Data Collection

Abbas, KM and Vaccine Impact (2024). vaccine-impact/hpv_vaccine_equity. [Data Collection]. Github. https://github.com/vaccine-impact/hpv_vaccine_equity

Abbas, KM, Vaccine Impact and Hadley, L (2024). lshtm-vimc/prime. [Data Collection]. Github. https://github.com/lshtm-vimc/prime

Abbott, S (2023). seabbs/badtobetter: Initial release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7799448

Abbott, S, Hellewell, J, Sherratt, K, Gostic, K, Hickson, J, Badr, HS, DeWitt, M, Azam, JM, EpiForecasts and Funk, S (2024). EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.13828203

Abbott, S, Russell, TW, Hellewell, J and Kucharski, AJ (2023). thimotei/legacy_ct_modelling: Final version. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10223417

Brady, OJ (2024). obrady/CATI_Vietnam. [Data Collection]. Github. https://github.com/obrady/CATI_Vietnam

Chatzilena, A and Van Leeuwen, E (2019). anastasiachtz/COMMAND_stan/. [Data Collection]. Github. https://github.com/anastasiachtz/COMMAND_stan/

Clark, R (2024). lshtm-tbmg/tbmod-pub-undernutrition. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.14160777

Domínguez, NT, Gruson, H, Pavlich-Mariscal, J, Gomez, G, Gámez López, ME, Cucunubá, ZM, tracelac, Hartgerink, C, Azam, J and ben18785 (2024). epiverse-trace/serofoi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.11095007

Etienne, RS, Valente, L, Phillimore, AB, Haegeman, B, Lambert, JW, Santos Neves, P, Xie, S, Bilderbeek, RJ, Hildenbrandt, H, Hauffe, T, Laudanno, G, Kristensen, N and Scherrer, R (2023). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=DAISIE

Finger, F, Funk, S, White, K, Siddiqui, MR, Edmunds, WJ and Kucharski, AJ (2019). Additional file 2: of Real-time analysis of the diphtheria outbreak in forcibly displaced Myanmar nationals in Bangladesh. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.7829816.v1

Fox, A and Choi, Y (2021). TheYongjinChoi/NYS-COVID19-Disparities-Survey. [Data Collection]. GitHub. https://github.com/TheYongjinChoi/NYS-COVID19-Disparities-Survey

Goodfellow, L (2024). lucy-gf/imd-covid. [Data Collection]. Github. https://github.com/lucy-gf/imd-covid

Gupte, PR, Kucharski, AJ, Russell, TW, Lambert, JW, Gruson, H, Taylor, T, Azam, JM, Degoot, AM and Funk, S (2024). cfr: Estimate Disease Severity and Case Ascertainment. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=cfr

Gupte, P, Van Leeuwen, E, Kucharski, A, Eggo, RM, Gruson, H, Jombart, T, Valle Campos, A and Lambert, JW (2024). finalsize: Calculate the Final Size of an Epidemic. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=finalsize

Haque, F, Lampe, FC, Hajat, S, Stavrianaki, K, Hasan, SMT, Faruque, ASG, Ahmed, T, Jubayer, S and Kelman, I (2024). S1 Data for: "Impacts of climate change on diarrhoeal disease hospitalisations: How does the global warming targets of 1.5–2°C affect Dhaka, Bangladesh?". [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0012139.s005

Hartgerink, C, Lambert, JW, Mané, K, Gruson, H and Ahadzie, B (2024). numberize: Convert Words to Numbers in Multiple Languages. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=numberize

Henderson, AD, Butler-Cole, BF, Wiedemann, M, Evans, D and Smith, R (2023). opensafely/openprompt-vaccine-long-covid. [Data Collection]. GitHub. https://github.com/opensafely/openprompt-vaccine-long-covid

Hodgson, D (2022). dchodge/nambcea. [Data Collection]. Github. https://github.com/dchodge/nambcea

Hou, Z, Lai, X, Liu, Y, Jit, M, Larson, H and Hai, F (2023). Assessing the impact of the 2018 Changchun Changsheng vaccine incident on childhood vaccination in China. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8158678

Hébert-Dufresne, L, Althouse, BM, Skrip, L and Bedson, J (2019). Social Mobilization Action Consortium: Community Engagement data from the 2014-2016 Sierra Leone Ebola outbreak. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.8247002.v1

Institute for Health Metrics and Evaluation (IHME) and London School of Hygiene and Tropical Medicine (2024). Measles Seroprevalence Systematic Review and Bias Assessment 1962-2019. [Data Collection]. Global Health Data Exchange (GHDx). https://ghdx.healthdata.org/record/ihme-data/measles-serosurvey-bias-systematic-review

Jarvis, CI, Coletti, P, Backer, J, Munday, JD, Faes, C, Beutels, P, Althaus, C, Low, N, Wallinga, J, Hens, N and Edmunds, J (2024). CoMix data (last round in BE, CH, NL and UK). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.11154065

Jensen, HT (2024). Model for "Estimating the health and macroeconomic burdens of tuberculosis in India, 2021-2040". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00004409.

Judge, C (2024). ciarajudge/EpiFusion. [Data Collection]. Github. https://github.com/ciarajudge/EpiFusion

Judge, C (2024). ciarajudge/EpiFusion_PublicationRepo. [Data Collection]. Github. https://github.com/ciarajudge/EpiFusion_PublicationRepo

Kapulu, MC, Muthumbi, E, Otieno, E, Rossi, O, Ferruzzi, P, Necchi, F, Acquaviva, A, Martin, LB, Orindi, B, Mwai, K, Mwanzu, A, Bigogo, GM, Verani, JR, Mbae, C, Nyundo, C, Agoti, CN, Nakakana, UN, Conti, V, Bejon, P, Kariuki, S, Scott, JAG, Micoli, F and Podda, A (2023). Replication Data for: Age-dependent acquisition of IgG antibodies to Shigella serotypes – a retrospective analysis of sero-prevalence in Kenyan children. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/F5AV5G

Krauer, F (2024). fkrauer/RSV-VACC-DE. [Data Collection]. Github. https://github.com/fkrauer/RSV-VACC-DE

Lambert, JW (2024). joshwlambert/DAISIEprepExtra. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6984486

Lambert, JW, Bilderbeek, R and Santos Neves, P (2024). DAISIEmainland. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6502547

Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App all datasets. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9821996.v1

Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App drug breakdown. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822077.v1

Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App economic data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822122.v1

Lim, A and Brady, OJ (2024). OpenDengue/master-repo. [Data Collection]. GitHub. https://github.com/OpenDengue/master-repo

London School of Hygiene & Tropical Medicine (2023). Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB60532

Mané, K, Jombart, T, Bah, B, Ahadzie, B, Mohammed, N, Degoot, AM, Gruson, H, Gupte, PR, Azam, JM, Lambert, JW and Hartgerink, C (2024). cleanepi: Clean and Standardize Epidemiological Data. [Data Collection]. Comprehensive R Archive Network. https://cran.r-project.org/package=cleanepi

Mezmur, H, Tefera, M, Jemal, M, Kahsay, B and Assefa, N (2024). Household fuel use and adverse pregnancy outcomes. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26406418.v1

Moirano, G, Fletcher, C, Semenza, JC and Lowe, R (2024). ghr/wnv_casecrossover. [Data Collection]. Gitlab. https://earth.bsc.es/gitlab/ghr/wnv_casecrossover

Neves, PS, Lambert, JW, Etienne, RS, Bilderbeek, R, Xie, S, Valente, L, Hildenbrandt, H, Scherrer, R and Yangshen0325 (2023). rsetienne/DAISIE. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4054058

Nightingale, E (2023). esnightingale/vl-collection-methods-xm. [Data Collection]. GitHub. https://github.com/esnightingale/vl-collection-methods-xm

Nightingale, E (2024). esnightingale/vl-disaggregation. [Data Collection]. Github. https://github.com/esnightingale/vl-disaggregation

Nilles, EJ and Kucharski, AJ (2024). enilles1/immunoepidemiology. [Data Collection]. Github. https://github.com/enilles1/immunoepidemiology

O'reilly, KM (2024). Interview Questions for WW Dashboards. [Data Collection]. Zenodo. https://zenodo.org/doi/10.5281/zenodo.11031718

Pearson, CAB and Hladish, T (2023). tjhladish/AbcSmc. [Data Collection]. Github. https://github.com/tjhladish/AbcSmc

Pearson, CAB, Hladish, T, Pillai, AN and Chao, D (2023). tjhladish/dengue-abm. [Data Collection]. Github. https://github.com/tjhladish/dengue-abm

Pung, R, Kucharski, AJ, Firth, J, Russell, TW, Rogers, T and Lee, V (2024). rachaelpung/temporal_networks. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.14032212

Richards, AS (2023). alexandrasrichards/natural_history_tb_disease. [Data Collection]. GitHub. https://github.com/alexandrasrichards/natural_history_tb_disease

Robert, A and Suffel, AM (2024). alxsrobert/measles_england_sir. [Data Collection]. Github. https://github.com/alxsrobert/measles_england_sir

Roell, Y, Pezzi, L, Lozano-Parra, A, Olson, D, Messina, J, Quandelacy, T, Drexler, JF, Brady, O, Karimzadeh, M and Jaenisch, T (2024). S1 Table for "Assessing vulnerability for future Zika virus outbreaks using seroprevalence data and environmental suitability maps". [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0012017.s001

Russell, TW (2023). Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10223385

Russell, TW and Kucharski, AJ (2024). thimotei/legacy_nAb_kinetics. [Data Collection]. Github. https://github.com/thimotei/legacy_nAb_kinetics/

Shearer, FM, Moyes, CL, Pigott, DM, Brady, OJ, Marinho, F, Deshpande, A, Longbottom, J, Browne, AJ, Kraemer, MUG, O'reilly, KM, Hombach, J, Yactayo, S, de Araújo, VEM, da Nóbrega, AA, Mosser, JF, Stanaway, JD, Lim, SS, Hay, SI, Golding, N and Reiner, RC (2018). Data from: Global yellow fever vaccination coverage from 1970 to 2016: an adjusted retrospective analysis. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.5ps8j

Sherratt, K, Abbott, S, Carnegie, A and Liu, Y (2023). Improving modelling for epidemic responses: reflections. [Data Collection]. Open Science Framework. https://doi.org/10.17605/OSF.IO/4JNCB

Sherratt, K and Funk, S (2024). epiforecasts/multi-model-information: Publication release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10891376

Simpson, KMJ, Mor, SM, Ward, MP, Collins, J, Flint, J, Hill-Cawthorne, GA and El Ghany, MA (2020). Dataset for "Genomic characterisation of Salmonella enterica serovar Wangata isolates obtained from different sources reveals low genomic diversity". [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0229697.s002

Skrip, L, Barcon, S, Davis, G, Yeabah, TO and Kromah, M (2024). Data collection tools and dataset from tracer study of Q4D Lab, a locally developed and owned coding and biostatistics program in Liberia. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26762368.v2

Sliversteri, S, Ssali, A, Bahemuka, UM, Nsubuga, D, Muwanga, M, Nsereko, C, Ssemwanga, E, Robert, A, Seeley, J, Elliott, A and Ruzagira, E (2024). Structural and social factors affecting COVID-19 vaccine uptake among healthcare workers and older people in Uganda: A qualitative analysis. Data file. [Data Collection]. PLOS Global Public Health. https://doi.org/10.1371/journal.pgph.0002188.s003

Tiley, K (2024). katietiley/Wolbachia_TPP_PPC. [Data Collection]. Github. https://github.com/katietiley/Wolbachia_TPP_PPC

Van zandvoort, K, Hassan, AI, Bobe, MO, Pell, CL, Ahmed, MS, Ortika, BD, Ibrahim, S, Abdi, MI, Karim, MA, Eggo, RM, Yusuf, S, Hinds, J, Soleman, SM, Cummings, R, Mcgowan, CR, Mulholland, EK, Satzke, C, Hergeeye, MA, Checchi, F and Flasche, S (2024). Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland. Data and analyses. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.11493115

Waterlow, N and Knight, G (2024). gwenknight/ecdc_data_age_sex. [Data Collection]. Github. https://github.com/gwenknight/ecdc_data_age_sex

Xiang, F and Frost, S (2019). xiangfstats/GenieR: A final release. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.2532305