Replication Data for: Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022 (doi:10.7910/DVN/EG6MEH)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Replication Data for: Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022

doi:10.7910/DVN/EG6MEH

Harvard Dataverse

2023-07-20

1

Lambisia, Arnold W.; Murunga, Nickson; Mutunga, Martin; Cheruiyot, Robinson; Maina, Grace; Makori, Timothy; Nokes, D.James; Agoti, Charles N., 2023, "Replication Data for: Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022", https://doi.org/10.7910/DVN/EG6MEH, Harvard Dataverse, V1, UNF:6:prw/VZIIJHN4aFHKLaZ63w== [fileUNF]

Replication Data for: Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022

doi:10.7910/DVN/EG6MEH

Lambisia, Arnold W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mutunga, Martin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Cheruiyot, Robinson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Maina, Grace (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Makori, Timothy (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nokes, D.James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Harvard Dataverse

Lambisia, Arnold W.

The Data Governance Committee

Lambisia, Arnold W.

2023-07-20

https://doi.org/10.7910/DVN/EG6MEH

Medicine, Health and Life Sciences, Enteric viruses, COVID-19, Rotavirus A, positivity rate, Kenya, paediatrics

<p>This is a replication dataset for the manuscript titled "<a href="">Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022</a>." <p>The main dataset is part of long-term surveillance of enteric viruses associated with diarrhoea. These datasets are part of long-term surveillance of enteric viruses associated with diarrhea among children under 13 years admitted to the KCH study. These datasets contain results of samples tested by real-time PCR between 1st Jan 2019 and 31st Dec 2022. Aside from the samples tested and results of the tests, it also contains the patients’ sociodemographic characteristics, cycle threshold, discharge outcome, and disease severity. The dataset is used to explore the prevalence and seasonality of five common viruses associated with diarrhoea (rotavirus group A, adenovirus 40/41, astrovirus, sapovirus, and norovirus)</p>

• Number of cases: 1613

• No. of variables per record: 4

• Type of File: text/tab-separated-values

UNF:6:Ho3m2J0ABc//Fx5w9gqPEg==

• Number of cases: 870

• No. of variables per record: 16

• Type of File: text/tab-separated-values

UNF:6:BL/Lg+5IaMOInpo1W+BxCg==

• serial - serial
• Date - Date
• rota_consent - rota_consent
• consent_refusal_reason - consent_refusal_reason
• serial - serial
• Ct_ADV40_41 - Ct_ADV40_41
• Ct_RVA - Ct_RVA
• Ct_NVGII - Ct_NVGII
• Ct_ASV - Ct_ASV
• Ct_SAP - Ct_SAP
• stool_date - stool_date
• age_months - age_months
• sex - sex
• temp - temp
• vomiting_durn - vomiting_durn
• vomiting_episode - vomiting_episode
• diarrhoea_durn - diarrhoea_durn
• diarrhoea_episode - diarrhoea_episode
• dehydration_status - dehydration_status
• outcome - outcome

f7244870 Location:

Summary Statistics: Min. 1.0; StDev 465.7773073046818; Mean 807.0; Valid 1613.0; Max. 1613.0;

Variable Format: numeric

Notes: UNF:6:xIeGmIjGXR4zu42ERkojRg==

f7244870 Location:

Variable Format: character

Notes: UNF:6:ucGxaAfeSfypFk/BJzWEOQ==

f7244870 Location:

Variable Format: character

Notes: UNF:6:LY8xXZn944gJLTqlC/ilwg==

f7244870 Location:

Variable Format: character

Notes: UNF:6:w7xCj3/V2bHRHSZzo7S7Pg==

f7244871 Location:

Summary Statistics: Max. 870.0; Mean 435.5; Min. 1.0; Valid 870.0; StDev 251.29166321229204

Variable Format: numeric

Notes: UNF:6:N1ie5cvb9nRKu4KEgKiPXQ==

f7244871 Location:

Summary Statistics: StDev 8.451209669485708; Valid 34.0; Min. 11.75; Mean 23.838997326470587; Max. 37.59;

Variable Format: numeric

Notes: UNF:6:0Zi9MUXYj9+wJyA1gFllsw==

f7244871 Location:

Summary Statistics: Max. 39.56412; Valid 138.0; Min. 15.65474415; Mean 24.015139608623187; StDev 5.201363887413204

Variable Format: numeric

Notes: UNF:6:5tm0ooRrO5CSGvMKktLi+Q==

f7244871 Location:

Summary Statistics: StDev 5.538579544695165; Mean 27.58719737382353; Min. 17.29668808; Valid 102.0; Max. 39.60014725

Variable Format: numeric

Notes: UNF:6:TG4gd3Kh6vZ1TO3vwjqVzQ==

f7244871 Location:

Summary Statistics: Mean 24.71202679736842; Valid 19.0; Max. 35.29440689; StDev 4.333329944009778; Min. 19.48098946

Variable Format: numeric

Notes: UNF:6:O/qEF9DDE/dkjLtFJZAhug==

f7244871 Location:

Summary Statistics: Valid 60.0; StDev 4.933584989436999; Max. 39.63056946; Mean 32.85214071233333; Min. 20.3243885

Variable Format: numeric

Notes: UNF:6:6TjMsrvUJMxuC58AX5dCxg==

f7244871 Location:

Variable Format: character

Notes: UNF:6:71puGfYskhg+MpGxDXPQ6w==

f7244871 Location:

Summary Statistics: Max. 156.0; Min. 0.361396313; Valid 870.0; StDev 27.206307564255575; Mean 22.919764465812648

Variable Format: numeric

Notes: UNF:6:APi2/+us5T3hQgQXWIK/+w==

f7244871 Location:

Variable Format: character

Notes: UNF:6:B+q5fnsfLnK9UurVD9A5BQ==

f7244871 Location:

Summary Statistics: Min. 32.6; StDev 1.197800562745831; Mean 37.59816091954023; Valid 870.0; Max. 40.7;

Variable Format: numeric

Notes: UNF:6:qeV2kcaGOb7wxYoB4X+O/w==

f7244871 Location:

Summary Statistics: Mean 3.5897858319604605; Max. 60.0; Min. 0.0; Valid 607.0; StDev 4.238137526087355

Variable Format: numeric

Notes: UNF:6:stUkq/Jd6li+pl9cDI2adA==

f7244871 Location:

Summary Statistics: Min. 0.0; Valid 610.0; Mean 4.304918032786884; Max. 30.0; StDev 4.123560652679256;

Variable Format: numeric

Notes: UNF:6:rOxLRXvLjDuR/sDIF3EtHQ==

f7244871 Location:

Summary Statistics: Valid 868.0; Mean 4.1831797235023025; Max. 60.0; Min. 0.0; StDev 4.9871662774184236

Variable Format: numeric

Notes: UNF:6:QHP01YV7skdcNAqm4vip3A==

f7244871 Location:

Summary Statistics: Max. 30.0; Mean 4.981609195402299; Valid 870.0; StDev 3.8531301440432784; Min. 0.0

Variable Format: numeric

Notes: UNF:6:EGobVlILm4lfPA36oRkI1w==

f7244871 Location:

Variable Format: character

Notes: UNF:6:p97x6I2E18e1unj+RnuRMA==

f7244871 Location:

Variable Format: character

Notes: UNF:6:Bsw/kGvx8wmBx9V4IqL29w==

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ALambisia_Enterics_Data_Dictionary.pdf

application/pdf

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ALambisia_Enterics_Readme.txt

text/plain

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Epi_Analysis_manuscript_script1.R

type/x-r-syntax

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Manuscript_Scripts_EV_July2023.Rmd

text/x-r-notebook