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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018 |
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Identification Number: |
doi:10.7910/DVN/OL399P |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2021-04-14 |
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Version: |
2 |
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Bibliographic Citation: |
Morobe, John M.; Kamau, Everlyn; Murunga, Nickson; Gatua, Winfred; Lewa, Clement; Cheruiyot, Robinson; Mutunga, Martin; Odundo, Calleb; Agoti, Charles N.; Nokes, David James, 2021, "Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018", https://doi.org/10.7910/DVN/OL399P, Harvard Dataverse, V2, UNF:6:25VkNi7AihwToeZ6rwVt0g== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018 |
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Identification Number: |
doi:10.7910/DVN/OL399P |
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Authoring Entity: |
Morobe, John M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kamau, Everlyn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Medicine, University of Oxford, Oxford, UK) |
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Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Gatua, Winfred (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Lewa, Clement (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Cheruiyot, Robinson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Mutunga, Martin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Odundo, Calleb (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Public Health, Pwani University, Kilifi, Kenya) |
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Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Morobe, John M. |
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Depositor: |
Morobe, John M. |
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Date of Deposit: |
2021-04-13 |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href="">Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018</a>."</p> <p>This study is part of a longitudinal surveillance study established to understand the epidemiology and disease burden of HRV associated pneumonia admissions to Kilifi County Hospital (KCH).It contains month and year of sample collection, Eligibles (Under fives with severe or very severe pneumonia),sample tested, sample positives for respiratory viruses, and HRV types detected. </p> |
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Notes: |
<strong>Notes on running code</strong> <br> Data analysis R code and python script is as provided below; <br> <ol> <li>HRV_monthly_distribution.do- Monthly distribution of human rhinovirus cases identified from surveillance of acute respiratory infections (ARI) in patients under 5 years old admitted to the Kilifi County Hospital, Kenya, 2007–2018. </li> <li>Figure2.R-This r code display Annual proportion of HRV species across the 12-years period. </li> <li>Rplots_figure3-Quarterly proportions of HRV types detected organised at the species level. </li> <li>HiLiter_figure_4.py-It displays nucleotides differences between sequences of the same HRV type. </li> <li>Pairwise_snps_Figure4-This shows the distribution plot of pairwise nucleotide differences between sequences of the same HRV type. This code is used to run multiple datasets i.e. RV-A12, RV-A49, RV-A78, RV-A101; RV-C2, RV-C3, RV-C6, RV-C11, RV-C21, RV-C38. </li> </ol> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p> |
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Notes: |
<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> |
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Other Study Description Materials |
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File Description--f4550324 |
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File: DATA_HRVA.tab |
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Notes: |
UNF:6:M2wy6BbQ+Nq9vcv4cYHgbA== |
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File Description--f4550325 |
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File: DATA_HRVB.tab |
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Notes: |
UNF:6:vupqnVRTd5WBEw9RErLQhw== |
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File Description--f4550323 |
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File: DATA_HRVC.tab |
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Notes: |
UNF:6:BQ2HIfjeJ6bCV97ycygBBA== |
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File Description--f4895502 |
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File: mpx_tested_mpx_positives_2007_2018.tab |
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Notes: |
UNF:6:xPbqoQdKOCdOrisV0PTN3w== |
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File Description--f4550317 |
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File: new_types_year.tab |
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Notes: |
UNF:6:KVL9TP2IAWSh2cPEoM+GOA== |
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File Description--f4550330 |
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File: RV-A101.tab |
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Notes: |
UNF:6:uu4a43QznVxNj4Dmpyhvmw== |
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File Description--f4551554 |
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File: RV-A12.tab |
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Notes: |
UNF:6:Lml9244glvWtOO9lWWpN5Q== |
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File Description--f4551549 |
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File: RV-A49.tab |
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Notes: |
UNF:6:jdHRkvuBuIKMcC1PWTUyCA== |
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File Description--f4551552 |
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File: RV-A78.tab |
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Notes: |
UNF:6:kkf2+H+P3yR2uZ+R7GGt7w== |
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File Description--f4551548 |
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File: RV-C11.tab |
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Notes: |
UNF:6:jIzVPWIW1hvklGAsuWQSKw== |
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File Description--f4551547 |
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File: RV-C21.tab |
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Notes: |
UNF:6:9AOEtA5UgKcr6fX0G7T19A== |
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File Description--f4551556 |
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File: RV-C2.tab |
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Notes: |
UNF:6:fZJreEg5NhdrDiAm3aXT1A== |
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File Description--f4551551 |
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File: RV-C38.tab |
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Notes: |
UNF:6:euTii2GEcSTExOci4dmLCw== |
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File Description--f4551555 |
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File: RV-C3.tab |
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Notes: |
UNF:6:MT0kucLmADWrT/mcEveg6A== |
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File Description--f4551553 |
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File: RV-C6.tab |
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Notes: |
UNF:6:S7xmJsZBj/AIvIqKN2WefA== |
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List of Variables: |
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Variables |
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f4550324 Location: |
Summary Statistics: Mean 2012.3240740740741; Min. 2007.0; Max. 2018.0; StDev 3.1999670083103764; Valid 108.0 Variable Format: numeric Notes: UNF:6:DXdrE3ZsBb5PTiIRUVP9kg== |
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f4550324 Location: |
Variable Format: character Notes: UNF:6:m6IR9zDkS9WMPHIPlAQmXQ== |
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f4550324 Location: |
Variable Format: character Notes: UNF:6:WfpiPlGO31QeygfiVTWx6A== |
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f4550324 Location: |
Summary Statistics: Min. 1.0; Max. 18.0; Mean 4.805555555555555; StDev 4.439538439706589; Valid 108.0; Variable Format: numeric Notes: UNF:6:nl7/t+Fmb9qBJjs+0LM9fA== |
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f4550324 Location: |
Summary Statistics: Valid 108.0; Mean 44.44444444467592; StDev 34.30779623746413; Min. 5.263157895; Max. 100.0 Variable Format: numeric Notes: UNF:6:sm24BOZrRiL/AA5K0G/nKw== |
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f4550325 Location: |
Summary Statistics: Mean 2013.0; Valid 39.0; StDev 3.3950428258673977; Max. 2018.0; Min. 2007.0 Variable Format: numeric Notes: UNF:6:e3Ch+EWCnDm2iO4ufwwL6w== |
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f4550325 Location: |
Variable Format: character Notes: UNF:6:3VzrLjONP+9dGkvSanR7Dg== |
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f4550325 Location: |
Variable Format: character Notes: UNF:6:Z99wkmI6WiAs02ul3q54hw== |
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f4550325 Location: |
Summary Statistics: Max. 3.0; Mean 1.3333333333333333; Min. 1.0; Valid 39.0; StDev 0.5773502691896257; Variable Format: numeric Notes: UNF:6:AZQKDmeVTB2A5f7/DMt3JQ== |
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f4550325 Location: |
Summary Statistics: Max. 100.0; Mean 82.05128205102564; StDev 26.665190580410417; Valid 39.0; Min. 25.0; Variable Format: numeric Notes: UNF:6:KpA77IoqHNpsmHIk23qU7w== |
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f4550323 Location: |
Summary Statistics: Max. 2018.0; Mean 2012.2444444444445; StDev 3.4358032641454654; Min. 2007.0; Valid 90.0; Variable Format: numeric Notes: UNF:6:xhhwTSEN38+lzw0PI0QDqw== |
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f4550323 Location: |
Variable Format: character Notes: UNF:6:331/dedf6lQR8j7UK6i3hg== |
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f4550323 Location: |
Variable Format: character Notes: UNF:6:kp9GvFVsmXxiWLdvB8us/Q== |
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f4550323 Location: |
Summary Statistics: Valid 90.0; Min. 1.0; StDev 4.87405677676933; Mean 5.544444444444444; Max. 22.0; Variable Format: numeric Notes: UNF:6:/rfMhhBkkcnnkcZDQshmMA== |
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f4550323 Location: |
Summary Statistics: Mean 53.33333333313333; Valid 90.0; Min. 3.846153846; Max. 100.0; StDev 34.469928981888934 Variable Format: numeric Notes: UNF:6:T8PVZPmQvWXQXY6RSN9ARw== |
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f4895502 Location: |
Summary Statistics: StDev 3.4641016151377544; Min. 1.0; Valid 144.0; Mean 6.5; Max. 12.0 Variable Format: numeric Notes: UNF:6:Kkm+DPInpLNe/UuZcx7uww== |
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f4895502 Location: |
Summary Statistics: StDev 3.4641016151377544; Max. 2018.0; Mean 2012.5; Min. 2007.0; Valid 144.0 Variable Format: numeric Notes: UNF:6:PLENJ5D+bZBsPN+Y1eXoyA== |
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f4895502 Location: |
Summary Statistics: Valid 144.0; Mean 52.631944444444436; Min. 16.0; StDev 25.859693108411534; Max. 142.0 Variable Format: numeric Notes: UNF:6:TlKV4RnwgBDM3ljHNQYNgA== |
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f4895502 Location: |
Summary Statistics: Valid 144.0; Max. 35.0; Min. 1.0; Mean 10.430555555555555; StDev 5.79926783150316 Variable Format: numeric Notes: UNF:6:cmNJnh2HdZB9ZOio8sBM+Q== |
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f4895502 Location: |
Variable Format: character Notes: UNF:6:xota+9o42bTHIF/PQ1gGlw== |
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f4895502 Location: |
Variable Format: character Notes: UNF:6:wsLAiFd2fbu/w56eWvr6IQ== |
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f4550317 Location: |
Summary Statistics: StDev 3.5010202594590707; Max. 2018.0; Valid 36.0; Mean 2012.5; Min. 2007.0 Variable Format: numeric Notes: UNF:6:fa9pFwRTNsvVMtphzDl13g== |
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f4550317 Location: |
Summary Statistics: Mean 53.33333333333332; Valid 36.0; Max. 144.0; Min. 0.0; StDev 47.898702636769976 Variable Format: numeric Notes: UNF:6:o/EkpTtgftk33GzP8izFCA== |
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f4550317 Location: |
Variable Format: character Notes: UNF:6:VEeIn+0vd3miMN1vqyBmxg== |
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f4550330 Location: |
Variable Format: character Notes: UNF:6:vuJEOU72qDyCy015GltBhA== |
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f4550330 Location: |
Variable Format: character Notes: UNF:6:i8A7YafNJ0C9ppGvsPqb4w== |
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f4550330 Location: |
Summary Statistics: Max. 39.0; Mean 20.373188405797116; Valid 276.0; Min. 0.0; StDev 13.028718152841916; Variable Format: numeric Notes: UNF:6:2fLAC6HkoQl29Pw9VB6aIQ== |
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f4551554 Location: |
Variable Format: character Notes: UNF:6:68It/ms6lS3cryme/6VgHQ== |
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f4551554 Location: |
Variable Format: character Notes: UNF:6:w9uSY+ZPI8TRQJccv/YXQw== |
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f4551554 Location: |
Summary Statistics: StDev 5.582389426661112; Min. 0.0; Valid 231.0; Max. 23.0; Mean 11.46753246753247 Variable Format: numeric Notes: UNF:6:4SQGto3d2VsQgH3PMNncLA== |
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f4551549 Location: |
Variable Format: character Notes: UNF:6:H6ktYQ9IotXnPFeFBcwCow== |
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f4551549 Location: |
Variable Format: character Notes: UNF:6:g4rSbdNUOXPkNXs0/N77nA== |
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f4551549 Location: |
Summary Statistics: Valid 703.0; Max. 34.0; Mean 16.351351351351347; Min. 0.0; StDev 7.981657766833947 Variable Format: numeric Notes: UNF:6:pYdo4Uu616BVs+xmmL0OCQ== |
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f4551552 Location: |
Variable Format: character Notes: UNF:6:KOrPp3yftEZqIIMAx7WJqA== |
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f4551552 Location: |
Variable Format: character Notes: UNF:6:bg/AT0hY4k6m0S3sz9Vt+A== |
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f4551552 Location: |
Summary Statistics: StDev 21.03371905919874; Max. 58.0; Min. 0.0; Mean 33.35087719298245; Valid 171.0 Variable Format: numeric Notes: UNF:6:5PsvKinmh5WczCnIB/fl3A== |
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f4551548 Location: |
Variable Format: character Notes: UNF:6:GzOtVcMxLGzhUZwXj6kfuw== |
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f4551548 Location: |
Variable Format: character Notes: UNF:6:F7+awvYEbhD9hI0dw5cUPQ== |
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f4551548 Location: |
Summary Statistics: StDev 10.02604679995799; Mean 14.05538461538462; Valid 325.0; Max. 38.0; Min. 0.0; Variable Format: numeric Notes: UNF:6:MfBlEi7uGMHOIqwbanvchQ== |
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f4551547 Location: |
Variable Format: character Notes: UNF:6:bN/jdu8NlidI1fTMEKUntw== |
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f4551547 Location: |
Variable Format: character Notes: UNF:6:uQDsvNxNZcPsFsyQDXk2QQ== |
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f4551547 Location: |
Summary Statistics: Max. 50.0; Min. 0.0; StDev 12.616726809976706; Mean 13.804761904761907; Valid 210.0; Variable Format: numeric Notes: UNF:6:4mSWETbthOWaQVNhlCZ8uw== |
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f4551556 Location: |
Variable Format: character Notes: UNF:6:eDZzSUQ9YXrmqcibhQ4W8w== |
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f4551556 Location: |
Variable Format: character Notes: UNF:6:sDqCzftPavGZbepyIcr2tw== |
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f4551556 Location: |
Summary Statistics: Max. 31.0; Min. 0.0; Valid 351.0; Mean 12.490028490028495; StDev 8.154878487264115 Variable Format: numeric Notes: UNF:6:AEvuxKWnBd7u8qXmJhfVFQ== |
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f4551551 Location: |
Variable Format: character Notes: UNF:6:qwoPYc8BG77VaMOiYNE1TQ== |
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f4551551 Location: |
Variable Format: character Notes: UNF:6:Y3D4wsyLX/OtiFH2GuyfAA== |
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f4551551 Location: |
Summary Statistics: Max. 31.0; Valid 325.0; Min. 0.0; StDev 10.30031301675415; Mean 15.421538461538464; Variable Format: numeric Notes: UNF:6:fziFPuSq61zUzhPuKnJMQQ== |
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f4551555 Location: |
Variable Format: character Notes: UNF:6:+FoQcoxHnGYsQMmOAnjjiQ== |
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f4551555 Location: |
Variable Format: character Notes: UNF:6:mudQGCbnWXmF5O6GnSertw== |
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f4551555 Location: |
Summary Statistics: Max. 55.0; Mean 23.410526315789483; Min. 0.0; Valid 190.0; StDev 19.86035626680139 Variable Format: numeric Notes: UNF:6:gxxw5PNfku35C1qgiRu8jA== |
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f4551553 Location: |
Variable Format: character Notes: UNF:6:cUWxfosysu0v6mo1hS6jxw== |
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f4551553 Location: |
Variable Format: character Notes: UNF:6:s2O4BV2k+kmGwduvBx7aTg== |
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f4551553 Location: |
Summary Statistics: Mean 14.329004329004341; Min. 0.0; StDev 7.687651213357828; Valid 231.0; Max. 29.0 Variable Format: numeric Notes: UNF:6:3vXMwTD5yUJNhZlGaOm74w== |
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Label: |
Figure2.R |
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Notes: |
text/x-r-source |
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Label: |
HiLiter_figure_4.py |
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Text: |
It displays nucleotides differences between sequences of the same HRV type |
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Notes: |
text/plain |
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Label: |
HRV_monthly_distribution.do |
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Notes: |
application/x-stata-syntax |
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Label: |
Jmwita_author_Codebook.xlsx |
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Notes: |
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet |
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Label: |
JMwita_HRV_Readme.txt |
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Notes: |
text/plain |
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Label: |
Pairwise_snps_Figure4.R |
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Text: |
This shows the distribution plot of pairwise nucleotide differences between sequences of the same HRV type |
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Notes: |
type/x-r-syntax |
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Label: |
Rplots_figure3.R |
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Text: |
This script displays distribution of HRV over the 12 year period |
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Notes: |
type/x-r-syntax |
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Label: |
species_Months-summary.txt |
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Notes: |
text/plain |
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Label: |
SuppFigure1.R |
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Notes: |
type/x-r-syntax |
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Label: |
Supplementary File 1.csv |
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Notes: |
text/csv |
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Label: |
types_Frequency-seqs.txt |
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Notes: |
text/plain |