Replication Data for: Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on (doi:10.7910/DVN/XJUA0Z)

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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
Entire Codebook

Replication Data for: Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on

doi:10.7910/DVN/XJUA0Z

Harvard Dataverse

2020-07-23

1

Kamau, Everlyn; Otieno, James R.; Lewa, Clement S.; Mwema, Anthony; Murunga, Nickson; Nokes, David James; Agoti, Charles N., 2020, "Replication Data for: Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on", https://doi.org/10.7910/DVN/XJUA0Z, Harvard Dataverse, V1, UNF:6:lRmpyQXvfZbKo2IVyePm4g== [fileUNF]

Replication Data for: Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on

doi:10.7910/DVN/XJUA0Z

Kamau, Everlyn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Otieno, James R. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Lewa, Clement S. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mwema, Anthony (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK)

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; School of Health and Human Sciences, Pwani University, Kilifi, Kenya)

Harvard Dataverse

Kamau, Everlyn

Kamau, Everlyn

2020-07-22

https://doi.org/10.7910/DVN/XJUA0Z

Medicine, Health and Life Sciences

<p>This study is part of a longitudinal surveillance study established to understand the epidemiology and disease burden of RSV associated pneumonia admissions to Kilifi County Hospital (KCH). Fields available in the data include month and year of sample collection, Eligibles (Under fives with severe or very severe pneumonia), RSVA and RSVB positives, proportion tested, and FUBAR all sequences output.</p>

<strong>Related Data</strong> <br> The Kilifi G gene sequences presented in the related publication are available in GenBank (accession numbers KP862065-KP862529, KX775722-KX775849 and MH742792-MH742925).

<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p>

<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>

Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on. ~manuscript in preparation

Respiratory Syncytial Virus genotype BA in Kilifi, Kenya: evolutionary dynamics, 15 years on. ~manuscript in preparation

• Number of cases: 252

• No. of variables per record: 9

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

UNF:6:g21am5MCCmakRt3K0iM/ow==

Analysis dataset (CSV format)

• Number of cases: 176

• No. of variables per record: 8

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

UNF:6:BO8m+8lpMSLHZQXrCKnPSQ==

Analysis dataset (CSV format)

• Site - Site
• Position - Position
• Partition - Partition
• &alpha; - &alpha;
• &beta; - &beta;
• beta_alpha - beta_alpha
• Prob[&alpha;>&beta;] - Prob[&alpha;>&beta;]
• Prob[&alpha;<&beta;] - Prob[&alpha;<&beta;]
• BayesFactor[&alpha;<&beta;] - BayesFactor[&alpha;<&beta;]
• month - month
• year - year
• eligible_1055 - eligible_1055
• tested - tested
• rsvb_bin - rsvb_bin
• tested_prop - tested_prop
• rsva_bin - rsva_bin
• monYr - monYr

f3988004 Location:

Summary Statistics: Max. 252.0; Mean 126.5; StDev 72.89032857656768; Min. 1.0; Valid 252.0

Variable Format: numeric

Notes: UNF:6:JuWX+Ryks4L045F0rBmy2g==

f3988004 Location:

Summary Statistics: Max. 319.0; Valid 252.0; StDev 72.89032857656768; Min. 68.0; Mean 193.5

Variable Format: numeric

Notes: UNF:6:wpSAq0Jp7GKKxCxWwM2QnQ==

f3988004 Location:

Summary Statistics: Max. 1.0; Valid 252.0; StDev 0.0; Mean 1.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:okIt3NlVxDs7dk5N8idSxw==

f3988004 Location:

Summary Statistics: Mean 1.8793571428571427; Valid 252.0; Max. 26.731; StDev 2.7559422347038547; Min. 0.271;

Variable Format: numeric

Notes: UNF:6:3d2jEM8k/XXfkaCi7VrTVQ==

f3988004 Location:

Summary Statistics: Valid 252.0; StDev 2.372050811101861; Max. 36.06; Mean 1.0046150793650794; Min. 0.113

Variable Format: numeric

Notes: UNF:6:2O2S21kwfGdCNQa7g2OyuQ==

f3988004 Location:

Summary Statistics: Min. -25.912; StDev 3.5611019343609787; Max. 31.913; Mean -0.8747619047619047; Valid 252.0

Variable Format: numeric

Notes: UNF:6:yKF40u9vE7naSwP+HYQSOA==

f3988004 Location:

Summary Statistics: Valid 252.0; Min. 0.0; Max. 1.0; StDev 0.26993777702556393; Mean 0.5623492063492064

Variable Format: numeric

Notes: UNF:6:knDqZICzMw4ztmalWB/JkQ==

f3988004 Location:

Summary Statistics: Min. 0.0; Max. 0.999; Valid 252.0; StDev 0.25071111384762346; Mean 0.36357142857142855

Variable Format: numeric

Notes: UNF:6:amQrY8jAJVHhitlAkLfwng==

f3988004 Location:

Summary Statistics: Mean 9.399388888888893; Valid 252.0; Min. 0.0; StDev 92.81038253127261; Max. 1340.058

Variable Format: numeric

Notes: UNF:6:3QsTdc/22hdz05c9++VrOw==

f3988005 Location:

Summary Statistics: Mean 6.409090909090909; Max. 12.0; Valid 176.0; Min. 1.0; StDev 3.4430430515091515;

Variable Format: numeric

Notes: UNF:6:Or8Te/uvJY0h0dZ4ktjMaw==

f3988005 Location:

Summary Statistics: Min. 2003.0; Mean 2009.840909090909; StDev 4.249064068067866; Valid 176.0; Max. 2017.0

Variable Format: numeric

Notes: UNF:6:sf6H6jCJUqWHlI2InurwkA==

f3988005 Location:

Summary Statistics: Min. 24.0; Mean 83.02272727272728; StDev 35.157759484188574; Valid 176.0; Max. 225.0

Variable Format: numeric

Notes: UNF:6:UcEq5K8cyCh/CufIW7Quzw==

f3988005 Location:

Summary Statistics: Max. 192.0; Valid 176.0; StDev 31.753146893848783; Mean 67.47727272727272; Min. 16.0;

Variable Format: numeric

Notes: UNF:6:haMBwV+fxhh39ZbbVmp/Bg==

f3988005 Location:

Summary Statistics: Min. 0.0; Valid 176.0; StDev 9.266023327819147; Mean 5.096590909090909; Max. 65.0;

Variable Format: numeric

Notes: UNF:6:4+4kplCSsGoACflZ52iyig==

f3988005 Location:

Summary Statistics: Max. 96.0; StDev 8.980236236154528; Valid 176.0; Min. 47.0; Mean 80.1875

Variable Format: numeric

Notes: UNF:6:ZQNDoX4aSJJVYiqVeV1MvA==

f3988005 Location:

Summary Statistics: StDev 12.395134152132062; Min. 0.0; Valid 176.0; Mean 8.420454545454545; Max. 58.0;

Variable Format: numeric

Notes: UNF:6:QPKmso/snWdlubxgB2fnjw==

f3988005 Location:

Variable Format: character

Notes: UNF:6:gmWGUcV435ZUiHsW5AKBCg==

Label:

EKamau_RSVB_GGene_Kilifi_Codebook.pdf

Text:

Contains variable or column header descriptions and value labels

application/pdf

Label:

EKamau_RSVB_GGene_Kilifi_Readme.txt

text/plain

Label:

FigS1.R

Text:

R analysis script - outputs figure 1 graph

type/x-r-syntax

Label:

RSVB_epidemics.R

Text:

R analysis script - outputs epidemics graph

type/x-r-syntax