A

Abbas, KM (2020). vaccine-impact/epi_covid. [Data Collection]. Github. https://github.com/vaccine-impact/epi_covid

Abbas, KM, Kang, GJ, Chen, D, Werre, SR and Marathe, A (2018). Repository for manuscript: "Demographics, perceptions, and socio-economic factors affecting influenza vaccination among adults in the United States". [Data Collection]. Github. https://github.com/gloriakang/influenza-vaccination-adults

Abbas, KM, Van Zandvoort, K, Brisson, M and Jit, M (2020). Effects of updated demography, disability weights, and cervical cancer burden on estimates of human papillomavirus vaccination impact at the global, regional, and national levels: a PRIME modelling study. [Data Collection]. The Lancet Global Health. https://doi.org/10.1016/S2214-109X(20)30022-X

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

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

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

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

Abbott, S, Bekker-Nielsen Dunbar, M and Smith, A (2020). seabbs/getTBinR. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2547405

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). Collated Results of the National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Tests, Hospital Admissions and Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/4L3OKY

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Continent Summary Reproduction Number (R) Based on Reported Cases. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/F9HVNL

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). Continent Summary Reproduction Number (R) Based on Reported Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/A12ADQ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Admissions. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/0NYGXE

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/UIM3MB

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). Local Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/ISLFJB

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National Reproduction Number (R) Based on Reported Cases. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/TTLQRN

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National Reproduction Number (R) Estimates Based on Reported Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/RBZVJE

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Belgium Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/NALGQJ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Brazil Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/METDW2

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Canada Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/2CNKZJ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Colombia Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/GI8EVP

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Germany Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/LNMJYJ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for India Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/PRP6CY

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for Italy Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/8DUSHZ

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2021). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for South Africa Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/17XS9I

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Deaths. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/QVWUJ5

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Hospital Admissions. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/CCE4XT

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United Kingdom Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/S07EZB

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/BZ7FPH

Abbott, S and Bosse, N (2022). epiforecasts/simplified-forecaster-evaluation. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7189308

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

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

Abbott, S and Funk, S (2021). epiforecasts/covid19.sgene.utla.rt. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5236661

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). Pathways to Low Fertility. [Data Collection]. Zenodo, London, United Kingdom. http://doi.org/10.5281/zenodo.3627833

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). Wuhan Seeding Vs Transmission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3630424

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). epiforecasts/WuhanSeedingVsTransmission: Resubmission to Wellcome Open Research. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3630424

Abbott, S, Gaythorpe, KA, Imai, N and Liu, Y (2020). seabbs/CovidInterventionReview: CC0 license. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3728162

Abbott, S, Hellewell, J, Lucas, T, Funk, S and Gimma, A (2023). epiforecasts/ringbp. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3749529

Abbott, S, Hickson, J, Badr, HS, Funk, S, Monticone, P, Ellis, P, Munday, JD, Allen, J, Pearson, CAB, DeWitt, M, Bosse, N and Meakin, S (2021). epiforecasts/EpiNow2. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957489

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

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

Abbott, S and Sherratt, K (2022). seabbs/ecdc-weekly-growth-forecasts. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7189620

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

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

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

Abdurahman, O, Last, A, Macleod, D, Habtamu, E, Versteeg, B, Greenland, K, Burton, MJ, Dumessa, G, Guye, M, Nure, R, Adugna, D and Miecha, H (2023). Data for risk factor survey of active trachoma in the Oromia region of Ethiopia. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003653.

Abotsi, RE, Nicol, MP, McHugh, G, Simms, V, Rehman, AM, Barthus, C, Ngwira, LG, Kwambana-Adams, B, Heyderman, RS, Odland, JØ, Ferrand, RA and Dube, FS (2021). Data from: The impact of long-term azithromycin on antibiotic resistance in HIV-associated chronic lung disease. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.5dv41ns71

Abouyannis, M, Boga, M, Amadi, D, Ouma, N, Nyaguara, A, Mturi, N, Berkley, JA, Adetifa, IMO, Casewell, NR, Lalloo, DG and Hamaluba, M (2023). The de-identified final dataset for the study population. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010987.s002

Abramsky, T, Harvey, S, Lees, S, Kapiga, S, Mtolela, G, Madaha, F, Hanson, C, Hashim, R and Kapinga, I (2023). MAISHA Study CRT01: Baseline and follow-up data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003591.

Abramsky, T, Harvey, S, Lees, S, Kapiga, S, Mtolela, G, Madaha, F, Hanson, C, Hashim, R and Kapinga, I (2023). MAISHA Study CRT02: Baseline and follow-up data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003592.

Adetifa, IMO, Uyoga, S, Gitonga, JN, Mugo, D, Otiende, M, Nyagwange, J, Karanja, HK, Tuju, J, Wanjiku, P, Aman, R, Mwangangi, M, Amoth, P, Kasera, K, Ng’ang’a, W, Rombo, C, Yegon, C, Kithi, K, Odhiambo, E, Rotich, T, Orgut, I, Kihara, S, Bottomley, C, Kagucia, EW, Gallagher, KE, Etyang, A, Voller, S, Lambe, T, Wright, D, Barasa, E, Tsofa, B, Bejon, P, Ochola-Oyier, LI, Agweyu, A, Scott, JAG and Warimwe, GM (2021). Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/FQUNVD

Adeyemi, OO, Ndodo, ND, Sulaiman, MK, Ayansola, OT, Buhari, OIN, Akanbi, OA, Bolarinwa, OA, Chukwu, C, Joel, IY, Omoare, AA, Wahab, KW, Obiekea, C, Buhari, MO, Ahumibe, A, Kolawole, CF, Okoi, C, Omotesho, OB, Mba, N, Adeniyi, O, Babatunde, O, Akintunde, N, Ayinla, G, Akande, OW, Odunola, RA, Saka, MJ, Musa, OI, Durotoye, IA, Ihekweazu, C, Adetifa, IM and Fadeyi, A (2023). SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control. S1 Data. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0280756.s003

Aiken, A and Rehman, AM (2023). MBIRA - Mortality from Bacterial Infections Resistant to Antibiotics study - underlying data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003168.

Alcayna, T, Fletcher, I, Gibb, R, Tremblay, L, Funk, S, Rao, B and Lowe, R (2022). Supplementary Material: Climate-sensitive disease outbreaks in the aftermath of extreme climatic events: a scoping review. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6376135

Aldridge, RW, Lewer, D, Beale, S, Johnson, AM, Zambon, M, Hayward, AC and Fragaszy, E (2020). Dataset: Seasonality and immunity to laboratory-confirmed seasonal coronaviruses (HCoV-NL63, HCoV-OC43, and HCoV-229E): results from the Flu Watch cohort study. [Data Collection]. UCL Institute of Health Informatics, London, United Kingdom. https://doi.org/10.14324/000.ds.10093909

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.

Alobo, M, Mgone, C, Wesonga, CA, Lawn, JE, Ezeaka, C, Okong, P, Temmerman, M, Molineux, E, Malata, A, Wazny, K and Kariuki, T (2021). Research priorities in maternal and neonatal health in Africa: results using the Child Health and Nutrition Research Initiative method involving over 900 experts across the continent. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/38GTU

Andreu, N, Phelan, J, de Sessions, PF, Cliff, JM, Clark, T and Hibberd, M (2017). Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. [Data Collection]. Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88801

Angkurawaranon, C, Nitsch, D, Larke, N, Rehman, AM, Smeeth, L and Addo, J (2016). Ecological Study of HIV Infection and Hypertension in Sub-Saharan Africa: Is There a Double Burden of Disease? [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0166375.

Ansari, HR, Templeton, TJ, Subudhi, AK, Ramaprasad, A, Tang, J, Lu, F, Naeem, R, Hashish, Y, Oguike, MC, Benavente, ED, Clark, TG, Sutherland, CJ, Barnwell, JW, Culleton, R, Cao, J and Pain, A (2016). Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. [Data Collection]. International Journal for Parasitology. https://doi.org/10.1016/j.ijpara.2016.05.009.

Arunga, S (2019). The management of microbial keratitis within Uganda’s primary health system: a situational analysis. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/MSLAOS

Ashall, J, Shah, S, Biggs, JR, Chang, JR, Jafari, Y, Brady, OJ, Mai, HK, Lien, LT, Do Thai, H, Nguyen, HAT, Anh, DD, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Rasschaert, F, Van Wesenbeeck, L, Yoshida, L, Hafalla, JCR, Hue, S and Hibberd, ML (2023). Dengue virus type 4 isolate DET-P-0428-1 polyprotein (POLY) gene, complete cds; and sfRNA2 lncRNA gene, partial sequence. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/OQ427062

Ashall, J, Shah, S, Biggs, JR, Chang, JR, Jafari, Y, Brady, OJ, Mai, HK, Lien, LT, Do Thai, H, Nguyen, HAT, Anh, DD, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Rasschaert, F, Van Wesenbeeck, L, Yoshida, L, Hafalla, JCR, Hue, S and Hibberd, ML (2023). Dengue virus type I isolate DEN-P-1098-1 polyprotein (POLY) gene, partial cds. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/OQ426566.1/

Assefa, N, Demissie, L, Teklemarriam, Z, Oundo, JO, Madrid, L, Dessie, Y and Scott, JAG (2021). Replication Data for: Seroprevalence of anti–SARS-CoV-2 antibodies in women attending antenatal care in eastern Ethiopia. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/XIWCXN

Athrey, G, Hodges, TK, Reddy, MR, Overgaard, H, Matias, A, Ridl, FC, Kleinschmidt, I, Caccone, A and Slotman, MA (2013). Data from: Effective population size of malaria mosquitoes: large impact of vector control. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.1rf75

Atkins, KE and Hodgson, D (2022). katiito/rsvvaccines_amr. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7185501

Atkins, K, Vanhoek, A, Watson, C, Baguelin, M, Choga, L, Patel, A, Raj, T, Jit, M and Griffiths, U (2015). Data from: Seasonal influenza vaccination delivery through community pharmacists in England: evaluation of the London pilot. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.rn931

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

Avoka, CK, Banke-Thomas, A, Beňová, L, Radovich, E and Campbell, OMR (2022). Use of motorised transport and pathways to childbirth care in health facilities: Evidence from the 2018 Nigeria Demographic and Health Survey. S1 Data. [Data Collection]. PLOS Global Public Health. https://doi.org/10.1371/journal.pgph.0000868.s009

Ayieko, P, Hashim, R, Grosskurth, H and Kapiga, S (2021). Hand hygiene intervention to optimise soil transmitted helminths infection control among primary school children: endline survey data from a cluster randomised trial. [Data Collection]. Mendeley Data. https://doi.org/10.17632/9wgnn35jcr.1

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

B

Bacigalupo, S, Ruby Chang, Y, Dixon, L, Gubbins, S, Kucharski, AJ and Drewe, J (2022). The importance of fine-scale predictors of wild boar habitat use in an isolated population. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.4mw6m90cx

Balogun, M, Banke-Thomas, A, Sekoni, A, Boateng, GO, Yesufu, V, Wright, O, Ubani, O, Abayomi, A, Afolabi, BB and Ogunsola, F (2021). Dataset of 1241 clients of RMNCH services during the COVID-19 outbreak in Lagos. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0251382.s002

Bandason, T, Dauya, E, Dakshina, S, McHugh, G, Chonzi, P, Munyati, S, Weiss, HA, Simms, V, Kranzer, K and Ferrand, RA (2018). Screening tool to identify adolescents living with HIV in a community setting in Zimbabwe: A validation study. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0204891.s001.

Banke-Thomas, A (2022). Intra-facility_maternal_deaths_Lagos_2018-2019. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20098148.v1

Banke-Thomas, A, Olubodun, T, Macharia, PM, Wong, KL, Gwacham-Anisiobi, U, Ogunyemi, O, Benova, L, Omolade Abejirinde, I, Makanga, PT, Wang, J, Stanton, C, Sundararajan, N, Shah, Y, Prasad, G, Kansal, M, Vispute, S, Shekel, T and Afolabi, BB (2023). A geospatial database of close to reality travel times to obstetric emergency care in 15 Nigerian conurbations. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.22699759.v1

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

Barnsley, G and Watson, OJ (2022). mrc-ide/covid-vaccine-impact-orderly. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6539430

Barsosio, HC, Gitonga, JN, Karanja, HK, Nyamwaya, DK, Omuoyo, DO, Kamau, E, Hamaluba, MM, Nyiro, JU, Kitsao, BS, Nyaguara, A, Mwakio, S, Newton, CR, Sang, R, Wright, D, Sanders, EJ, Seale, AC, Agoti, CN, Berkley, JA, Bejon, P and Warimwe, GM (2019). Replication Data for: Congenital Microcephaly Unrelated to Flavivirus Exposure in Coastal Kenya. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/4EB9PG

Baschieri, A (2016). Unintended childbearing and family welfare in rural Malawi. [Data Collection]. UK Data Service, Colchester, Essex, United Kingdom. http://dx.doi.org/10.5255/UKDA-SN-850869

Bastiaens, GJH, Tiono, AB, Okebe, J, Pett, HE, Coulibaly, SA, Gonçalves, BP, Affara, M, Ouédraogo, A, Bougouma, EC, Sanou, GS, Nébié, I, Bradley, J, Lanke, KHW, Niemi, M, Sirima, SB, d’Alessandro, U, Bousema, T and Drakeley, C (2018). Data from: Safety of single low-dose primaquine in glucose-6-phosphate dehydrogenase deficient falciparum-infected African males: two open-label, randomized, safety trials. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.230ps

Beale, S, Lewer, D, Aldridge, RW, Johnson, AM, Zambon, M, Hayward, A and Fragaszy, E (2020). Household Transmission of Seasonal Coronavirus Infections: Results from the Flu Watch cohort study. [Data Collection]. University College London. https://doi.org/10.5522/04/12383873.v1

Bell, S, Clarke, R, Mounier-Jack, S and Paterson, P (2020). Parents’ and guardians’ views on the acceptability of a future COVID-19 vaccine for themselves and their children: cross-sectional survey and qualitative interview data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001862.

Bell, S, Clarke, R, Mounier-Jack, S, Paterson, P, Ismail, S and Ojo-Aromokudu, O (2021). COVID-19 vaccination beliefs, attitudes, and behaviours among health and social care workers in the UK: Survey dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002525.

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.

Benest, J (2022). ISIDLSHTM/CoBeDOA. [Data Collection]. GitHub. https://github.com/ISIDLSHTM/CoBeDOA

Benest, J (2022). ISIDLSHTM/CoBeDOA_Data. [Data Collection]. GitHub. https://github.com/ISIDLSHTM/CoBeDOA_Data

Benest, J, Rhodes, S, Evans, TG and White, RG (2022). ISIDLSHTM/Model_Size_Selection. [Data Collection]. Github. https://github.com/ISIDLSHTM/Model_Size_Selection

Benova, L, Moller, A and Moran, AC (2019). Qualitative data for: "The landscape of validation of global maternal and newborn health indicators through key informant interviews". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001403.

Bhattarai, S, Adhikari, A, Rayamajhee, B, Dhungana, J, Singh, M, Koirala, S and Shakya, DR (2022). Data_Sheet_1_Participatory Approach to Develop Evidence-Based Clinical Ethics Guidelines for the Care of COVID-19 Patients: A Mixed Method Study From Nepal. [Data Collection]. Frontiers. https://doi.org/10.3389/fpubh.2022.873881.s001

Biggs, JR, Sy, AK, Ashall, J, Santoso, MS, Brady, OJ, Reyes, MAJ, Quinones, MA, Jones-Warner, W, Tandoc, AO, Sucaldito, NL, Huynh, KM, Le, TL, Hung, DT, Nguyen, HAT, Dang, DA, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Menten, J, Rasschaert, F, Van Wesenbeeck, L, Masyeni, S, Haryanto, S, Yohan, B, Cutiongco-de la Paz, E, Yoshida, L, Hue, S, Capeding, MRZ, Padilla, CD, Sasmono, RT, Hafalla, JCR and Hibberd, ML (2022). A summary of data collected from suspected dengue patients included in the study population from Indonesia, Vietnam and the Philippines. [Data Collection]. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010365.s001

Biggs, J, Sy, AK, Ashall, J, Santoso, MS, Brady, OJ, Reyes, MAJ, Quinones, MA, Jones-Warner, W, Tandoc, AO, Sucaldito, NL, Huynh, KM, Le, TL, Hung, DT, Nguyen, HAT, Dang, DA, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Menten, J, Rasschaert, F, Van Wesenbeeck, L, Masyeni, S, Haryanto, S, Yohan, B, Cutiongco-de la Paz, E, Yoshida, L, Hue, S, Capeding, MRZ, Padilla, CD, Sasmono, RT, Hafalla, JCR and Hibberd, ML (2022). Demographic characteristics of the reporting study population at enrolment. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010365.s002

Biggs, J, Sy, AK, Ashall, J, Santoso, MS, Brady, OJ, Reyes, MAJ, Quinones, MA, Jones-Warner, W, Tandoc, AO, Sucaldito, NL, Huynh, KM, Le, TL, Hung, DT, Nguyen, HAT, Dang, DA, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Menten, J, Rasschaert, F, Van Wesenbeeck, L, Masyeni, S, Haryanto, S, Yohan, B, Cutiongco-de la Paz, E, Yoshida, L, Hue, S, Capeding, MRZ, Padilla, CD, Sasmono, RT, Hafalla, JCR and Hibberd, ML (2022). Sensitivity (95%CI) of NS1 RDTs in capturing DENV1-4 infections stratified by immune status among patients from Vietnam (N:1,217). [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010365.s003

Blassel, L, Tostevin, A, Villabona-arenas, CJ, Peeters, M, Hue, S and Gascuel, O (2021). Archive of figure generating data. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1008873.s007

Blencowe, H (2017). Global and regional prevalence of neural tube defects estimates in 2015: Data sources, methods and results. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.264.

Blencowe, H, Bradley, E, Lawn, JE, Ohuma, E, Okwaraji, Y, Suarez Idueta, L and Yargawa, J (2022). Vulnerable Newborn Measurement Collaboration. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003095.

Blencowe, H, Cousens, S, Bianchi jassir, F, Say, L, Chou, D, Mathers, C, Hogan, D, Shiekh, S, Qureshi, Z, You, D and Lawn, J (2015). National, regional, and worldwide estimates of stillbirth rates in 2015, with trends from 2000: a systematic analysis. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.25.

Blencowe, H, Krasevec, J, de Onis, M, Black, RE, An, X, Stevens, GA, Borghi, E, Hayashi, C, Estevez, D, Cegolon, L, Shiekh, S, Ponce Hardy, V, Lawn, JE and Cousens, S (2019). Supporting information for National, regional, and worldwide estimates of low birthweight rates in 2015, with trends from 2000: a systematic analysis. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001090.

Bolt, H (2023). ehr-lshtm/acute_kidney_injury_seasonality_ML. [Data Collection]. GitHub. https://github.com/ehr-lshtm/acute_kidney_injury_seasonality_ML

Bonnet, G, Pizzitutti, F, Gonzales-Gustavson, EA, Gabriël, S, Pan, WK, Garcia, HH, Bustos, JA, Vilchez, P and O’Neal, SE (2022). Dataset for calcified NCC (Matapalo area villages). [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1010118.s006

Bonnet, G, Pizzitutti, F, Gonzales-Gustavson, EA, Gabriël, S, Pan, WK, Garcia, HH, Bustos, JA, Vilchez, P and O’Neal, SE (2022). Dataset for epilepsy figures (Tumbes region). [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1010118.s005

Borghi, J, Mamdani, M, Abdulla, S, Mayumana, I, Mashasi, I, Binyaruka, P, Patouillard, E, Njau, I and Maestad, O (2014). Evaluation of a pay for performance programme in Pwani region in Tanzania: A controlled before and after study, IMPACT. [Data Collection]. Ifakara Health Institute, Dar es Salaam, Tanzania. https://doi.org/10.17890/ihi.2012.12.99

Borghi, J, Mamdani, M, Abdulla, S, Mayumana, I, Mashasi, I, Binyaruka, P, Patouillard, E, Njau, I and Maestad, O (2014). Evaluation of a pay for performance programme in Pwani region in Tanzania: A controlled before and after study, PROCESS. [Data Collection]. Ifakara Health Institute, Dar es Salaam, Tanzania. https://doi.org/10.17890/ihi.2012.01.99

Bosse, NI, Abbott, S, Bracher, J, Van leeuwen, E, Cori, A and Funk, S (2023). Data for "Human judgement forecasting of COVID-19 in the UK" by Bosse et. al (2023). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7897288

Bosse, N, Abbott, S and Funk, S (2022). epiforecasts/covid.german.forecasts. [Data Collection]. Github. https://github.com/epiforecasts/covid.german.forecasts

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

Bosse, N, Bracher, J, Abbott, S and Funk, S (2023). epiforecasts/transformation-forecast-evaluation. [Data Collection]. Github. https://github.com/epiforecasts/transformation-forecast-evaluation

Bott, S, Neuman, M, Helleringer, S, Desclaux, A, Asmar, KE, Obermeyer, CM and MATCH Study Group (2014). Rewards and challenges of providing HIV testing and counselling services: health worker perspectives from Burkina Faso, Kenya and Uganda. [Data Collection]. Health policy and planning. https://doi.org/10.1093/heapol/czu100

Bottomley, C (2021). christian-bottomley/mixture_model_sarscov2. [Data Collection]. Github. https://github.com/christian-bottomley/mixture_model_sarscov2

Bousema, T, Stresman, G, Baidjoe, AY, Bradley, J, Knight, P, Stone, W, Osoti, V, Makori, E, Owaga, C, Odongo, W, China, P, Shagari, S, Doumbo, OK, Sauerwein, RW, Kariuki, S, Drakeley, C, Stevenson, J and Cox, J (2017). Data from: The impact of hotspot-targeted interventions on malaria transmission in Rachuonyo south district in the western Kenyan highlands: a cluster-randomized controlled trial. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.nr8d8

Bower, H, Akpogheneta, O, Kanneh, Z, Jusu, B, Kanneh, L, Alhasan, F, Gbakie, M and Shieffelin, J (2020). Data for: "Boosting understanding of Lassa Fever virus epidemiology: field testing a novel assay to identify past Lassa Fever virus infection in blood and oral fluids of survivors and unexposed controls in Sierra Leone". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001992.

Bower, H and Glynn, J (2017). Data from: A systematic review and meta-analysis of seroprevalence surveys of ebolavirus infection. [Data Collection]. Dryad Digital Repository. https://doi.org/10.5061/dryad.gn95r.2.

Bower, H, el Karsany, M, Adam, Abd Alhadi Adam Hussein, Idriss, MI, Alzain, MA, Alfakiyousif, MEA, Mohamed, R, Mahmoud, I, Albadri, O, Mahmoud, SAA, Abdalla, OI, Eldigail, M, Elagib, N, Arnold, U, Gutierrez8, B, Pybus, OG, Carter, DP, Pullan, ST, Jacob, ST, Abdallah, TM, Gannon, B and Fletcher, TE (2021). Data for: "Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002018.

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

Brady, OJ (2018). Microcephaly and potential exposure data in Brazil 2015-2017. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.7359197.v1

Brady, OJ (2013). Model of adult Aedes aegypti survival/mortality at different temperatures. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.865034.v1

Brady, OJ (2013). Model of adult Aedes albopictus survival/mortality at different temperatures. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.865035.v1

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

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/

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

Brotons, P, Bassat, Q, Lanaspa, M, Henares, D, Perez-Arguello, A, Madrid, L, Balcells, R, Acacio, S, Andres-Franch, M, Marcos, MA, Valero-Rello, A and Muñoz-Almagro, C (2017). Nasopharyngeal bacterial load as a marker for rapid and easy diagnosis of invasive pneumococcal disease in children from Mozambique: Supporting data for the manuscript results. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0184762.s001

Burr, SE, Camara, B, Oluwalana, C, Bojang, E, Bottomley, C, Bojang, A, Bailey, RL, D'Alessandro, U and Roca, A (2017). Data for: "Does azithromycin given to women in labour decrease ocular bacterial infection in neonates? A double-blind, randomized trial". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000626.

C

Cairns, M, Woukeu, A and Tagbor, H (2015). Screening and treatment of malaria in pregnancy in West Africa. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.2.

Camacho, A, Kucharski, AJ, Aki-Sawyerr, Y, White, MA, Flasche, S, Baguelin, M, Pollington, TM, Carney, J, Glover, R, Smout, E, Tiffany, A, Edmunds, WJ and Funk, S (2015). Bed capacity for Ebola patients in Sierra Leone. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1304889.v1

Camacho, A, Kucharski, A, Funk, S, Breman, J, Piot, P and Edmunds, J (2014). Potential for large outbreaks of Ebola virus disease: Supplementary Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.27.

Cameron, DW, Panesar, P, Jones, A, Aldous, A, Kranzer, K, Halpin, E, Fifer, H, Macrae, B, Curtis, C and Pollara, G (2016). Attitudes and Behaviours to Antimicrobial Prescribing following introduction of a Smartphone App. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0154202.s004

Campbell, O, Cegolon, L, Macleod, D and Benova, L (2016). Length of Stay After Childbirth in 92 Countries and Associated Factors in 30 Low- and Middle-Income Countries: Compilation of Reported Data and a Cross-sectional Analysis from Nationally Representative Surveys. [Data Collection]. PLOS Medicine. https://doi.org/10.1371/journal.pmed.1001972

Candido, DS, Claro, IM, de Jesus, JG, Souza, WM, Moreira, FRR, Dellicour, S, Mellan, TA, du Plessis, L, Pereira, RHM, Sales, FCS, Manuli, ER, Thézé, J, Almeida, L, Menezes, MT, Voloch, CM, Fumagalli, MJ, Coletti, TM, da Silva, CAM, Ramundo, MS, Amorim, MR, Hoeltgebaum, HH, Mishra, S, Gill, MS, Carvalho, LM, Buss, LF, Prete, CA, Ashworth, J, Nakaya, HI, Peixoto, PS, Brady, OJ, Nicholls, SM, Tanuri, A, Rossi, Átila D., Braga, CK, Gerber, AL, de C. Guimarães, AP, Gaburo, N, Alencar, CS, Ferreira, AC, Lima, CX, Levi, JE, Granato, C, Ferreira, GM, Francisco, RS, Granja, F, Garcia, MT, Moretti, ML, Perroud, MW, Castiñeiras, Terezinha M. P. P., Lazari, CS, Hill, SC, de Souza Santos, AA, Simeoni, CL, Forato, J, Sposito, AC, Schreiber, AZ, Santos, MNN, de Sá, CZ, Souza, RP, Resende-Moreira, LC, Teixeira, MM, Hubner, J, Leme, PAF, Moreira, RG, Nogueira, ML, Ferguson, NM, Costa, SF, Proenca-Modena, JL, Vasconcelos, ATR, Bhatt, S, Lemey, P, Wu, C, Rambaut, A, Loman, NJ, Aguiar, RS, Pybus, OG, Sabino, EC and Faria, NR (2020). Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil. [Data Collection]. Dryad. http://doi.org/10.5061/dryad.rxwdbrv5z

Candido, DS, Claro, IM, de Jesus, JG, Souza, WM, Moreira, FRR, Dellicour, S, Mellan, TA, du Plessis, L, Pereira, RHM, Sales, FCS, Manuli, ER, Thézé, J, Almeida, L, Menezes, MT, Voloch, CM, Fumagalli, MJ, Coletti, TM, da Silva, CAM, Ramundo, MS, Amorim, MR, Hoeltgebaum, HH, Mishra, S, Gill, MS, Carvalho, LM, Buss, LF, Prete, CA, Ashworth, J, Nakaya, HI, Peixoto, PS, Brady, OJ, Nicholls, SM, Tanuri, A, Rossi, Átila D., Braga, CK, Gerber, AL, de C. Guimarães, AP, Gaburo, N, Alencar, CS, Ferreira, AC, Lima, CX, Levi, JE, Granato, C, Ferreira, GM, Francisco, RS, Granja, F, Garcia, MT, Moretti, ML, Perroud, MW, Castiñeiras, Terezinha M. P. P., Lazari, CS, Hill, SC, de Souza Santos, AA, Simeoni, CL, Forato, J, Sposito, AC, Schreiber, AZ, Santos, MNN, de Sá, CZ, Souza, RP, Resende-Moreira, LC, Teixeira, MM, Hubner, J, Leme, PAF, Moreira, RG, Nogueira, ML, Ferguson, NM, Costa, SF, Proenca-Modena, JL, Vasconcelos, ATR, Bhatt, S, Lemey, P, Wu, C, Rambaut, A, Loman, NJ, Aguiar, RS, Pybus, OG, Sabino, EC and Faria, NR (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. [Data Collection]. Science. https://doi.org/10.1126/science.abd2161

Carrillo-Larco, RM, Bernabe-ortiz, A, Miranda, JJ, Xue, H and Wang, Y (2017). Maternal perception & BMI [complete no dates]. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0175685.s001

Carter, N, Webb, E, Lebina, L, Motsomi, K, Bosch, Z, Martinson, N and MacPherson, P (2023). Data supporting "Prevalence of subclinical pulmonary tuberculosis and its association with HIV in household contacts of tuberculosis in two South African provinces: analysis of a cluster-randomised trial". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003373.

Carvalho, MS, Freitas, LP, Cruz, OG, Brasil, P and Bastos, LS (2020). Dengue and microcephaly cases in Brazil used in Carvalho et al. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3489427

Cerqueira-Silva, T, de Araujo Oliveira, V, Paixão, ES, Júnior, JB, Penna, GO, Werneck, GL, Pearce, N, Barreto, ML, Boaventura, VS and Barral-Netto, M (2022). Duration of protection of CoronaVac plus heterologous BNT162b2 booster in the Omicron period in Brazil. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6657862

Chan, K, Tusting, LS, Bottomley, C, Saito, K and Lines, J (2022). Replication Data for: Malaria transmission and prevalence in rice-growing versus non-rice-growing villages in Africa: a systematic review and meta-analysis. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/PXF0JX

Chandler, C, Webb, EL, Maiteki-Sebuguzi, C, Nayiga, S, Nabirye, C, Diliberto, D, Ssemmondo, E, Dorsey, G, Kamya, MR and Staedke, SG (2017). The impact of an intervention to introduce malaria rapid diagnostic tests on fever case management in a high transmission setting in Uganda: A mixed-methods cluster-randomized trial (PRIME). [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0170998.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ogobara, J and Greenwood, B (2020). AZ-SMC Trial - School child parasitaemia dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001934.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ouedraogo, J and Greenwood, B (2020). AZ-SMC Trial - Cross-sectional dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001932.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ouedraogo, J and Greenwood, B (2020). AZ-SMC Trial - Drug administration dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001931.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O and Ouedraogo, J (2020). AZ-SMC Trial - In vivo treatment efficacy dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001935.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ouedraogo, J and Greenwood, B (2020). AZ-SMC Trial - Person-Time dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001928.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ouedraogo, J and Greenwood, B (2020). AZ-SMC Trial - Weekly survey dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001933.

Chandramohan, D, Dicko, A, Zongo, I, Sagara, I, Cairns, M, Kuepfer, I, Diarra, M, Barry, A, Tapily, A, Nikiema, F, Yerbanga, S, Coumare, S, Thera, I, Traore, A, Milligan, P, Tinto, H, Doumbo, O, Ouedraogo, J and Greenwood, B (2020). Data repository for AZ-SMC - a trial of seasonal malaria chemoprevention combined with azithromycin in African children. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/data.00001752.

Chapman, LAC, Barnard, RC, Russell, TW, Abbott, S, Van Zandvoort, K, Davies, NG and Kucharski, AJ (2021). Unexposed populations and potential COVID-19 burden in European countries as of 21st November 2021. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5772162

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

Chapman, LAC, Shukla, P and Lo, NC (2021). Comparison of COVID-19 vaccine prioritization strategies in the United States. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4516525

Chapman, LA, Aubry, M, Maset, N, Russell, T, Knock, ES, Lees, JA, Mallet, H, Cao-Lormeau, V and Kucharski, AJ (2023). Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7790839

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

Checchi, F (2022). francescochecchi/mortality_capture_recapture_analysis. [Data Collection]. Github. https://github.com/francescochecchi/mortality_capture_recapture_analysis

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

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

Chihana, M and Crampin, AC (2015). Karonga HDSS INDEPTH Core Dataset 2003 - 2011. [Data Collection]. INDEPTH Network. https://doi.org/10.7796/INDEPTH.MW011.CMD2011.v4

Chihana, M and Crampin, AC (2015). Malawi - Karonga HDSS INDEPTH Core Dataset 2003 - 2012 Release 2015. [Data Collection]. INDEPTH Network. https://doi.org/10.7796/INDEPTH.MW011.CMD2012.v1

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

Choi, Y, Campbell, H, Amirthalingam, G, Van Hoek, AJ and Miller, E (2017). Additional file 1: 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_D2.v1

Choko, A and Corbett, EL (2023). Baseline data for the fishermen’s schistosomiasis and HIV services (FISH) cluster randomized trial in Mangochi, Malawi. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003363.

Choko, A, Corbett, E and Fielding, K (2018). Baseline and primary data for the partner-provided HIV self-testing and linkage (PASTAL) adaptive multi-arm multi-stage cluster randomized trial in Blantyre, Malawi. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000923.

Choko, A, Webb, E and Corbett, E (2016). Initial Accuracy of HIV Rapid Test Kits Stored in Suboptimal Conditions and Validity of Delayed Reading of Oral Fluid Tests. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.105.

Choko, A, Webb, E and Corbett, L (2015). Uptake, accuracy, safety and linkage into care over two years of promoting annual self-testing for HIV in Blantyre, Malawi: a community-based prospective study. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.7.

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

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

Clifford, S and Hackman, J (2023). Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7618847

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

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

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

Coker, OO, Chaiprasert, A, Ngamphiw, C, Tongsima, S, Regmi, SM, Clark, T, Ong, RTH, Teo, Y, Prammananan, T and Palittapongarnpim, P (2016). Mycobacterium tuberculosis Nonthaburi genotype raw reads. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/sra/SRX1094545

Colbourn, T, Waites, W, Manheim, D, Sturniolo, S, Kerr, CC, Panovska-Griffiths, J and Colbourn, G (2020). ptti/ptti: Modelling the health and economic impacts of different testing and tracing strategies for COVID-19 in the UK. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4298798

Coletti, P, Wambua, J, Gimma, A, Willem, L, Vercruysse, S, Vanhoutte, B, Jarvis, CI, Van zandvoort, K, Edmunds, WJ, Beutels, P and Hens, N (2020). CoMix social contact data (Belgium). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4035001

Coletti, P, Wambua, J, Gimma, A, Willem, L, Vercruysse, S, Vanhoutte, B, Jarvis, CI, Van Zandvoort, K, Edmunds, J, Beutels, P and Hens, N (2020). Social contact data from CoMix survey (Belgium). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4035001

Coll, F, Mallard, K, Preston, M, Bentley, S, Parkhill, J, Mcnerney, R, Martin, N and Clark, T (2012). In Silico Spoligotyping. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://web.archive.org/web/20140726124623/http://pathogenseq.lshtm.ac.uk/

Coll, F, Mcnerney, R, Guerra-Assunção, JA, Glynn, JR, Perdigão, J, Viveiros, M, Portugal, I, Pain, A, Martin, N and Clark, TG (2014). Data for: "A robust SNP barcode for typing Mycobacterium tuberculosis complex strains". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000414.

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/

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

Colón-González, FDJ, Gibb, R, Khan, K, Watts, A, Lowe, R and Brady, OJ (2022). Projecting the future incidence and burden of dengue in Southeast Asia. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/85XWQ

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

Colón-González, FJ, Sewe, MO, Tompkins, AM, Sjödin, H, Casallas, A, Rocklöv, J, Caminade, C and Lowe, R (2021). Projecting the risk of mosquito-borne diseases in a warmer and more urbanised world: a multi-model multi-scenario intercomparison study. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/HPAEY

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

Cox, SE, White, LV, Faguer, B, Edwards, T, Lee, N, Solon, J, Ariyoshi, K, Castro, MC, Saludar, NR, Saito, N and Calapis, RW (2020). Co-morbidities (malnutrition, diabetes, anaemia, HIV, hypertension) and quality of life in persons with tuberculosis in the Philippines. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.11695467.v1

Cox, S and Faguer, B (2021). Patterns of non-communicable comorbidities at start of tuberculosis treatment in three regions of the Philippines: St-ATT cohort baseline data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002476.

Cox, S and Faguer, B (2021). St-ATT: The Starting Anti-Tuberculosis Treatment Cohort in the Philippines. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002313.

Cresswell, J, Drabo, S, Filippi, V, Ganaba, R, Guissou, R, Ilboudo, P, Ouedrago, D, Powell-Jackson, T, Somé, H, Soubeiga, A, Storeng, K and Yaogo, M (2015). Productivity, family planning and reproductive health in Burkina Faso: the PopDev study. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.13.

Cresswell, J, Filippi, V, Ganaba, R, Diallo, HA, Sarrassat, S and Somé, H (2018). Alive & Thrive Evaluation in Burkina Faso: endline data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.280.

Cresswell, J, Ganaba, R, Sarrassat, S, Cousens, S, Somé, H, Diallo, AH and Filippi, V (2017). Alive & Thrive Evaluation in Burkina Faso: baseline data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.173.

D

Damilola R. Oresegun, Peter Thorpe, Benavente, E, Campino, S, Fauzi Muh, Moon, RW, Clark, T and Cox-Singh, J (2021). Getting close to nature – Plasmodium knowlesi reference genome sequences from contemporary clinical isolates. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5598263

Daniele, M, Ouedraogo, D, Some, H, Ganaba, R, Sarrassat, S, Cousens, S, Rossier, C and Filippi, V (2019). Dataset for "Involving male partners in maternity care in Burkina Faso: a randomized controlled trial". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001021.

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.

Davidson, J, Banerjee, A, Smeeth, L and Warren-Gash, C (2022). Codelists for: "Acute cardiovascular events after SARS-CoV-2 infection in England in 2020: a self-controlled case series study". [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002763.

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

Davidson, J, Mcdonald, H, Strongman, H, Cadogan, S, Banerjee, A, Smeeth, L and Warren-Gash, C (2022). Codelists for: "Effect of cardiovascular risk profile on severe outcomes of COVID-19 in England in 2020: a population-based cohort study". [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002762.

Davidson, J, Warren-Gash, C, Banerjee, A, McDonald, H and Smeeth, L (2021). Codelists for: "The effect of influenza vaccine on acute cardiovascular events in people with varying cardiovascular risk: a self-controlled case-series study in England, 2008-2019". [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002675.

Davidson, J, Warren-Gash, C and McDonald, H (2021). Clinical codelist - CPRD Gold - solid organ transplant. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002709.

Davidson, J, Warren-Gash, C and Mcdonald, H (2021). Clinical codelist - CPRD Gold - aplastic anaemia. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002681.

Davidson, J, Warren-Gash, C and Mcdonald, H (2021). Clinical codelist - CPRD Gold - bone marrow or stem cell transplant. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002683.

Davidson, J, Warren-Gash, C and Mcdonald, H (2021). Clinical codelist - CPRD Gold - chemotherapy and radiotherapy. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002684.

Davidson, J, Warren-Gash, C and Mcdonald, H (2021). Therapy codelist - CPRD Gold - oral steroids. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002702.

Davidson, J, Warren-Gash, C, Mcdonald, H, Banerjee, A, Gayle, A, Strongman, H, Evans, D, Clay, S, Forbes, H, Mansfield, KE, Carreira, H, Bhaskaran, K, Bhate, K, Smeeth, L, Dedman, D, Mathur, R, Cadogan, S and LSHTM EHR team (2021). Codelists 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". [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002269.

Davies, NG (2021). CSV-format data for: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5105920

Davies, NG (2020). cmmid/covid-age. [Data Collection]. Github. https://github.com/cmmid/covid-age

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

Davies, NG (2020). nicholasdavies/covidm-alpha. [Data Collection]. Github. https://github.com/nicholasdavies/covidm-alpha

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 Variant of Concern 202012/01 in England". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4549674

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

Davies, NG and Gardner, A (2018). Data from: Monogamy promotes altruistic sterility in insect societies. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.gt8b5

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

Dawa, J, Emukule, GO, Barasa, E, Widdowson, MA, Anzala, O, Van Leeuwen, E, Baguelin, M, Chaves, SS and Eggo, RM (2020). Additional file 3 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12831246.v1

Dawa, J, Emukule, GO, Barasa, E, Widdowson, MA, Anzala, O, Van leeuwen, E, Baguelin, M, Chaves, SS and Eggo, RM (2020). Additional file 1 of Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12831240.v1

Day, LT, Ruysen, H, Gordeev, VS, Gore-langton, GR, Boggs, D, Cousens, S, Moxon, SG, Blencowe, H, Baschieri, A, Rahman, AE, Tahsina, T, Zaman, SB, Hossain, T, Rahman, QS, Ameen, S, Arifeen, SE, KC, A, Shrestha, SK, KC, NP, Singh, D, Jha, AK, Jha, B, Rana, N, Basnet, O, Joshi, E, Paudel, A, Shrestha, PR, Jha, D, Bastola, RC, Ghimire, JJ, Paudel, R, Salim, N, Shamba, D, Manji, K, Shabani, J, Shirima, K, Mkopi, N, Mrisho, M, Manzi, F, Jaribu, J, Kija, E, Assenga, E, Kisenge, R, Pembe, A, Hanson, C, Mbaruku, G, Masanja, H and Lawn, JE (2018). EN-BIRTH Data Collection Tools. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000951.

Day, LT, Ruysen, H, Gordeev, VS, Gore-langton, GR, Boggs, D, Cousens, S, Moxon, SG, Blencowe, H, Baschieri, A, Rahman, AE, Tahsina, T, Zaman, SB, Hossain, T, Rahman, QS, Ameen, S, Arifeen, SE, KC, A, Shrestha, SK, KC, NP, Singh, D, Jha, AK, Jha, B, Rana, N, Basnet, O, Joshi, E, Paudel, A, Shrestha, PR, Jha, D, Bastola, RC, Ghimire, JJ, Paudel, R, Salim, N, Shamba, D, Manji, K, Shabani, J, Shirima, K, Mkopi, N, Mrisho, M, Manzi, F, Jaribu, J, Kija, E, Assenga, E, Kisenge, R, Pembe, A, Hanson, C, Mbaruku, G, Masanja, H and Lawn, JE (2018). EN-BIRTH Data Collector Training - Handbook and Manual. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000952.

Day, LT, Ruysen, H, Gordeev, VS, Gore-langton, GR, Boggs, D, Cousens, S, Moxon, SG, Blencowe, H, Baschieri, A, Rahman, AE, Tahsina, T, Zaman, SB, Hossain, T, Rahman, QS, Ameen, S, Arifeen, SE, KC, A, Shrestha, SK, KC, NP, Singh, D, Jha, AK, Jha, B, Rana, N, Basnet, O, Joshi, E, Paudel, A, Shrestha, PR, Jha, D, Bastola, RC, Ghimire, JJ, Paudel, R, Salim, N, Shamba, D, Manji, K, Shabani, J, Shirima, K, Mkopi, N, Mrisho, M, Manzi, F, Jaribu, J, Kija, E, Assenga, E, Kisenge, R, Pembe, A, Hanson, C, Mbaruku, G, Masanja, H and Lawn, JE (2018). EN-BIRTH Data Collector Training – Training Module material. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000954.

Day, LT, Ruysen, H, Gordeev, VS, Gore-langton, GR, Boggs, D, Cousens, S, Moxon, SG, Blencowe, H, Baschieri, A, Rahman, AE, Tahsina, T, Zaman, SB, Hossain, T, Rahman, QS, Ameen, S, Arifeen, SE, KC, A, Shrestha, SK, KC, NP, Singh, D, Jha, AK, Jha, B, Rana, N, Basnet, O, Joshi, E, Paudel, A, Shrestha, PR, Jha, D, Bastola, RC, Ghimire, JJ, Paudel, R, Salim, N, Shamba, D, Manji, K, Shabani, J, Shirima, K, Mkopi, N, Mrisho, M, Manzi, F, Jaribu, J, Kija, E, Assenga, E, Kisenge, R, Pembe, A and Lawn, JE (2018). Every Newborn Birth Indicator Research Tracking in Hospitals (EN-BIRTH) - Supplementary Materials. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000955.

Day, LT, Ruysen, H, Gordeev, VS, Gore-langton, GR, Boggs, D, Cousens, S, Moxon, S, Blencowe, H, Baschieri, A, Rahman, AE, Tahsina, T, Zaman, SB, Hossain, T, Rahman, QS, Ameen, S, Arifeen, SE, KC, A, Shrestha, SK, KC, NP, Singh, D, Jha, AK, Jha, B, Rana, N, Basnet, O, Joshi, E, Paudel, A, Shrestha, PR, Jha, D, Bastola, RC, Ghimire, JJ, Paudel, R, Salim, N, Shamba, D, Manji, K, Shabani, J, Shirima, K, Mkopi, N, Mrisho, M, Manzi, F, Jaribu, J, Kija, E, Assenga, E, Kisenge, R, Pembe, A, Hanson, C, Mbaruku, G, Masanja, H and Lawn, JE (2018). EN-BIRTH Data Collector Training - Supporting Annexes. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000953.

De figueiredo, A (2021). Impact of vaccine passports on inclination to accept COVID-19 vaccinations in the UK. [Data Collection]. OSF. https://osf.io/xh9p7/

DeCelles, J, Kaufman, Z, Bhauti, K, Hershow, R, Weiss, H, Chaibva, C, Moyo, N, Braunschweig, E, Mantula, F, Hatzold, K and Ross, D (2019). Voluntary medical male circumcision uptake through soccer in Zimbabwe. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/FI4R2V

Delves, M, Lafuente-Monasterio, MJ, Upton, L, Ruecker, A, Leroy, D, Gamo, F and Sinden, R (2019). Table 1 - Fueling Open Innovation for Malaria Transmission-Blocking Drugs: Hundreds of Molecules Targeting Early Parasite Mosquito Stages. [Data Collection]. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.02134

Demissie, SD, Larson, H, Chantler, T, Kozuki, N, Karafillakis, E, Landegger, J, Kiapi, L, Gebrekirstos, P, Mohammad, S, Wodajo, S and Langston, A (2019). Closing the immunisation gap in Ethiopia: a formative evaluation of 'The Fifth Child Project'. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/Z75DUF

Dennis, M, Chelwa, N, Owolabi, O, Cresswell, J, Filippi, V and Campbell, O (2017). Zambia Signal Functions study 2016 dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.276.

Dennis, M, Radovich, E, Wong, K, Owolabi, O, Cavallaro, F, Mbizvo, MT, Binagwaho, A, Waiswa, P, Lynch, C and Benova, L (2017). Pathways to increased coverage: an analysis of time trends in contraceptive need and use among adolescents and young women in Kenya, Rwanda, Tanzania, and Uganda. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.3907207

Der, J, Grint, D, Narh, CT, Bonsu, F and Grant, AD (2019). Data for "Where are patients missed in the tuberculosis diagnostic cascade? A prospective cohort study in Ghana". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001529.

Derrick, T (2019). EXTENDED DATA [The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment]. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9696263.v1

Dhalla, K, Cousens, S, Bowman, R, Wood, M and Murdoch, I (2016). Is Beta Radiation Better than 5 Flurouracil as an Adjunct for Trabeculectomy Surgery When Combined with Cataract Surgery? A Randomised Controlled Trial. [Data Collection]. PLOS One. https://journals.plos.org/plosone/10.1371/journal.pone.0161674.s001

Diamond, C, Gong, H, Sun, FY, Liu, Y, Quilty, B, Jit, M, Yang, J, Yu, H, Edmunds, WJ and Baguelin, M (2021). EIDECDIA/China_influenza_seasonality. [Data Collection]. Github. https://github.com/EIDECDIA/China_influenza_seasonality

Diez Benavente, E, Florez de Sessions, P, Moon, RW, Holder, AA, Blackman, MJ, Roper, C, Drakeley, CJ, Pain, A, Sutherland, CJ, Hibberd, ML, Campino, S and Clark, TG (2017). Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pgen.1007008

Dobreva, Z, Gimma, A, Rohan, H, Djoudalbaye, B, Tshangela, A, Jarvis, CI, Van Zandvoort, K and Quaife, M (2022). Additional file 1 of Characterising social contacts under COVID-19 control measures in Africa. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.21316250.v1

Dodd, PJ, Looker, C, Plumb, ID, Bond, V, Schaap, A, Shanaube, K, Muyoyeta, M, Vynnycky, E, Godfrey-faussett, P, Corbett, EL, Beyers, N, Ayles, H and White, RG (2019). Social contact data for Zambia and South Africa (CODA dataset). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.2548692

Dodd, PJ, Looker, C, Plumb, ID, Bond, V, Schaap, A, Shanaube, K, Muyoyeta, M, Vynnycky, E, Godfrey-faussett, P, Corbett, E, Beyers, N, Ayles, H and White, R (2015). Age- and Sex-Specific Social Contact Patterns and Incidence of Mycobacterium tuberculosis Infection: Interview Questionnaire. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.35.

Downs, LO, Campbell, C, Abouyannis,, M, Otiende, M, Kapulu, M, Obiero, CW, Hamaluba, M, Ngetsa, C, Andersson, M, Githinji, G, Warimwe, G, Baisley, K, Scott, JAG, Matthews, PC and Etyang, A (2023). Replication Data for: Where Do Those Data Go? Reuse of screening results from clinical trials to estimate population prevalence of HBV infection in adults in Kilifi, Kenya. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/FPUH4R

Doyle, A (2024). Data for: Young People’s use of Technology, and mental health and well-being. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003320.

Doyle, AM, Floyd, S, Baisley, K, Orindi, B, Kwaro, D, Mthiyane, TN, Muuo, S, Shahmanesh, M, Ziraba, A and Birdthistle, I (2018). Who are the male sexual partners of adolescent girls and young women? Comparative analysis of population data in three settings prior to DREAMS roll-out. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0198783

Doyle, AM and Seeley, J (2019). Health service provision for and utilisation by young people (10-24 years) study conducted between September 2016 and August 2017 within the Africa Health Research Institute’s Population Intervention Programme Surveillance Area in northern KwaZulu-Natal. [Data Collection]. AHRI Data Repository. https://doi.org/10.23664/AHRI.HSYP.Data

Drabo, S, Kagambega, A, Keita, A, Kontiebo, S, Montel, L, Filippi, V, Soubeiga, A, Storeng, K, Da, S, Allahissem, C, Gali Gali, I and Yaogo, M (2015). Productivity, family planning and reproductive health in Burkina Faso: PopDev qualitative data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.19.

Drake, C, Hernandez, A, Liu, Y, Schwartz, AH and Sundaram, M (2021). yangclaraliu/armslist_scraping. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5185707

Dube, A and Crampin, AC (2016). Malawi - Karonga HDSS INDEPTH Core Dataset 2003 - 2014 (Release 2016). [Data Collection]. INDEPTH Data Repository. https://doi.org/10.7796/INDEPTH.MW011.CMD2014.v1

Dube, A and Crampin, AC (2017). Malawi - Karonga HDSS INDEPTH Core Dataset 2003-2015 (Release 2017). [Data Collection]. INDEPTH Data Repository. http://indepth-ishare.org/index.php/catalog/128

de Lencastre, H, Manna, S, Dunne, EM, Ortika, BD, Pell, CL, Kama, M, Russell, FM, Mungun, T, Mulholland, KE, Hinds, J and Satzke, C (2018). Discovery of a Streptococcus pneumoniae serotype 33F capsular polysaccharide locus that lacks wcjE and contains a wcyO pseudogene. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0206622

E

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

Ekoriko, P (2023). lshtm-public/rds-ui. [Data Collection]. Bitbucket. https://bitbucket.org/lshtm-public/rds-ui

Emery, JC, Dodd, PJ, Banu, S, Frascella, B, Garden, FL, Horton, KC, Hossain, S, Law, I, van Leth, F, Marks, GB, Nguyen, HB, Nguyen, HV, Onozaki, I, Quelapio, MID, Richards, AS, Shaikh, N, Tiemersma, EW, White, RG, Zaman, K, Cobelens, F and Houben, RM (2023). epidemery/subclinical_transmission. [Data Collection]. GitHub. https://github.com/epidemery/subclinical_transmission

Emes, ET and Naylor, N (2023). Trescovia/AHHME. [Data Collection]. Github. https://github.com/Trescovia/AHHME

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

Endo, A, Abbott, S, Kucharski, AJ and Funk, S (2020). Extended data: Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3740348

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

Endo, A and Kucharski, AJ (2020). akira-endo/COVID19_backwardtracing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4050267

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

Endo, A, Uchida, M, Hayashi, N, Liu, Y, Atkins, KE, Kucharski, AJ and Funk, S (2021). akira-endo/schooldynamics_FluMatsumoto14-15: Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5604502

Endo, A, Uchida, M, Liu, Y, Atkins, KE, Kucharski, AJ and Funk, S (2022). akira-endo/schooldynamics_FluMatsumoto14-15: Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5604502

Enria, L, Waterlow, N, Rogers, N, Brindle, H, Lal, S, Eggo, RM, Lees, S and Roberts, C (2020). Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001860.

Enria, L, Waterlow, N, Rogers, N, Brindle, H, Lal, S, Eggo, RM, Lees, S and Roberts, C (2020). Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Qualitative Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001859.

Enria, L, Waterlow, N, Rogers, N, Brindle, H, Lal, S, Eggo, RM, Lees, S and Roberts, C (2021). Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Quantitative Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002015.

Etyang, AO, Kapesa, S, Odipo, E, Bauni, E, Kyobutungi, C, Abdalla, M, Mutner, P, Musani, SK, Macharia, A, Williams, TN, Cruickshank, JK, Smeeth, L and Scott, JAG (2023). Replication Data for: Effect of Previous Exposure to Malaria on Blood Pressure in Kilifi, Kenya: A Mendelian Randomization Study. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/NCFR6X

Evans, B and Jombart, T (2021). Analysis of changes in worldwide routine immunisation coverage in 2020. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5746754

Eyre, MT, Burns, R, Kirkby, V, Smith, C, Denaxas, S, Nguyen, V, Hayward, A, Shallcross, L, Fragaszy, E and Aldridge, RW (2021). Impact of baseline cases of cough and fever on UK COVID-19 diagnostic testing rates: estimates from the Bug Watch community cohort study - Supplementary material, code and data. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/5J6DY

F

Fabian, ID, Stacey, A, Foster, A, Kivelä, TT, Munier, F, Cassoux, N and Bowman, R (2020). Global Retinoblastoma Presentation 2017 data, on behalf of the Global Retinoblastoma Study Group. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3727687

Falconer, J and Parajuli, A (2018). Draft search strategies for: "Novel strategies and approaches for testing populations at risk for sexually transmitted infections: A systematic review protocol". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001047.

Fielding, K (2021). Adjunctive host-directed therapies for pulmonary tuberculosis: data from a prospective, open-label, phase 2, randomised controlled trial. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002277.

Fielding, K (2021). Data set for describing resistance and identifying risk factors for resistance to Mycobacterium tuberculosis, among highly TB exposed gold miners in South Africa. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002424.

Fielding, K (2020). Data set for the comparison of the performance of QuantiFERON-TB Gold Plus with QuantiFERON-T Gold in-tube among highly TB exposed gold miners in South Africa. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001891.

Fielding, K (2019). TB Fast Track dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001531.

Fielding, K, Lewis, J and Jiang, S (2013). Effectiveness of electronic reminders to improve medication adherence in tuberculosis patients: a cluster-randomised trial. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.4.

Filippi, V (2016). The effects of obstetric complications and their costs on the long-term economic and social well being of women and their families. [Data Collection]. UK Data Service, Colchester, Essex, United Kingdom. http://dx.doi.org/10.5255/UKDA-SN-852317

Filippi, V, Cresswell, J, Yaogo, M, Ganaba, R, Powell-jackson, T, Soubeiga, A, Drabo, S, Storeng, K, Ilboudo, P, Ouedraogo, D and Some, H (2019). Productivity, family planning and reproductive health in Burkina Faso 2013-2014. [Data Collection]. UK Data Service. http://doi.org/10.5255/UKDA-SN-852089

Finch, E and Kucharski, AJ (2022). EmilieFinch/covid-reinfection. [Data Collection]. Github. https://github.com/EmilieFinch/covid-reinfection

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

Finger, F, Genolet, T, Mari, L, de Magny, GC, Manga, NM, Rinaldo, A and Bertuzzo, E (2016). Mobile phone data highlights the role of mass gatherings in the spreading of cholera outbreaks. [Data Collection]. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1522305113.

Fischer, N, Darmstadt, GL, Shahunja, K, Crowther, JM, Kendall, L, Gibson, RA, Ahmed, T and Relman, DA (2021). 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". [Data Collection]. Stanford Digital Repository. https://purl.stanford.edu/dk954yp6586

Flaherty, KE, Grembi, JA, Ramachandran, VV, Haque, F, Khatun, S, Rahman, M, Maples, S, Becker, TK, Spormann, AM, Schoolnik, GK, Hryckowian, AJ and Nelson, EJ (2021). High-throughput low-cost nl-qPCR for enteropathogen detection: A proof-of-concept among hospitalized patients in Bangladesh. S1 Dataset. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0257708.s004

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

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

Floyd, S, Ayles, H, Schaap, A, Shanaube, K, MacLeod, D, Phiri, M, Griffith, S, Bock, P, Beyers, N, Fidler, S and Hayes, R (2018). Aggregate data for "Towards 90-90: Findings after two years of the HPTN 071 (PopART) cluster-randomized trial of a universal testing-and-treatment intervention in Zambia". [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0197904.s005

Floyd, S, Schaap, A, Hensen, B and Mulubwa, C (2018). Dataset for: "Community based distribution of oral HIV self-testing kits in Zambia: a cluster-randomised trial nested in four HPTN 071 (PopART) intervention communities". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000980.

Floyd, S and Schaap, A (2023). Dataset for: "The impact of community-based, peer-led sexual and reproductive health services on knowledge of HIV-status among adolescents and young people aged 15-24 in Lusaka, Zambia: the Yathu Yathu cluster randomized trial". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003310.

Foster, N (2024). ASCENT-Ethiopia health economics. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003721.

Foster, N, Hanifa, Y, Pillai, N, Roycent, T, Fielding, K, Vassall, A and Grant, AD (2018). XPHACTOR cross-sectional patient cost dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000791.

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.

Francis, SC (2017). iGugu Main Study Data PLOS Medicine. [Data Collection]. INDEPTH Data Repository. https://doi.org/10.7796/iGUGU.MAIN.STUDY.DATA.PLOS.MEDICINE.v1

Francis, SC, Hou, Y, Baisley, K, Van de wijgert, J, Watson-Jones, D, Ao, TT, Herrera, C, Maganja, K, Andreasen, A, Coulton, GR, Hayes, RJ and Shattock, RJ (2015). Data for: "Immune activation in the female genital tract: Expression profiles of soluble proteins in women at high risk for HIV infection". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.104.

Frison, S (2020). Wasting prevention CHNRI dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001552.

Fu, H (2023). hfu915/dynamice_mrmaps. [Data Collection]. Github. https://github.com/hfu915/dynamice_mrmaps

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

Fu, Y, Wang, D, Chuang, J and Fu, H (2022). Social contact data for Taiwan. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6385758

Fujisawa, K, Silcott-Niles, C, Simonson, P, Lamattina, D, Humeres, CA, Bhattacharyya, T, Mertens, P, Thunissen, C, O’Rourke, V, Pańczuk, M, Whitworth, JA, Salomón, OD and Miles, MA (2021). Consolidated results of dogs in the 2018 and 2019 studies. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009552.s001

Funk, S (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

Funk, S (2018). Socialmixr: Social Mixing Matrices for Infectious Disease Modelling. [Data Collection]. The Comprehensive R Archive Network. https://CRAN.R-project.org/package=socialmixr https://github.com/sbfnk/socialmixr

Funk, S (2022). epiforecasts/ons_severity_estimates. [Data Collection]. Github. https://github.com/epiforecasts/ons_severity_estimates

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

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

G

García, GA, Janko, M, Hergott, DEB, Donfack, OT, Smith, JM, Mba Eyono, JN, DeBoer, KR, Nguema Avue, RM, Phiri, WP, Aldrich, EM, Schwabe, C, Stabler, TC, Rivas, MR, Cameron, E, Guerra, CA, Cook, J, Kleinschmidt, I and Bradley, J (2023). Additional file 1 of Identifying individual, household and environmental risk factors for malaria infection on Bioko Island to inform interventions. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.22610438.v1

Gaskell, KM, El kheir, N, Mirfendesky, M, Rampling, T, Marks, M, Houlihan, CF, Lemonge, N, Bristowe, H, Aslam, S, Kyprianou, D, Nastouli, E, Goldblatt, D, Fielding, K and Moore, DAJ (2023). S1 Data for: "Comparison of new and emerging SARS-CoV-2 variant transmissibility through active contact testing. A comparative cross-sectional household seroprevalence study". [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0284372.s003

Giannini, F and Abbas, K (2023). fionagi/GASImpactModel. [Data Collection]. GitHub. https://github.com/fionagi/GASImpactModel

Gibb, R (2023). rorygibb/dengue_vietnam_ms: v1.0.0: Code base for Nature Communications MS. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10159288

Gibb, R and Mollentze, N (2021). rorygibb/pathogen_discovery: Viral discovery Biology Letters code. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5714490

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

Gibbs, H (2023). hamishgibbs/ghana_cdr_aggregation. [Data Collection]. Github. https://github.com/hamishgibbs/ghana_cdr_aggregation

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

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

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/

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

Gibbs, H, Waterlow, NR, Cheshire, J, Danon, L, Liu, Y, Grundy, C, Kucharski, AJ and Eggo, RM (2021). Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic - Estimates for Local Authority Districts. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5013619

Gibbs, H, Waterlow, NR, Cheshire, J, Danon, L, Liu, Y, Grundy, C, Kucharski, AJ and Eggo, RM (2022). hamishgibbs/facebook_population_2020_2021. [Data Collection]. Github. https://github.com/hamishgibbs/facebook_population_2020_2021

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). 99% credible set SNPs for leprosy association at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s016

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Analysis of pleiotropy at the leprosy association at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s018

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Association statistics for imputed classical HLA alleles and leprosy risk in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s022

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Chromatin state at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s020

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Genome-wide association study of leprosy in Malawi and Mali. S2 Table. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s015

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Leprosy association statistics for suggestive associations in Malawi. S1 Table. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s014

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Regulatory function at the chromosome 10q24 leprosy association. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s021

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Replication of previously-published leprosy associated non-HLA SNPs in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s023

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Replication of previously-published leprosy associated non-HLA SNPs in Malawi and Mali stratified by multibacillary and paucibacillary disease. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s024

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). SNP quality control summary in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s026

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Sample quality control summary in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s025

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Selection signatures at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s019

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Study populations and leprosy association statistics at rs2015583 in the Chinese replication analysis. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s017

Gimma, A (2021). amygimma/comix_uk_summary_analysis. [Data Collection]. Github. https://github.com/amygimma/comix_uk_summary_analysis

Gimma, A, Munday, JD, Wong, KLM, Coletti, P, Van Zandvoort, K, Prem, K, Klepac, P, Rubin, GJ, Funk, S, Edmunds, WJ and Jarvis, CI (2022). Mean contacts by age and date. [Data Collection]. PLOS Medicine. https://doi.org/10.1371/journal.pmed.1003907.s015

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Austria). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4775972

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Croatia). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6535325

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Finland). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6542663

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (France). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5040870

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Hungary). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6535343

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Italy). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5041112

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Lithuania). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6542667

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Poland). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5041128

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Portugal). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5041140

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Slovakia). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6535356

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Spain). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5040839

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Switzerland). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6542656

Gimma, A, Wong, KL, Van Xandvoort, K, Jarvis, CI and Edmunds, WJ (2021). CoMix social contact data (UK). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4905745

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Denmark). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5040530

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2022). CoMix social contact data (Estonia). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6535312

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Greece). [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.5137218

Gimma, A, Wong, KL, Coletti, P and Jarvis, CI (2021). CoMix social contact data (Slovenia). [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.5137239

Gina, P, Randall, PJ, Muchinga, TE, Pooran, A, Meldau, R, Peter, JG and Dheda, K (2017). Early morning urine collection to improve urinary lateral flow LAM assay sensitivity in hospitalised patients with HIV-TB co-infection. [Data Collection]. BMC Infectious Diseases. https://doi.org/10.1186/s12879-017-2313-0

Glynn, J (2020). Systematic analysis of infectious disease outcomes by age. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001787.

Glynn, JR (2023). Dataset codebook for a 30-year population-based study examining the contribution of remote M.tuberculosis infection to tuberculosis. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002829.

Glynn, JR, Bower, H, Houlihan, C, Oza, S, Checchi, F, Johnson, S, Turay, C, Sesay, D, Mansaray, SH, Kamara, O, Kamara, JA, Bangura, MS, Montesano, C, Dicks, S, Samuel, D, Tedder, R and Sebba, C (2017). Asymptomatic infection and family contact patterns in households of Ebola Virus Disease survivors, Sierra Leone 2015. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.41.

Glynn, JR, Fielding, K, Mzembe, T, Sichali, L, Banda, L, Mclean, E, Kanjala, C, Crampin, AC, Ponnighaus, J, Warndorff, D and Fine, P (2021). Data for: “BCG revaccination in Malawi: 30-year follow-up of a large, randomised, double-blind placebo-controlled trial”. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002443.

Gon, G (2020). CLEAN study dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001937.

Gon, G (2020). Data for "HANDS project - Hand-hygiene of Attendants for Newborn Deliveries and Survival". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001945.

Goncalves, B (2021). Data for: "Estimation of country-level incidence of early-onset invasive Group B Streptococcus disease in infants using Bayesian methods". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002118.

Gonçalves, BP (2023). BronnerG/Hosp_Vacc_analysis: v1. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8252908

Gonçalves, BP, Kapulu, MC, Sawa, P, Guelbéogo, WM, Tiono, AB, Grignard, L, Stone, WJR, Hellewell, J, Lanke, K, Bastiaens, GJH, Bradley, J, Nébié, I, Ngoi, JM, Oriango, R, Mkabili, D, Nyaurah, M, Midega, J, Wirth, DF, Marsh, K, Churcher, TS, Bejon, P, Sirima, SB, Drakeley, C and Bousema, T (2018). Data from: Examining the human infectious reservoir for Plasmodium falciparum malaria in areas of differing transmission intensity. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.c3n63

Gourlay, A, Birdthistle, I, Mthiyane, NT, Orindi, BO, Muuo, S, Kwaro, D, Shahmanesh, M, Baisley, K, Ziraba, A and Floyd, S (2019). Awareness and uptake of layered HIV prevention programming for young women: analysis of population-based surveys in three DREAMS settings in Kenya and South Africa. [Data Collection]. BMC Public Health. https://doi.org/10.1186/s12889-019-7766-1

Graham, S (2023). grahams99/Enhanced_surveillance_questionnaire. [Data Collection]. Github. https://github.com/grahams99/Enhanced_surveillance_questionnaire

Grant, AD, Baisley, K, Mzembe, T and Edwards, A (2019). Incidence of tuberculosis infection among adolescents in rural KwaZulu-Natal, South Africa, 2017-2018. [Data Collection]. AHRI Data Repository. https://data.ahri.org/index.php/catalog/912/

Grant, AD and Kielmann, K (2022). Qualitative and Quantitative Data for Tuberculosis Infection Prevention and Control in KwaZulu-Natal and Western Cape, South Africa, 2018-2021. [Data Collection]. UK Data Service, Colchester, Essex, United Kingdom. https://doi.org/10.5255/UKDA-SN-854435

Grant-McAuley, W, Klock, E, Laeyendecker, O, Piwowar-Manning, E, Wilson, E, Clarke, W, Breaud, A, Moore, A, Ayles, H, Kosloff, B, Shanaube, K, Bock, P, Mandla, N, van Deventer, A, Fidler, S, Donnell, D, Hayes, R and Eshleman, SH (2021). Evaluation of multi-assay algorithms for identifying individuals with recent HIV infection: HPTN 071 (PopART). Minimum dataset, seroconverters. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0258644.s004

Grenié, M, Gruson, H, Silge, J and Tucker, C (2022). Rekyt/funrar. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.596011

Gruson, H and Grenié, M (2022). fundiversity: Easy Computation of Functional Diversity Indices. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4761754

Gruson, H and actions-user (2022). Bisaloo/asymptor. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4326986

H

Hanifa, Y, Fielding, K, Chihota, VN, Adonis, L, Charalambous, S, Karstaedt, A, McCarthy, K, Nicol, MP, Ndlovu, NT, Sahid, F, Churchyard, G and Grant, AD (2016). Diagnostic Accuracy of Lateral Flow Urine LAM Assay for TB Screening of Adults with Advanced Immunosuppression Attending Routine HIV Care in South Africa. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0156866.

Hanifa, Y, Fielding, K, Grant, AD and Churchyard, GJ (2016). Data for: "The utility of repeat Xpert MTB/RIF testing to diagnose tuberculosis in HIV-positive adults with initial negative result". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.284.

Hanifa, Y, Fielding, K, Grant, AD and Churchyard, GJ (2016). XPHACTOR Clinical Score dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.204.

Hanifa, Y, Telisinghe, L, Fielding, KL, Malden, JL, Churchyard, GJ, Grant, AD and Charalambous, S (2015). The diagnostic accuracy of urine lipoarabinomannan test for tuberculosis screening in a South African correctional facility. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1399199.v1

Haque, F, Ball, RL, Khatun, S, Ahmed, M, Kache, S, Chisti, MJ, Sarker, SA, Maples, SD, Pieri, D, Korrapati, TV, Sarnquist, C, Federspiel, N, Rahman, MW, Andrews, JR, Rahman, M and Nelson, EJ (2017). Evaluation of a Smartphone Decision-Support Tool for Diarrheal Disease Management in a Resource-Limited Setting. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0005290.s003

Haque, F, Rahman, M, Banu, NN, Sharif, AR, Jubayer, S, Shamsuzzaman, A, Alamgir, A, Erasmus, JH, Guzman, H, Forrester, N, Luby, SP and Gurley, ES (2019). Syndromic survey de-identified data in SPSS. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0212218.s005

Haque, F, Rahman, M, Banu, NN, Sharif, AR, Jubayer, S, Shamsuzzaman, A, Alamgir, A, Erasmus, JH, Guzman, H, Forrester, N, Luby, SP and Gurley, ES (2019). De-identified clinical survey data in SPSS. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0212218.s006

Haque, F, Rahman, M, Banu, NN, Sharif, AR, Jubayer, S, Shamsuzzaman, A, Alamgir, A, Erasmus, JH, Guzman, H, Forrester, N, Luby, SP and Gurley, ES (2019). De-identified symptom duration data in SPSS. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0212218.s007

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

Harvey, S, Lees, S, Mshana, G, Pilger, D, Hansen, C, Kapiga, S and Watts, C (2018). Additional files for: "A cluster randomized controlled trial to assess the impact on intimate partner violence of a 10-session participatory gender training curriculum delivered to women taking part in a group-based microfinance loan scheme in Tanzania (MAISHA CRT01): study protocol". [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6077129.v1

Hayes, R, Floyd, S, Schaap, A, Shanaube, K, Bock, P, Sabapathy, K, Griffith, S, Donnell, D, Piwowar-Manning, E, El-Sadr, W, Beyers, N, Ayles, H and Fidler, S (2017). A universal testing and treatment intervention to improve HIV control: One-year results from intervention communities in Zambia in the HPTN 071 (PopART) cluster-randomised trial. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pmed.1002292.

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

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, 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

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

Hensen, B, Ayles, H, Mulubwa, C, Floyd, S, Schaap, A, Chiti, B, Phiri, M, Mwenge, L, Simwinga, M, Fidler, S, Hayes, R, Bond, V and Mwinga, A (2019). Community-based distribution of oral HIV self-testing kits: experimental evidence from Zambia. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/NGY29G

Hensen, B, Phiri, MM, Sigande, L, Schaap, A, Simuyaba, M, Zulu-Phiri, R, Mwape, L, Floyd, S, Fidler, S, Hayes, R, Simwinga, M and Ayles, H (2024). Cross sectional survey data for self-reported ever and recent (last 12 months) STI testing. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003742.

Herbst, K, Pillay, D, Baisley, K, Barnighausen, T and Dlamini, S (2018). DREAMS baseline study in females aged 15-24 years in rural KwaZulu Natal, South Africa, 2006-2015. [Data Collection]. INDEPTH Network. https://doi.org/10.7796/AHRI.DREAMS.DREAMS.AGYW.Baseline.2018.v1

Herbst, K, Pillay, D, Baisley, K, Barnighausen, T and Koole, O (2018). DREAMS baseline study in young men aged 20-29 years in rural KwaZulu Natal, South Africa, 2006-2015. [Data Collection]. INDEPTH Network. https://doi.org/10.7796/AHRI.DREAMS.DREAMS.Male.Baseline.2018.v1

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

Hodcroft, E, Zuber, M, Harkins, E, Neher, R, Wagner, C, Huddleston, J, Bedford, T, Moncla, LH, Hadfield, J, fzhang12, Sibley, T, Saleh, A, falnaji, Xueying, aniafijarczyk, Nezu, T, Müller, NF, Gall, A, Brito, A, Villabona Arenas, CJ, Bell, S, Kozyreva, V, Eren, Puller, V, Han, AX, irak, Rimaz, H, Ghafari, M, Sato, T and Lee, H (2024). emmahodcroft/ncov_2021: Release for Geneva Manuscript. [Data Collection]. Zenodo, London, United Kingdom. https://doi.org/10.5281/zenodo.10524847

Hodgson, D (2024). dchodge/rsvmabmat. [Data Collection]. GitHub. https://github.com/dchodge/rsvmabmat

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

Homolka, S, Zallet, J, Albert, H, Witt, A and Kranzer, K (2019). Acceptability and sensory qualities of fortified rice in Nepal. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9888155.v2

Horby, P, Thai, PQ, Hens, N, Yen, NTT, Mai, LQ, Thoang, DD, Linh, NM, Huong, NT, Alexander, N, Edmunds, WJ, Duong, TN, Fox, A and Hien, NT (2018). Social Contact Data for Vietnam. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1289473

Horton, KC, Sumner, T, Houben, Rein M G J, Corbett, EL and White, RG (2018). A Bayesian approach to understanding gender differences in tuberculosis disease burden. [Data Collection]. American Journal of Epidemiology. https://doi.org/10.1093/aje/kwy131

Hughes, R, Kitsao-Wekulo, P, Bhopal, S, Kimani-Murage, E, Hill, Z and Kirkwood, B (2020). The Nairobi Early Childcare in Slums (NECS) Study. [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001780.

I

Imam, A, Gathara, D, Aluvaala, J, Maina, M and English, M (2022). Additional file 1 of Evaluating the effects of supplementing ward nurses on quality of newborn care in Kenyan neonatal units: protocol for a prospective workforce intervention study. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.21275873.v1

J

Jacob, PE, Lee, A, Murray, L and Funk, S (2017). rbi: R Interface to LibBi. [Data Collection]. The Comprehensive R Archive Network. https://cran.r-project.org/package=rbi

Jaramillo, JF, Olano, VA, Vargas, S, Sarmiento-Senior, D, Overgaard, HJ and Alexander, N (2013). Escuelas saludables: reduciendo las enfermedades de diarrea y dengue en las escuelas rurales de Anapoima y La Mesa, Cundinamarca. [Data Collection]. Universidad El Bosque, Bogotá, Colombia. http://hdl.handle.net/20.500.12495/9389

Jarju, S, Senghore, E, Brotherton, H, Saidykhan, A, Jallow, S, Krubally, E, Sinjanka, E, Ndene, MN, Bajo, F, Sanyang, MM, Saidy, B, Bah, A, Mohammed, NI, Forrest, K, Clarke, E, Dalessandro, U, Sesay, AK, Usuf, E, Cerami, C, Roca, A, Kampmann, B and De silva, T (2022). Circulation of respiratory viruses during the COVID-19 pandemic in the Gambia. [Data Collection]. Open Science Framework. https://doi.org/10.17605/OSF.IO/TSF78

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

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

Jeandron, A, Cumming, O, Rumedeka, BB, Saidi, JM and Cousens, S (2018). Dataset for "Confirmation of cholera by rapid diagnostic test amongst patients admitted to the cholera treatment centre in Uvira, Democratic Republic of the Congo". [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0201306.s002

Johnson, A (2015). National Survey of Sexual Attitudes and Lifestyles, 2010-2012. [Data Collection]. UK Data Service, Essex, United Kingdom. http://doi.org/10.5255/UKDA-SN-7799-2

Johnson, C, Kumwenda, M, Meghji, J, Choko, AT, Phiri, M, Hatzold, K, Baggaley, R, Taegtmeyer, M, Terris-Prestholt, F, Desmond, N and Corbett, EL (2021). Additional file 1 of ‘Too old to test?’: A life course approach to HIV-related risk and self-testing among midlife-older adults in Malawi. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14369899.v1

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

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

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

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

Jombart, T, Cori, A, Didelot, X, Cauchemez, S, Fraser, C and Ferguson, N (2014). Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1003457

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/

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/

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

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

Jombart, T, actions-user, Gruson, H and Pavlich-Mariscal, J (2022). epiverse-trace/blueprints: 0.0.2. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7062318

Jung, S, Endo, A, Kinoshita, R and Nishiura, H (2021). SungmokJung/Projection_Japan_COVID19 v1.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4576936

Jung, S, Miura, F, Endo, A and Murayama, H (2023). SungmokJung/mpox_global: Initial release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10056592

K

Kakande, A, Ssemata, AS, Muhumuza, R, Atujuna, M, Abaasa, A, Fox, J, Ndekezi, D, Tshabalala, G, Nematadzira, T, Hornschuh, S, Nomvuyo, M, Ahmed, N, Maluadzi, M, Weiss, H, Seeley, J, Dietrich, JJ, Stranix-Chibanda, L, Webb, E, PrEPVacc Study Group and ITAPS team (2023). Data for: PrEP preference among adolescent boys and young men in three sub-Saharan African countries. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003232.

Kanjala, C, Glynn, JR and Fine, P (2020). Effect of repeat BCG on all-cause mortality: a double-blind randomised placebe-controlled trial in Malawi. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001872.

Kansiime, S (2021). Blood pressure levels among children in rural Uganda: results from 1,913 children in a general population survey. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002387.

Kansiime, S, Hansen, C, Hayes, R, Ruzagira, E and PrEPVacc study team (2023). Dataset for: Developing HIV risk prediction tools in four African settings. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003540.

Karat, AS, Omar, T, von Gottberg, A, Tlali, M, Chihota, VN, Churchyard, GJ, Fielding, KL, Johnson, S, Martinson, NA, McCarthy, K, Wolter, N, Wong, EB, Charalambous, S and Grant, AD (2016). Autopsy Prevalence of Tuberculosis and Other Potentially Treatable Infections among Adults with Advanced HIV Enrolled in Out-Patient Care in South Africa: Lesedi Kamoso study data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.122.

Karat, A, Tlali, M, Fielding, K, Charalambous, S, Chihota, VN, Churchyard, GJ, Hanifa, Y, Johnson, S, McCarthy, K, Martinson, NA, Omar, T, Kahn, K, Chandramohan, D and Grant, AD (2016). Measuring mortality due to HIV-associated tuberculosis among adults in South Africa: comparing verbal autopsy, minimally-invasive autopsy, and research data. Data from the Lesedi Kamoso study. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.169.

Karkey, A, Jombart, T, Walker, AW, Thompson, CN, Torres, A, Dongol, S, Tran Vu Thieu, N, Pham Thanh, D, Tran Thi Ngoc, D, Voong Vinh, P, Singer, AC, Parkhill, J, Thwaites, G, Basnyat, B, Ferguson, N and Baker, S (2016). The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water. S2 Dataset. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0004346.s008

Karuga, RN, Mireku, M, Muturi, N, McCollum, R, Vallieres, F, Kumar, M, Taegtmeyer, M and Otiso, L (2019). Supportive supervision of close-to-community providers of health care: Findings from action research conducted in two counties in Kenya. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0216444

Karumbi, J, Gorst, S, Gathara, D, Young, B and Williamson, P (2023). Survey Questions for LMIC stakeholders. [Data Collection]. PLOS Global Public Health. https://doi.org/10.1371/journal.pgph.0002574.s001

Katumba, K, Tann, CJ, Webb, EL, Tenywa, P, Nampijja, M, Seeley, J and Greco, G (2023). The economic burden incurred by families caring for a young child with developmental disability in Uganda: User costing questionnaire. [Data Collection]. PLOS Global Public Health. https://doi.org/10.1371/journal.pgph.0000953.s002

Katumba, K, Tann, C, Webb, E, Tenywa, P, Nampijja, M, Seeley, J and Greco, G (2023). Data supporting "The economic burden incurred by families caring for a young child with developmental disability in Uganda". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003311.

Kazembe, L, Watts, P, Phillips, G, Petticrew, M, Hayes, R, Bottomley, C, Yu, G, Schmidt, E, Tobi, P, Moore, D, Frostick, C, Lock, K and Renton, A (2013). Physical Activity in Deprived Communities in London: Examining Individual and Neighbourhood-Level Factors. [Data Collection]. PLoS One. https://doi.org/10.1371/journal.pone.0069472

Kazungu, JS and Adetifa, I (2017). Replication Data for: Crude childhood vaccination coverage in West Africa: trends and predictors of completeness. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://dx.doi.org/10.7910/DVN/YQYES9

Keating, P, Murray, J, Schenkel, K, Merson, L and Seale, A (2021). Support files for: "Electronic data collection, management and analysis tools used for outbreak response in low- and middle-income countries: a systematic review and stakeholder survey". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002527.

Keddie, S (2022). shk313/diagnostic-test-metaanalysis/CrAg. [Data Collection]. GitHub. https://github.com/shk313/diagnostic-test-metaanalysis/tree/main/CrAg

Keddie, SH (2023). shk313/Evaluating-sensitivity-and-specificity-from-LCM-a-simulation-study. [Data Collection]. Github. https://github.com/shk313/Evaluating-sensitivity-and-specificity-from-LCM-a-simulation-study

Keddie, S, Bärenbold, O, Keogh, R and Bradley, J (2022). Stan models for diagnostic tests accuracy simulation; Accompaniment for Journal Article. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6616490

Kelly, C, Dube, A and Mortimer, K (2018). Data for: "From kitchen to classroom: Assessing the impact of cleaner burning biomass-fuelled cookstoves on primary school attendance in Karonga district, northern Malawi". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.282.

Kelly, H, Weiss, H, Benavente Moreno, Y, de Sanjose, S and Mayaud, P (2017). Antiretroviral therapy, high-risk human papillomavirus and cervical intraepithelial neoplasia: a systematic review and meta-analysis. [Data Collection]. Mendeley Data. http://dx.doi.org/10.17632/cg8k3d7rc8.1

Khan, PY (2024). Data for: Karachi adult tuberculosis prevalence and child Mycobacterium tuberculosis infection survey, 2018-2019. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003788.

Kibirige, D, Sekitoleko, I, Balungi, P, Kyosiimire-Lugemwa, J and Lumu, W (2022). Additional file 1 of Clinical, metabolic, and immunological characterisation of adult Ugandan patients with new-onset diabetes and low vitamin D status. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.21130068.v1

Kibondo, UA, Odufuwa, OG, Ngonyani, SH, Mpelepele, AB, Matanilla, I, Ngonyani, H, Makungwa, NO, Mseka, AP, Swai, K, Ntabaliba, W, Stutz, S, Austin, JW and Moore, SJ (2022). Additional file 3 of Influence of testing modality on bioefficacy for the evaluation of Interceptor® G2 mosquito nets to combat malaria mosquitoes in Tanzania. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19582050.v1

Kim, C, Abbas, KM and vaccine-impact (2023). vaccine-impact/vaccine_amr. [Data Collection]. Github. https://github.com/vaccine-impact/vaccine_amr

Kim, ES, Adriko, M, Aidah, W, Oseku, KC, Lokure, D, Sabapathy, K and Webb, EL (2023). The impact of dual- versus single-dosing and fatty food co-administration on albendazole efficacy against hookworm among children in Mayuge district, Uganda: Results from a 2x2 factorial randomised controlled trial. S1 Data. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0011439.s006

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

Kisesa HIV Open Cohort study and ALPHA Network (2022). ALPHA HIV Incidence and Mortality Data, Kisesa 1994-2016. [Data Collection]. DataFirst, Cape Town, South Africa. https://doi.org/10.25828/SGBS-Q698

Kissler, SM, Klepac, P, Tang, M, Conlan, AJ and Gog, JR (2020). skissler/haslemere. [Data Collection]. Github. https://github.com/skissler/haslemere

Klepac, P, Kucharski, AJ, Conlan, AJ, Kissler, S, Tang, M, Fry, H and Gog, JR (2020). Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project. [Data Collection]. Medrxiv. https://doi.org/10.1101/2020.02.16.20023754

Knight, G (2018). Code for "The relative fitness of drug resistant Mycobacterium tuberculosis: a modelling study of household transmission in Lima, Peru". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.1205418

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

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

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

Knight, GM, Zimic, M, Funk, S, Gilman, RH, Friedland, JS and Grandjean, L (2018). Follow up time from The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6480617.v1

Knight, GM, Waterlow, N, Wildfire, J and Clements, AJ (2023). aj-clements/Vivli-AMR-KG. [Data Collection]. Github. https://github.com/aj-clements/Vivli-AMR-KG/

Koltai, M (2021). Source data for "Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5534768

Koltai, M (2023). mbkoltai/RSV-CEA-Kenya-South-Africa. [Data Collection]. Github. https://github.com/mbkoltai/RSV-CEA-Kenya-South-Africa

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

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

Koltai, M (2020). sysbio-curie/exact-stoch-log-mod. [Data Collection]. GitHub. https://github.com/sysbio-curie/exact-stoch-log-mod

Kraemer, MUG, Sinka, ME, Duda, KA, Mylne, A, Shearer, FM, Brady, OJ, Messina, JP, Barker, CM, Moore, CG, Carvalho, RG, Coelho, GE, Van Bortel, W, Hendrickx, G, Schaffner, F, Wint, GRW, Elyazar, IRF, Teng, H and Hay, SI (2015). Data from: The global compendium of Aedes aegypti and Ae. albopictus occurrence. [Data Collection]. Dryad Digital Repository. https://doi.org/10.5061/dryad.47v3c

Krauer, F (2022). fkrauer/RSV-seasonality-public. [Data Collection]. Github. https://github.com/fkrauer/RSV-seasonality-public

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

Kretzschmar, MEE, Tosas Auguet, O, Betley, JR, Stabler, R, Patel, A, Ioannou, A, Marbach, H, Hearn, P, Aryee, A, Goldenberg, SD, Otter, JA, Desai, N, Karadag, T, Grundy, C, Gaunt, M, Cooper, BS, Edgeworth, JD and Kypraios, T (2016). Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data. [Data Collection]. PLOS Medicine. https://doi.org/10.1371/journal.pmed.1001944.s005

Krug, C, Lynch, C, Cavallaro, F and Wong, K (2020). Evaluating the informed push model intervention in Senegal. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001570.

Krug, C, Neuman, M, Rosen, JE, Weinberger, M, Wallach, S, Lagaay, M, Punton, M, Prakash, A, Nsanya, MK, Ayieko, P, Kapiga, S, Ajayi, YP, Crawford, EE, Tenaw, E, Mussa, M, Shrestha, SK, Bottomley, C, Hargreaves, J and Doyle, AM (2023). Evaluating the adolescents 360 approach in Ogun (Nigeria), Nasarawa (Nigeria), Oromia (Ethiopia) and Mwanza (Tanzania) – Study data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003599.

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

Kucharski, AJ (2021). adamkucharski/covid-import-model. [Data Collection]. Github. https://github.com/adamkucharski/covid-import-model

Kucharski, AJ, Funk, S, Eggo, RM, Mallet, H, Edmunds, WJ and Nilles, EJ (2016). S1 Dataset for "Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013–14 French Polynesia Outbreak". [Data Collection]. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0004726.s016

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

Kucharski, AJ, Wenham, C, Brownlee, P, Racon, L, Widmer, N, Eames, KTD and Conlan, AJK (2018). Reported contacts dataset for "Structure and consistency of self-reported social contact networks in British secondary schools". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.1371/journal.pone.0200090.s002

Kucharski, AJ, Kama, M, Watson, CH, Aubry, M, Funk, S, Henderson, AD, Brady, OJ, Vanhomwegen, J, Manuguerra, J, Lau, CL, Edmunds, WJ, Aaskov, J, Nilles, EJ, Cao-Lormeau, V, Hue, S and Hibberd, ML (2018). adamkucharski/fiji-denv3-2014. [Data Collection]. Github. https://github.com/adamkucharski/fiji-denv3-2014

Kucharski, A, Conlan, AJK and Eames, K (2015). School's Out: Seasonal Variation in the Movement Patterns of School Children. S1 Dataset. Reported individual travel patterns. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0128070.s004

Kucharski, A and Edmunds, J (2015). Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks: Simulation and Inference code. [Data Collection]. PLOS Computational Biology. http://doi.org/10.1371/journal.pcbi.1004154.s010

Kucharski, A, Mills, H, Pinsent, A, Fraser, C, Kerkhove, MV and Riley, S (2015). Data from: Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.2g43n

L

Lal, S, Ndyomugenyi, R, Alexander, N, Lagarde, M, Paintain, L, Magnussen, P, Chandramoham, D and Clarke, S (2015). Health facility utilisation changes during the introduction of community case management of malaria in South Western Uganda: An interrupted time series approach. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.9.

Lalli, M, Ruysen, H, Blencowe, H, Yee, K, Clune, K, DeSilva, M, Leffler, M, Hillman, E, El-Noush, H, Mulligan, J, Murray, JC, Silver, K and Lawn, JE (2018). Saving Lives at Birth; development of a retrospective theory of change, impact framework and prioritised metrics. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.3990024.v1

Lambert, J, Gruson, H, Kucharski, AJ, Gupte, P, Salmon, M, Campos, AV and Monticone, P (2023). epiverse-trace/epiparameter. [Data Collection]. Github. https://github.com/epiverse-trace/epiparameter/

Lambert, J, Gruson, H, Kucharski, AJ and Tamayo Cuartero, C (2024). epiverse-trace/simulist. [Data Collection]. Github. https://github.com/epiverse-trace/simulist

Lammie, PJ, Kamgno, J, Nguipdop-Djomo, P, Gounoue, R, Téjiokem, M and Kuesel, AC (2016). Loa loa Alben Trial data. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0004492.s002.

Landay, A, Reither, K, Katsoulis, L, Beattie, T, Gardiner, N, Lenz, N, Said, K, Mfinanga, E, Pohl, C, Fielding, KL, Jeffery, H, Kagina, BM, Hughes, EJ, Scriba, TJ, Hanekom, WA, Hoff, ST, Bang, P, Kromann, I, Daubenberger, C, Andersen, P and Churchyard, GJ (2015). Data from: Safety and immunogenicity of H1/IC31®, an adjuvanted TB subunit vaccine, in HIV-infected adults with CD4+ Lymphocyte counts greater than 350 cells/mm3: a phase II, multi-centre, double-blind, randomized, placebo-controlled trial. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.r61r8

Langan, S, Smeeth, L, Margolis, DJ and Thomas, SL (2013). Herpes Zoster Vaccine Effectiveness against Incident Herpes Zoster and Post-herpetic Neuralgia in an Older US Population: A Cohort Study. [Data Collection]. PLOS Medicine. https://doi.org/10.1371/journal.pmed.1001420

Lawn, JE, Waiswa, P, Waiswa, JA, Kwesiga, D, Blencowe, H, Baschieri, A, Gordeev, VS and EN-INDEPTH Collaborator Group (2020). Every Newborn INDEPTH (EN-INDEPTH) Study - Additional Materials. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001556.

Lazarus, JV, Ratzan, S, Palayew, A, Billari, FC, Binagwaho, A, Kimball, S, Larson, HJ, Melegaro, A, Rabin, K, White, TM and El-Mohandes, A (2020). COVID-SCORE: A global survey to assess public perceptions of government responses to COVID-19 (COVID-SCORE-10). [Data Collection]. PLoS One. https://doi.org/10.1371/journal.pone.0240011

Le Polain, O, Flasche, S, Prieto, D and Edmunds, J (2014). Age-Dependent Prevalence of Nasopharyngeal Carriage of Streptococcus pneumoniae before Conjugate Vaccine Introduction: Supporting Information. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.72.

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

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

Leclerc, QJ (2023). qleclerc/phage_antibiotic_dynamics. [Data Collection]. Github.

Leclerc, QJ, Fuller, NM, Knight, LE, Funk, S and Knight, GM (2020). COVID19 settings of transmission - collected reports database. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12173343.v5

Leclerc, QJ, Lindsay, JA and Knight, GM (2019). Summary table of the elements recorded in the 43 studies included in our review from Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.8850671.v1

Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App drug breakdown (groups). [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822104.v1

Leclerc, QJ, Naylor, NR, Aiken, AM, Coll, F and Knight, GM (2019). AR.IA App species breakdown. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.9822179.v1

Leclerc, QJ, Nightingale, E and Abbott, S (2020). qleclerc/nhs_pathways_report. [Data Collection]. Github. https://github.com/qleclerc/nhs_pathways_report

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

Lee, SA (2022). sophie-a-lee/spatial_smooth_framework: Data and R code to accompany 'A Bayesian modelling framework to quantify multiple sources of spatial variation for disease mapping'. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7054456

Lee, SA, Economou, T, de Castro Catão, R, Barcellos, C and Lowe, R (2021). Data and R code to accompany 'The impact of climate suitability, urbanisation, and connectivity on the expansion of dengue in 21st century Brazil' (version 1.0.0). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5710715

Leng, T and Flasche, S (2020). tsleng93/SocialBubble: Social Bubble (including density dependence). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3982789

Lenhart, A, Morrison, AC, Paz-Soldan, VA, Forshey, BM, Cordova-Lopez, JJ, Astete, H, Elder, JP, Sihuincha, M, Gotlieb, EE, Halsey, ES, Kochel, TJ, Scott, TW, Alexander, N and McCall, PJ (2020). The impact of insecticide treated curtains on dengue virus transmission: A cluster randomized trial in Iquitos, Peru. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0008097.s003

Leung, K, Jit, M, Lau, EHY and Wu, JT (2018). Social contact data for Hong Kong. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.1165562

Leung, K, Jit, M, Lau, EHY and Wu, JT (2020). Social contact data for Hong Kong. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3874808

Li, M, Taylor, EG, Atkins, KE, Chapman, GB and Galvani, AP (2016). Stimulating Influenza Vaccination via Prosocial Motives. S3 Dataset. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0159780.s006

Limbada, M, Ayles, H and Macleod, D (2021). A Comparison of Different Community Models of ART Delivery Amongst Stable HIV+ Patients in two Urban Settings in Zambia - Study Protocol. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002116.

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

Lindsay, S, Carrasco-Tenezaca, M, Jawara, M, Bradley, J, D'Alessandro, U, Jeffries, D, Pinder, M and Knudsen, J (2021). Supplementary data files & video for Carrasco-Tenezaca published in the Journal of the Royal Society Interface, 'The relationship between house height and mosquito house entry: an experimental study in rural Gambia. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14483475.v1

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

Liu, Y (2020). yangclaraliu/COVID19_NPIs_vs_Rt. [Data Collection]. Github. https://github.com/yangclaraliu/COVID19_NPIs_vs_Rt

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

Liu, Y, Funk, S and Flasche, S (2020). yangclaraliu/2019nCoV_proportion_asym: WOR Submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3709941

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

Liu, Y, Procter, SR, Pearson, CAB, Madriz Montero, A, Torres-Rueda, S, Asfaw, E, Uzochukwu, B, Drake, T, Bergren, E, Eggo, RM, Ruiz, F, Ndembi, N, Nonvignon, J, Jit, M and Vassall, A (2023). yangclaraliu/covid_vac_africa: BMCMed_R3. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7618748

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

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://yangcliu.shinyapps.io/demo/

Loganathan, T, Ng, C, Lee, W and Jit, M (2016). Technical appendix to "The hidden health and economic burden of rotavirus gastroenteritis in Malaysia: an estimation using multiple data sources". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.98.

Lotto Batista, M, Rees, EM, Gómez, A, López, S, Castell, S, Kucharski, AJ, Ghozzi, S, Müller, GV and Lowe, R (2023). Data and R-code to accompany 'Towards an Early Warning System for Leptospirosis in North-Eastern Argentina'. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7865638

Lovell-Read, FA, Funk, S, Obolski, U, Donnelly, CA and Thompson, RN (2021). Supplementary material from "Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study". [Data Collection]. The Royal Society. https://doi.org/10.6084/m9.figshare.c.5416023.v1

Lowe, R (2021). Data and R code to accompany 'Combined effects of hydrometeorological hazards and urbanisation on dengue risk in Brazil: a spatiotemporal modelling study'. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4632204

Lucinde, RK, Mugo, D, Bottomley, C, Karani, A, Gardiner, E, Aziza, R, Gitonga, JN, Karanja, H, Nyagwange, J, Tuju, J, Wanjiku, P, Nzomo, E, Kamuri, E, Thuranira, K, Agunda, S, Nyutu, G, Etyang, AO, Adetifa, IMO, Kagucia, E, Uyoga, S, Otiende, M, Otieno, E, Ndwiga, L, Agoti, CN, Aman, RA, Mwangangi, M, Amoth, P, Kasera, K, Nyaguara, A, Ng’ang’a, W, Ochola, LB, Namdala, E, Gaunya, O, Okuku, R, Barasa, E, Bejon, P, Tsofa, B, Ochola-Oyier, LI, Warimwe, GM, Agweyu, A, Scott, JAG and Gallagher, KE (2022). Stan code and input data for estimating adjusted seroprevalence. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0265478.s005

le Polain de Waroux, O, Flasche, S, Kucharski, AJ, Langendorf, C, Ndazima, D, Mwanga-Amumpaire, J, Grais, RF, Cohuet, S and Edmunds, WJ (2018). Data for: Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections. [Data Collection]. Mendeley Data. https://doi.org/10.17632/rdskdgxrh3.1

M

MRC/UVRI and White, R (2022). Respondent-Driven Sampling and Total Population Data from a Rural Ugandan Cohort, 2010: Special Licence Access. [Data Collection]. UK Data Service, Essex, United Kingdom. https://doi.org/10.5255/UKDA-SN-7462-1

Mandeng, SE, Awono-Ambene, HP, Bigoga, JD, Ekoko, WE, Binyang, J, Piameu, M, Mbakop, LR, Fesuh, BN, Mvondo, N, Tabue, R, Nwane, P, Mimpfoundi, R, Toto, JC, Kleinschmidt, I, Knox, TB, Mnzava, AP, Donnelly, MJ, Fondjo, E and Etang, J (2019). Spatial and temporal development of deltamethrin resistance in malaria vectors of the Anopheles gambiae complex from North Cameroon. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0212024

Mansfield, KE, Douglas, IJ, Nitsch, D, Thomas, SL, Smeeth, L and Tomlinson, L (2017). Read Code List - Arrhythmia. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.216.

Mansfield, KE, Douglas, IJ, Nitsch, D, Thomas, SL, Smeeth, L and Tomlinson, LA (2017). Code lists for: "Acute kidney injury and infections in patients taking antihypertensive drugs: a self-controlled case series analysis". [Project]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.211.

Mansfield, KE, Douglas, IJ, Nitsch, D, Thomas, SL, Smeeth, L and Tomlinson, LA (2017). ICD-10 Code List - Arrhythmia. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.221.

Mansfield, KE, Douglas, IJ, Nitsch, D, Thomas, SL, Smeeth, L and Tomlinson, LA (2017). ICD-10 Code List - Cardiac Failure. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.219.

Mansfield, KE, Douglas, IJ, Nitsch, D, Thomas, SL, Smeeth, L and Tomlinson, LA (2017). ICD-10 Code List - Diabetes Mellitus. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.226.