Replication Data for: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya (doi:10.7910/DVN/VV12WS)

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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: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya

doi:10.7910/DVN/VV12WS

Harvard Dataverse

2020-03-30

1

Luka, Martha M.; Murunga, Nickson; Otieno, Grieven Paul; Nokes, David James, 2020, "Replication Data for: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya", https://doi.org/10.7910/DVN/VV12WS, Harvard Dataverse, V1, UNF:6:C/W4dpKyKisMZOv1PtfVWg== [fileUNF]

Replication Data for: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya

doi:10.7910/DVN/VV12WS

Luka, Martha M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Otieno, Grieven Paul (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Harvard Dataverse

Luka, Martha M.

Luka, Martha M.

2020-03-18

https://doi.org/10.7910/DVN/VV12WS

Medicine, Health and Life Sciences

<p>This is a replication data for the paper: <i>'Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya.'</i></p> <p>The package contains surveillance and sequence data on respiratory viruses and acute respiratory infection symptoms among primary school children in Kilifi, Kenya. </p>

Publications based on this data collection should acknowledge this source by means of bibliographic citation.

<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>

Replication Data for: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya. ~submitted manuscript

Replication Data for: Molecular epidemiology of human rhinovirus from one-year surveillance within a school setting in rural coastal Kenya. ~submitted manuscript

• Number of cases: 42

• No. of variables per record: 4

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

UNF:6:BNdu3Rl5zSZL/PAke3sN5A==

• Number of cases: 253

• No. of variables per record: 11

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

UNF:6:dN0pEG3GBD3ZNxwmdNZDOg==

This is data from one year surveillance of respiratory viruses and acute respiratory infection symptoms among primary school children in Kilifi that were positive for HRV and sequenced

• Number of cases: 1859

• No. of variables per record: 25

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

UNF:6:Liqcby0Igo7F2r5+331erA==

STATA file versio 15

• Type - Type
• Frequency - Frequency
• Group - Group
• label - label
• person - person
• date - date
• type - type
• species - species
• study_no - study_no
• group - group
• Grade - Grade
• Group - Group
• rhino - rhino
• date_swab - date_swab
• actualseq - actualseq
• classgrade - class cohort
• part_type - Level of pariticipant: Pupil or Teacher
• classsize - Number of students in the class
• classcat - Category of class student population
• date_anthro
• month
• year
• age_years
• agecat - Age category
• sex - Sex
• person_ari - Are there other persons in your household who have symptoms of ARI?
• person_ari_inschool - person_ARI_inSchool
• swab_collected - Nasal swab collected?
• unwell_fortnight - Have you been ill in the last two weeks?
• cough - Cough in the last two weeks?
• nasal_disch - Nasal Discharge in the last two weeks?
• sorethroat - Sore Throat in the last two weeks?
• mpx_tested
• rhino - 14 ct_value
• rhino_bin
• partlevel - partlevel
• sameschool
• subtype
• species
• study_no - group(study_no)

f3781490 Location:

Variable Format: character

Notes: UNF:6:dywbeWhd7lnn+DwCHI7FGA==

f3781490 Location:

Summary Statistics: Min. 0.0; Valid 42.0; Max. 16.0; StDev 4.357433207515161; Mean 4.809523809523809

Variable Format: numeric

Notes: UNF:6:1ejgJsjjTJXfQG0frROHIQ==

f3781490 Location:

Variable Format: character

Notes: UNF:6:sFsk7cO/ypJVrHGZkFx+SQ==

f3781490 Location:

Summary Statistics: Max. 21.3; Min. 1.0; StDev 6.1305810809615675; Valid 42.0; Mean 11.15

Variable Format: numeric

Notes: UNF:6:wKG7uES0Ylq4VfLtqKoSiw==

f3781488 Location:

Summary Statistics: StDev 39.16477223093633; Max. 144.0; Valid 253.0; Min. 1.0; Mean 63.9604743083004

Variable Format: numeric

Notes: UNF:6:Zg5Tr69j2csFuTGuc0xKEw==

f3781488 Location:

Variable Format: character

Notes: UNF:6:2Ny5INP0HUANdg0nXtEQyQ==

f3781488 Location:

Variable Format: character

Notes: UNF:6:A6zy4LGZRdzUdfnxFTmmRw==

f3781488 Location:

Variable Format: character

Notes: UNF:6:jpqH8hR6obujZovL5+zLMg==

f3781488 Location:

Summary Statistics: Max. 100800.0; Mean 100422.97233201581; StDev 288.3750231787586; Valid 253.0; Min. 100006.0

Variable Format: numeric

Notes: UNF:6:MZdR1gEiHLvedKk6s0unQA==

f3781488 Location:

Variable Format: character

Notes: UNF:6:qK034XHJyuHvZ0zMy7ydsQ==

f3781488 Location:

Variable Format: character

Notes: UNF:6:L0Ot3nDlDfo8+9Aq7UTmwg==

f3781488 Location:

Variable Format: character

Notes: UNF:6:ZD2ribMFzw5MUQZQFmtODg==

f3781488 Location:

Summary Statistics: Mean 30.085858846284584; Max. 34.90981293; Min. 21.38475227; Valid 253.0; StDev 2.9886038164521334

Variable Format: numeric

Notes: UNF:6:ly+geV30EBwElP4IcH/MIQ==

f3781488 Location:

Variable Format: character

Notes: UNF:6:re0oGOVm5mRfckJX/q+2lw==

f3781488 Location:

Variable Format: character

Notes: UNF:6:rkJ807Qk+I4wnqF+czcChA==

f3769796 Location:

Summary Statistics: Min. 1.0; Max. 14.0; Mean 5.695535233996769; Valid 1859.0; StDev 3.407841977595765

Variable Format: numeric

Notes: UNF:6:nmn1vF7pmRWngNUmUHMcaw==

f3769796 Location:

Summary Statistics: Mean 1.0172135556750936; Valid 1859.0; StDev 0.1301013230593188; Max. 2.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:cSReaZRJYcXUomoo713b9g==

f3769796 Location:

Summary Statistics: Mean 63.25615763546793; Valid 1827.0; Min. 30.0; StDev 20.671187283142316; Max. 95.0;

Variable Format: numeric

Notes: UNF:6:q3oX8CtAFhVdv99Vc+rDRA==

f3769796 Location:

Summary Statistics: Mean 1.677613574165302; StDev 0.46751797101501197; Valid 1827.0; Min. 1.0; Max. 2.0

Variable Format: numeric

Notes: UNF:6:so9u/nHZHME9PFGkZpNuxA==

f3769796 Location:

Variable Format: character

Notes: UNF:6:q53g4cdt5XUOIiKBLtPNlg==

f3769796 Location:

Summary Statistics: Max. 10.0; Mean 5.645508337816028; StDev 2.7556957352480365; Min. 1.0; Valid 1859.0

Variable Format: numeric

Notes: UNF:6:o8LzgDRQXb1F5xDRYvjMFA==

f3769796 Location:

Summary Statistics: Min. 2017.0; Max. 2018.0; Valid 1859.0; StDev 0.46210956759430666; Mean 2017.308768154922

Variable Format: numeric

Notes: UNF:6:0A9gC4HZ4QiAxq6Ulk66VA==

f3769796 Location:

Summary Statistics: StDev 4.393262940256079; Mean 9.492374727668812; Min. 3.0; Max. 42.0; Valid 1836.0;

Variable Format: numeric

Notes: UNF:6:ZS/6hjpllC6bXyFkeMjpcw==

f3769796 Location:

Summary Statistics: StDev 0.7796970140797748; Mean 2.2244008714596966; Valid 1836.0; Min. 1.0; Max. 4.0;

Variable Format: numeric

Notes: UNF:6:Xz0dOl52N6IP//iX6Ts+cQ==

f3769796 Location:

Summary Statistics: Max. 1.0; Min. 0.0; Valid 1859.0; StDev 0.4998825868461204; Mean 0.4841312533620226

Variable Format: numeric

Notes: UNF:6:hBRPThXU5E9AO2ba3gRYZw==

f3769796 Location:

Summary Statistics: Mean 1.6976869284561857; Min. 0.0; Valid 1859.0; StDev 3.3315289382844653; Max. 9.0

Variable Format: numeric

Notes: UNF:6:BQg11e+pM9iaGgIy6Q28vg==

f3769796 Location:

Summary Statistics: Valid 303.0; StDev 0.4996228332878582; Min. 0.0; Max. 1.0; Mean 0.5346534653465346

Variable Format: numeric

Notes: UNF:6:Kyw6e2xXshV/xQ4P6/ESjw==

f3769796 Location:

Summary Statistics: Mean 1.0; StDev 0.0; Valid 1859.0; Max. 1.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:RF9KJ08NWt3IopHL4LPOFg==

f3769796 Location:

Summary Statistics: Max. 1.0; StDev 0.04634889695280618; Min. 0.0; Valid 1859.0; Mean 0.9978483055406132

Variable Format: numeric

Notes: UNF:6:paUGX/n1FZUreoAKjGD5sA==

f3769796 Location:

Summary Statistics: Mean 0.7439483593329742; Max. 10.0; StDev 0.5361623686895328; Min. 0.0; Valid 1859.0;

Variable Format: numeric

Notes: UNF:6:3u9eBkj+DxAoaFbeIhk7QA==

f3769796 Location:

Summary Statistics: Mean 0.8902635825712758; Valid 1859.0; StDev 0.4411635528070802; Min. 0.0; Max. 10.0;

Variable Format: numeric

Notes: UNF:6:UW4e46CUrpPoQ25iGUj8RQ==

f3769796 Location:

Summary Statistics: Valid 1859.0; Max. 10.0; StDev 0.6079620023460367; Min. 0.0; Mean 0.22754168908015132

Variable Format: numeric

Notes: UNF:6:9z1LAsv7U2PtZx9rxNFV2A==

f3769796 Location:

Summary Statistics: Max. 1.0; Valid 1859.0; Min. 1.0; StDev 0.0; Mean 1.0;

Variable Format: numeric

Notes: UNF:6:RF9KJ08NWt3IopHL4LPOFg==

f3769796 Location:

Summary Statistics: Max. 39.842845916748; Valid 1859.0; Mean 6.361004855569938; StDev 12.772754246840014; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:9nN7m/BtkFb8XaubQf6DJA==

f3769796 Location:

Summary Statistics: Min. 0.0; Valid 1859.0; StDev 0.5047849772488886; Mean 1.761699838622915; Max. 2.0

Variable Format: numeric

Notes: UNF:6:mvBj5POpWPyhZxvs6xjglQ==

f3769796 Location:

Summary Statistics: Max. 3.0; Mean 1.4588488434642248; Min. 1.0; Valid 1859.0; StDev 0.531870157700979;

Variable Format: numeric

Notes: UNF:6:YZMNBX4AhyrLf7Z8nbLmgQ==

f3769796 Location:

Summary Statistics: Min. 0.0; Max. 1.0; StDev 0.23398736195025094; Valid 1859.0; Mean 0.05809575040344306

Variable Format: numeric

Notes: UNF:6:x/djfQFNt8lmPprvTnhNlA==

f3769796 Location:

Variable Format: character

Notes: UNF:6:plYF52PeuQuOsqGgjEp5qw==

f3769796 Location:

Summary Statistics: Max. 3.0; Mean 1.7588932806324111; StDev 0.8735361680997994; Min. 1.0; Valid 253.0

Variable Format: numeric

Notes: UNF:6:NABuVND1TPCz3xGFy0ar6g==

f3769796 Location:

Summary Statistics: StDev 116.47785094293798; Min. 1.0; Valid 1859.0; Max. 371.0; Mean 211.17697686928216;

Variable Format: numeric

Notes: UNF:6:BHtTeHgr7DzP9bBABXaKfg==

Label:

2_data_analysis.do

Text:

STATA code (do file)

application/x-stata-syntax

Label:

3_hrv_props_by_class.do

Text:

STATA code (do file)

application/x-stata-syntax

Label:

4_hrv_chart.do

Text:

STATA code for generating graphs

application/x-stata-syntax

Label:

MLuka_SPReD_School_HRV_codebook.pdf

Text:

Contains variable description and value labels

application/pdf

Label:

reinfection.csv

text/csv

Label:

SPReD_school_HRV.R

Text:

R script (R version 3.6.2)

type/x-r-syntax