|
View: |
Part 1: Document Description
|
|
Citation |
|
|---|---|
|
Title: |
Replication Data for: Rhinovirus transmission dynamics across different social structures |
|
Identification Number: |
doi:10.7910/DVN/KSOPCI |
|
Distributor: |
Harvard Dataverse |
|
Date of Distribution: |
2023-07-31 |
|
Version: |
1 |
|
Bibliographic Citation: |
Luka, Martha M.; Otieno, James R.; Kamau, Everlyn; Morobe, John M.; Murunga, Nickson; Adema, Irene; Nyiro, Joyce U.; Macharia,Peter M.; Bigogo, Godfrey; Otieno, Nancy A.; Nyawanda, Bryan O.; Rabaa, Maia A.; Emukule, Gideon O.; Onyango, Clayton; Munywoki, Patrick K.; Agoti, Charles N.; Nokes, D.James, 2023, "Replication Data for: Rhinovirus transmission dynamics across different social structures", https://doi.org/10.7910/DVN/KSOPCI, Harvard Dataverse, V1, UNF:6:5Iz4Zr91WomokGKyjKfRMA== [fileUNF] |
|
Citation |
|
|
Title: |
Replication Data for: Rhinovirus transmission dynamics across different social structures |
|
Identification Number: |
doi:10.7910/DVN/KSOPCI |
|
Authoring Entity: |
Luka, Martha M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
Otieno, James R. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Kamau, Everlyn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Morobe, John M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Adema, Irene (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Nyiro, Joyce U. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Macharia,Peter M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Bigogo, Godfrey (KEMRI-Centre for Global Health Research) |
|
|
Otieno, Nancy A. (KEMRI-Centre for Global Health Research) |
|
|
Nyawanda, Bryan O. (KEMRI-Centre for Global Health Research) |
|
|
Rabaa, Maia A. (Coronavirus and Other Respiratory Viruses Division (CORVD), National Center for Immunization and Respiratory Diseases (NCIRD), U.S. Centers of Disease Control and Prevention (CDC) , Atlanta , Georgia, USA.) |
|
|
Emukule, Gideon O. (KEMRI-Centre for Global Health Research) |
|
|
Onyango, Clayton (U.S. Centers of Disease Control and Prevention (CDC) |
|
|
Munywoki, Patrick K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Nokes, D.James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
|
|
Distributor: |
Harvard Dataverse |
|
Access Authority: |
Luka, Martha M. |
|
Access Authority: |
Nokes, D.James |
|
Access Authority: |
The Data Governance Committee |
|
Depositor: |
Luka, Martha M. |
|
Date of Deposit: |
2023-07-31 |
|
Holdings Information: |
https://doi.org/10.7910/DVN/KSOPCI |
|
Study Scope |
|
|
Keywords: |
Medicine, Health and Life Sciences, rhinovirus, transmission, social structures, phylogenetics, molecular epidemiology |
|
Abstract: |
<p>This is a replication dataset for the publication titled: "<a href="">Rhinovirus transmission dynamics across different social structures </a>."</p> <p>This dataset aims to compare rhinovirus dynamics from five previous studies conducted in Kenya in four different social structures. The studies are (i) intensive household surveillance in coastal Kenya (Dec 2009 - May 2010), (ii) surveillance of respiratory viruses within a public primary school (May 2017 – April 2018), (iii) outpatient surveillance of acute respiratory illness within the Kilifi Health and Demographic Surveillance System (KHDSS) (Dec 2015 - Nov 2016), and (iv) countrywide surveillance of severe acute respiratory syndrome illness (SARI) among inpatients and influenza-like illness (ILI) among outpatients via sentinel hospital reporting (Jan 2014 - Dec 2014). (v) We used contemporaneous data from long-term surveillance of severe pneumonia among pediatric inpatients at the Kilifi County Hospital (KCH) for comparison with the households, school, and KHDSS studies datasets. The primary dataset contains VP4/2 sequence data, alongside necessary metadata (e.g. date of sampling, site where collection, respective study). Secondary datasets generated from the primary data are also included (described in section 4 - Contents). </p> |
|
Methodology and Processing |
|
|
Sources Statement |
|
|
Data Access |
|
|
Other Study Description Materials |
|
|
File Description--f7266276 |
|
|
File: anonym_metadata.tab |
|
|
|
|
Notes: |
UNF:6:fvVWoU1FnO2+TydQBF7N4A== |
|
File Description--f7266271 |
|
|
File: overall_genetic_distances_per_type.tab |
|
|
|
|
Notes: |
UNF:6:6po1ejojBbcxwWNfPLWfdA== |
|
File Description--f7266275 |
|
|
File: phylogeography_links.tab |
|
|
|
|
Notes: |
UNF:6:dSQS89asRbBNc8q8VZ/84Q== |
|
File Description--f7266273 |
|
|
File: supp_table3_data.tab |
|
|
|
|
Notes: |
UNF:6:vE0QJVWOKWn4y+oZx0ddAA== |
|
List of Variables: |
|
|
Variables |
|
|
f7266276 Location: |
Summary Statistics: StDev 688.1389988796848; Mean 1190.0261272650646; Max. 2380.0; Valid 2373.0; Min. 1.0 Variable Format: numeric Notes: UNF:6:G5OvdQAOyWPrcLSuHMJzsQ== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:22l0mgSY41uAh0yul76/0g== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:nTgm1YB7zVkPhXzMQ/utLw== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:WZsWhqVvkSwoYf2d2zX/MA== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:CkqJLCFOI+cTV16THz6vrQ== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:3bNPMAZl3gknZVeI+6mxyw== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:1NL9WFYwC37A5aRufKN5hQ== |
|
f7266276 Location: |
Variable Format: character Notes: UNF:6:UUTo6X3kUIMOdC5DkrjT8Q== |
|
f7266271 Location: |
Variable Format: character Notes: UNF:6:EQZo2ArV1eswSrc12Tu6yA== |
|
f7266271 Location: |
Summary Statistics: Mean 24.875; Max. 64.0; Min. 8.0; StDev 14.93951480350358; Valid 40.0; Variable Format: numeric Notes: UNF:6:qjJy1ui/6DViU56UfeBrvg== |
|
f7266271 Location: |
Variable Format: character Notes: UNF:6:v/iCaxk0NKwFLGpMOB1RUQ== |
|
f7266271 Location: |
Summary Statistics: Valid 40.0; Max. 0.0663572; StDev 0.017704993974683076; Min. 0.0; Mean 0.016172344999999998; Variable Format: numeric Notes: UNF:6:7U6qnDFw3JV6uaA40RkT+Q== |
|
f7266275 Location: |
Variable Format: character Notes: UNF:6:hdkqA2e3HPOENPzGd16A/A== |
|
f7266275 Location: |
Variable Format: character Notes: UNF:6:A/YYJ/1DnHllhX36ZQOWJg== |
|
f7266275 Location: |
Summary Statistics: StDev 6426.979781467187; Valid 111.0; Max. 37291.32954; Mean 1498.7856383751803; Min. 3.003966327 Variable Format: numeric Notes: UNF:6:gaYBbRI3UpOVKwxBmTgSxA== |
|
f7266275 Location: |
Summary Statistics: Valid 111.0; Min. 0.429507832; Max. 1.0; StDev 0.17827718442769586; Mean 0.7922718796576577 Variable Format: numeric Notes: UNF:6:XtS8hKhqYLW6jwgIXWuKNA== |
|
f7266275 Location: |
Variable Format: character Notes: UNF:6:/NhOzctzHBIRRf8J/Xwb6A== |
|
f7266273 Location: |
Variable Format: character Notes: UNF:6:/UzG1yVpkC8+nXUubcuEag== |
|
f7266273 Location: |
Variable Format: character Notes: UNF:6:Qfuwbx0wdgQZ6Hxu9rKYpA== |
|
f7266273 Location: |
Variable Format: character Notes: UNF:6:KtiqEezYB2wBhoPK6bWhVQ== |
|
Label: |
anonym_sequences.fasta |
|
Text: |
This dataset cobtains rhinovirus VP4/2 sequence data generated across 4 social scales by five previous studies in Kenya: (i) households, (ii) school, (iii) Kilifi HDSS (KHDSS) ,(iv) Countrywide and (v) Kilifi County Hospital (KCH) |
|
Notes: |
application/octet-stream |
|
Label: |
Fig4_suppTable3.R |
|
Notes: |
type/x-r-syntax |
|
Label: |
Fig5_suppFig2.R |
|
Notes: |
type/x-r-syntax |
|
Label: |
Figures_1_2_5A_table1_SuppFig1.R |
|
Notes: |
type/x-r-syntax |
|
Label: |
LUKA_HRV_SocialScales_Data_Dictionary.pdf |
|
Notes: |
application/pdf |
|
Label: |
LUKA_HRV_SocialScales_Readme.txt |
|
Notes: |
text/plain |
|
Label: |
mapShapefiles.zip |
|
Notes: |
application/zipped-shapefile |