, Matthew; Weerasuriya, Chathika Krishan; Gomez, Gabriela B; Sumner, Tom; Bozzani, Fiammetta; White, Richard G

liang-yu12/vd_covid. (2021) Lin, Liang Yu

Extended Data: Iron supplementation of breastfed Gambian infants from 6 weeks to 6 months of age: Protocol for a randomised controlled trial. (2021) Stelle, Isabella; Bah, Mamadou; Silverio, Sergio A.; Verhoef, Hans; Comma, Ebrima; Prentice, Andrew M.; Moore, Sophie E.; Cerami, Carla

jarvisc1/2020-reporting. (2021) Jarvis, Christopher I.; Jombart, Thibaut

epiforecasts/forecast.vocs. (2021) Abbott, Sam; Bracher, Johannes

Chjulian/sheffield_HT: Characterising within-hospital SARS-CoV-2 transmission events. (2021) Lindsey, Benjamin B.; Villabona-Arenas, Christian Julian; Atkins, Katherine E.; Campbell, Finlay

r-spatialecology/shar. (2021) Hesselbarth, Maximilian; actions-user; Sciaini, Marco; Hereñú, Darío; Gruson, Hugo; Etherington, Thomas

Dataset and R code for article "Topical emollient therapy with sunflower seed oil alters the skin microbiota of young children with severe acute malnutrition in Bangladesh: a randomised, controlled study". (2021) Fischer, Natalie; Darmstadt, Gary L; Shahunja, KM; Crowther, Jonathan M; Kendall, Lindsay; Gibson, Rachel A; Ahmed, Tahmeed; Relman, David A

epiforecasts/epinowcast. (2021) Abbott, Sam; Monticone, Pietro

rmjlros/COVID19_care_home_NPIs. (2021) Rosello, Alicia; Abbott, Sam; Barnard, Rosanna C.

PierreMasselot/Paper--2021--JRSS_SA--Machine_Learning_Thresholds. (2021) Masselot, Pierre

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". (2021) Strongman, Helen; Carreira, Helena folder_zip

hamishgibbs/ghana_rt_npi_mobility. (2021) Gibbs, Hamish

Paul-Mee/clic_brazil. (2021) Mee, Paul; Alexander, Neal; Colón-González, Felipe J

Decision Modelling for Health Economic Evaluation R Code. (2021) Williams, Jack; Naylor, Nichola; Briggs, Andrew

nfadai/Clements2021. (2021) Clements, Alastair J; Fadai, Nabil T

lshtm-vimc/dynamice. (2021) Fu, Han; Abbas, Kaja M.

mbkoltai/covid_lmic_model: Model fitting excess mortality data in Mogadishu v1.0. (2021) Koltai, Mihaly

francescochecchi/mortality_small_area_estimation. (2021) Checchi, Francesco; Testa, Adrienne; Gimma, Amy; Koum-Besson, Emilie; Warsame, Abdihamid

ropensci/drake. (2021) Landau, Will; Landau, Will; Bond-Lamberty, Ben; Strasiotto, Matthew; McBain, Miles; Müller, Kirill; Mahr, TJ; Hughes, Ellis; Ross, Noam; Bell, Kendon; Ingerson, Sean; Aden-Buie, Garrick; Gomolka, Matthias; Knoblauch, Nicholas; Albers, Sam; brendanf; evalparse; Denney, Bill; Muir, Chris; Barrett, Malcolm; Krug, Rainer M; Kehayas, Vassilis; Schratz, Patrick; Zhao, Bruce; Hlynur; Gruson, Hugo; Jasper; Ooms, Jeroen; Walthert, Lorenz; Dray, Matt

d-mayerova/Vaccine_confidence_Albania. (2021) Mayerová, Daniela; Abbas, Kaja M.

o2geosocial: Reconstruction of Transmission Chains from Surveillance Data. (2021) Robert, Alexis; Funk, Sebastian; Kucharski, Adam J.; Jombart, Thibaut

cmmid/coronavirus_immunity. (2021) Waterlow, Naomi R.; Van Leeuwen, Edwin; Davies, Nicholas; Flasche, Stefan; Eggo, Rosalind M.

petedodd/NotTB. (2021) Dodd, Peter J

Results of the Web-Delphi process to INAMI stakeholders (three rounds). (2021) Oliveira, Mónica Duarte; Dimitrovová, Klára; Angelis, Aris; Kanavos, Panos; Bana e Costa, Carlos

NickyMcC/CasualAgeMixing. (2021) Mccreesh, Nicky

Results of the Web-Delphi process to YLV stakeholders (three rounds). (2021) Oliveira, Mónica Duarte; Dimitrovová, Klára; Angelis, Aris; Kanavos, Panos; Bana e Costa, Carlos

Analysis of non-communicable disease reports contributing to UN high-level meeting process (2000-2020). (2021) Millington, James; Okpako, Oritsematosan; Herrick, Clare

MatchThem: Matching and Weighting Multiply Imputed Datasets. (2021) Pishgar, Farhad; Greifer, Noah; Leyrat, Clemence; Stuart, Elizabeth

rachaelpung/serial_interval_covid_b.1.617.2. (2021) Pung, Rachael

fsera/COVIDWeather. (2021) Sera, Francesco; Abbott, Sam; Roye, Dominic

reichlab/covidHubUtils. (2021) Wang, Serena Yijin; Stark, Ariane; Evan Ray; Bosse, Nikos; Reich, Nicholas G; Sherratt, Katharine; Shah, Apurv; Wattanachit, Nutcha; Khoale1096; Huang, Yuxin David; Gerding, Aaron; Gruson, Hugo; Cramer, Estee; Shandross, Li; Abbott, Sam; Funk, Sebastian

DidDrog11/smoking_covid_bayes. (2021) Simons, David

LSHTM-ORK/ODK_Biometrics. (2021) Roberts, Chrissy; Stott, Callum

Code to replicate "Quantifying impacts of the COVID-19 pandemic through life expectancy losses". (2021) Aburto, José Manuel; Schöley, Jonas; Kashnitsky, Ilya; Knowles, Ian; Zhang, Luyin; Rahal, Charles; Missov, Trifon I; Dowd, Jennifer B; Mills, Melinda C; Kashyap, Ridhi

Global intent to accept COVID-19 vaccines. (2021) De Figueiredo, Alex

tomsumner/CORTIS_HR_CE. (2021) Sumner, Tom

Software and results for: An agent-based model for simulating the impact of social norms on active commuting interventions. (2021) Greener, Robert; Lewis, Daniel; Reades, Jon; Miles, Simon; Cummins, Steven

KamTan/MediationSimulation. (2021) Tanner, Kamaryn T; Sharples, Linda D; Daniel, Rhian M; Keogh, Ruth H

gwenknight/hai_first_wave. (2021) Knight, Gwen

lwyakob/COVIDquarantine. (2021) Yakob, Laith

nicholasdavies/amr-competition-diversity: Full release for publication. (2021) Davies, Nicholas G.

mexhaz: Mixed Effect Excess Hazard Models. (2021) Charvat, Hadrien; Belot, Aurélien

Analysis for: The changing relationship between genetic risk and cognitive decline across birth cohorts. (2021) Courtin, Emilie; Greener, Robert; Weiss, Jordan; Ware, Erin B.; Dowd, Jennifer B.; Rehkopf, David

Optimising health and economic impacts of COVID-19 vaccine rollout strategies in the WHO European Region. (2021) Liu, Yang; Sandmann, Frank G.; Barnard, Rosanna C.; Pearson, Carl A.B.; CMMID Working-19 Working Group; Pastore, Roberta; Pebody, Richard; Flasche, Stefan; Jit, Mark

katholt/srst2. (2021) Inouye, Michael; Dashnow, Harriet; Pope, Bernie; Wick, Ryan; Holt, Kathryn E.

Methods and Code. (2021) Castaneda-Guzman, Mariana; Mantilla-Saltos, Gabriel; Murray, Kris A.; Settlage, Robert; Escobar, Luis E

PierreMasselot/emdr. (2021) Masselot, Pierre

nikosbosse/mirmeth: Alpha version. (2021) Bosse, Nikos

cmmid/covid_quar_test_import_risk. (2021) Quilty, Billy

qleclerc/COVID_bed_occupancy. (2021) Leclerc, Quentin J.

rachaelmburke/hivhospital. (2021) Burke, Rachael

t-pollington/developments_tau_statistic. (2021) Pollington, Timothy M; Tildesley, Michael J; Hollingsworth, T Déirdre; Chapman, Lloyd A. C.

Additional file 1 of A framework for handling missing accelerometer outcome data in trials. (2021) Tackney, Mia S.; Cook, Derek G.; Stahl, Daniel; Ismail, Khalida; Williamson, Elizabeth; Carpenter, James

BugBunny/oRphanhood. (2021) Timaeus, Ian

kieshaprem/nsum: Release of NSUM codes version 1.0. (2021) Prem, Kiesha

kieshaprem/synthetic-contact-matrices. (2021) Prem, Kiesha

anavica/mcc_ccattr_NCC. (2021) Vicedo-Cabrera, A. M.; Gasparrini, Antonio; Royé, Dominic

mauzenbergs/polio_vdpv. (2021) Auzenbergs, Megan; Fountain, Holly; Macklin, Grace; Lyons, Hil; O'reilly, Kathleen M.

KITmetricslab/covid19-forecast-hub-de. (2021) Bracher, J.; Wolffram, D.; Deuschel, J.; Görgen, K.; Ketterer, J.L.; Ullrich, A.; Abbott, Sam; Barbarossa, M.V.; Bertsimas, D.; Bhatia, S.; Bodych, M.; Bosse, Nikos I.; Burgard, J.P.; Castro, L.; Fairchild, G.; Fuhrmann, J.; Funk, Sebastian; Gogolewski, K.; Gu, Q.; Heyder, S.; Hotz, T.; Kheifetz, Y.; Kirsten, H.; Krueger, T.; Krymova, E.; Li, M.L.; Meinke, J.H.; Michaud, I.J.; Niedzielewski, K.; Ożański, T.; Rakowski, F.; Scholz, M.; Soni, S.; Srivastava, A.; Zieliński, J.; Zou, D.; Gneiting, T.; Schienle, M.

R code for the paper "Probabilistic seasonal dengue forecasting in Vietnam: A modelling study using superensembles". (2021) Colón-González, Felipe J.; Soares Bastos, Leonardo; Hofmann, Barbara; Hopkin, Alison; Harpham, Quillon; Crocker, Tom; Amato, Rosanna; Ferrario, Iacopo; Moschini, Francesca; James, Samuel; Malde, Sajni; Ainscoe, Eleanor; Sinh Nam, Vu; Quang Tan, Dang; Duc Khoa, Nguyen; Harrison, Mark; Tsarouchi, Gina; Lumbroso, Darren; Brady, Oliver J.; Lowe, Rachel

BayesSUR: Bayesian Seemingly Unrelated Regression. (2021) Banterle, Marco; Zhao, Zhi; Bottolo, Leonardo; Richardson, Sylvia; Leoncio, Waldir; Lewin, Alexandra; Zucknick, Manuela; Zhao, Zhi

cmmid/uk_movement_communities_covid. (2021) Gibbs, Hamish

johntaz/HDPS-Diagnostics. (2021) Tazare, John

cmmid/covidTestVac. (2021) Pearson, Carl A. B.

Datasets and code for "Mapping the plague through natural language processing". (2021) Krauer, Fabienne; Schmid, Boris V.

Data and R code to accompany 'Spatial connectivity in mosquito-borne disease models: a systematic review of methods and assumptions'. (2021) Lee, Sophie A.

ojal/KenyaSerology. (2021) Brand, Samuel; Ojal, John

rachaelmburke/tbcovidblantyre. (2021) Burke, Rachael

Additional file 2 of Comparative diagnostic accuracy studies with an imperfect reference standard – a comparison of correction methods. (2021) Umemneku Chikere, Chinyereugo M; Wilson, Kevin J; Allen, A Joy; Vale, Luke

Eyedeet/Systematic_review. (2021) Suffel, Anne Marie

TheYongjinChoi/NYS-COVID19-Disparities-Survey. (2021) Fox, Ashley; Choi, Yongjin

cmmid/quar_test_contact_tracing. (2021) Quilty, Billy

NickyMcC/WithinClinics. (2021) McCreesh, Nicky

knowah/bssnper2. (2021) Kessler, Noah J.

CEmimix ADO file. (2021) Leurent, Baptiste; Cro, Suzie

erees/seasonalHCoV. (2021) Rees, Eleanor

katholt/sonneityping: v20210201. (2021) Holt, Kathryn E.; Hawkey, Jane; Paranagama, Kalani

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". (2021) Quilty, Billy J; Hellewell, Joel; Clifford, Samuel; CMMID COVID-19 working group description

Data for: "Estimating force of infection from serologic surveys with imperfect tests". (2021) Alexander, Neal; Carabali, Mabel; Lim, Jacqueline K.

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. (2021) Davies, Nicholas G.; Jarvis, Christopher I.; CMMID COVID-19 Working Group; Edmunds, W. John; Jewell, Nicholas P.; Diaz-Ordaz, Karla; Keogh, Ruth H.

Data and R code accompanying the manuscript "The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia". (2021) Pavelka, Martin; van Zandvoort, Kevin; Abbott, Sam; Sherratt, Katharine; Majdan, Marek; Jarcuska, Pavel; Krajci, Marek; Flasche, Stefan; Funk, Sebastian

Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". (2021) Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C.; Jarvis, Christopher I.; Kucharski, Adam J.; Munday, James; Pearson, Carl A. B.; Russell, Timothy W.; Tully, Damien C.; Washburne, Alex D.; Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D.; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M.; Funk, Sebastian; Jit, Mark; Atkins, Katherine E.; Edmunds, W. John

Country Level COVID-19 Vaccination Prioritisation Decision Support Tool for WHO EUR. (2021) Liu, Yang; Sandmann, Frank; Barnard, Rosanna C.; Pearson, Carl A. B.; LSHTM CMMID COVID-19 Working Group; Davies, Nicholas G.; Jit, Mark

jdmunday/SchoolHouseholdNetworksCOVID: Initial release. (2021) Munday, James D.

jdmunday/CoMix_schools_reopening. (2021) Munday, James D.; Jarvis, Christopher I.

LloydChapman/COVID_homeless_modelling. (2021) Chapman, Lloyd A. C.

PierreMasselot/primr. (2021) Masselot, Pierre

jarvisc1/comix_uk_covid_restrictions. (2021) Jarvis, Christopher

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". (2021) Powell-Jackson, Timothy; Kovacs, Roxanne; Borghi, Josephine description

S1 File for "Multi-criteria suitability analysis for neglected and underutilised crop species in South Africa". (2021) Mugiyo, Hillary; Chimonyo, Vimbayi G P; Sibanda, Mbulisi; Kunz, Richard; Nhamo, Luxon; Masemola, Cecelia R; Dalin, Caroline; Modi, Albert T; Mabhaudhi, Tafadzwa

epiforecasts/covid19.nhs.data: Initial release. (2021) Abbott, Sam; Meakin, Sophie

opensafely/covid-vs-noncovid-deaths-research. (2021) Bhaskaran, Krishnan; Inglesby, Peter

cmmid/SA2UK. (2021) Pearson, Carl A. B.; Russell, Timothy W.; Kucharski, Adam J.

supingling/glycaemic-control. (2021) Ling, Suping

uk_tier_data. (2021) Gibbs, Hamish; Jarvis, Christopher I.; Eggo, Rosalind M.

WINRATIOTEST: Stata module to calculate the unmatched Win Ratio for prioritised outcomes. (2021) Gregson, John; Collier, Timothy