espicc-somaliland-digaale-survey-2019-carriage
Data and code accompanying the preprint "Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland".
https://github.com/kevinvzandvoort/espicc-somaliland-digaale-survey-2019-carriage
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Data and code accompanying the preprint "Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland".
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README.md
Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland. Data and analyses.
This repository contains the data and code used for all analyses described in our manuscript:
Van Zandvoort K, Hassan AI, Bobe MO, Pell CL, Ahmed MS, Ortika BD, Ibrahim S, Abdi MI, Karim MA, Eggo RM, Ali SY, Hinds J, Soleman MS, Cummings R, McGowan C, Mulholland K, Hergeeye MA, Satzke C, Checchi F, Flasche S, Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland. Preprint available at https://doi.org/10.1101/2024.02.09.24302568.
This work is part of a larger study: Evaluating Strategies for Pneumococcal Immunization Campaigns in Crises (ESPICC).
This analysis is closely linked to our previous manuscript and analysis on Social contacts and other risk factors for respiratory infections among internally displaced people in Somaliland.
How to download
You can clone the repository or download the zip from this URL: https://github.com/kevinvzandvoort/espicc-somaliland-digaale-survey-2019-carriage/archive/refs/heads/main.zip.
Questionnaires
This survey was implemented using Open Data Kit. Android tablets were provided by LSHTM Open Data Kit https://opendatakit.lshtm.ac.uk.
- Questionnaires were programmed as multiple forms in xlsx, and can be found in the
./questionnaire/xlsxfolder in the espicc-somaliland-digaale-survey-2019 repository. - Only the additional swab related form has been added to this repository, as the
./questionnaire/xlsx/s5_swab.xlsxfile. - Th file was converted to an xls file to work on an ODK server, and used with ODK Collect during fieldwork. Unlike some of the other forms, no manual edits were made to this xls file.
Included data sets
Only a subset of the data collected using all survey forms has been used for this analysis.
Data has been anonymized, and links between individual household members have been removed.
The anonymized data can be used to replicate all analyses, figures, and tables in the manuscript.
All data is stored in the ./data folder. A data dictionary is provided in ./data/data_dictionary.xlsx
The following datasets are included:
participant_data.csv- Reported household- and individual-level risk-factors
- collected with the
s1_household,s2_contacts,s3_anthropometry, ands5_swabforms.
lab_data.csv- Results from microbiological analyses
- Nasopharyngeal swabs assessed using lytA qPCR and serotyped using microarray
serotypes_by_vaccine.csv- Serotypes included in different PCV products
other_data/*- Pneumococcal carriage prevalence by age from studies conducted in the Gambia, Kenya, Uganda, and Malawi
- Serotype-specific invasiveness estimates from Løchen et al (2022; https://doi.org/10.1371/journal.pcbi.1009389)
- Temperature data from our test (s0test) and pilot (s1pilot) shipment.
poststratification_data/*- Estimated population size of specific strata, from the main
espicc-somaliland-digaale-survey-2019repository
- Estimated population size of specific strata, from the main
Figures and tables
Code for the analysis can be found in the ./scripts folder.
The analysis can be replicated by running the index.R file (in R), which sources these scripts.
Figures and tables will be created in a newly formed ./output folder
Owner
- Login: kevinvzandvoort
- Kind: user
- Repositories: 2
- Profile: https://github.com/kevinvzandvoort
Citation (CITATION.cff)
# YAML 1.2
---
authors:
-
affiliation: "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom"
family-names: "van Zandvoort"
given-names: Kevin
orcid: "https://orcid.org/0000-0002-7770-0537"
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affiliation: "Republic of Somaliland Ministry of Health Development, Somaliland"
family-names: Hassan
given-names: "Abdirahman Ibrahim"
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affiliation: "Save the Children International, Somaliland"
family-names: Bobe
given-names: "Mohamed Omer"
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affiliation: "Murdoch Children's Research Institute, Australia"
family-names: Pell
given-names: "Casey L"
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affiliation: "Save the Children International, Somaliland"
family-names: Ahmed
given-names: "Mohamed Saed"
-
affiliation: "Murdoch Children's Research Institute, Australia"
family-names: Ortika
given-names: "Belinda D"
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affiliation: "Save the Children International, Somaliland"
family-names: Ibrahim
given-names: "Saed"
-
affiliation: "Save the Children International, Somaliland"
family-names: Abdi
given-names: "Mohamed Ismail"
-
affiliation: "Republic of Somaliland Ministry of Health Development, Somaliland"
family-names: Karim
given-names: "Mustapha A"
-
affiliation: "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom"
family-names: "Eggo"
given-names: "Rosalind M"
orcid: "https://orcid.org/0000-0002-0362-6717"
-
affiliation: "Republic of Somaliland Ministry of Health Development, Somaliland"
family-names: Ali
given-names: "Saleban Yusuf"
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affiliation: "Institute for Infection and Immunity, St. George’s, University of London, United Kingdom"
family-names: Hinds
given-names: "Jason"
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affiliation: "Republic of Somaliland Ministry of Health Development, Somaliland"
family-names: Soleman
given-names: "Saeed Mohamood"
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affiliation: "Save the Children, United Kingdom"
family-names: Cummings
given-names: "Rachael"
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affiliation: "Department of Public Health, Environments and Society, London School of Hygiene & Tropical Medicine, United Kingdom"
family-names: McGowan
given-names: "Catherine R"
orcid: "https://orcid.org/0000-0001-6941-6539"
-
affiliation: "Murdoch Children's Research Institute, Australia"
family-names: Mulholland
given-names: "E Kim"
orcid: "https://orcid.org/0000-0001-7947-680X"
-
affiliation: "Murdoch Children's Research Institute, Australia"
family-names: Satzke
given-names: "Catherine"
orcid: "https://orcid.org/0000-0003-3164-8849"
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affiliation: "Republic of Somaliland Ministry of Health Development, Somaliland"
family-names: Hergeeye
given-names: "Mohamed Abdi"
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affiliation: "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom"
family-names: "Checchi"
given-names: "Francesco"
orcid: "https://orcid.org/0000-0001-9030-5382"
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affiliation: "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom"
family-names: "Flasche"
given-names: "Stefan"
orcid: "https://orcid.org/0000-0002-5808-2606"
license: MIT
message: "If you use this data, please cite it using these metadata."
title: "Pre-vaccination carriage prevalence of Streptococcus pneumoniae serotypes among internally displaced people in Somaliland. Data and analyses."
version: "v1.0.0"
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