BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Local outputs and comparative analysis
Creators: name: Meurisse, Marjan
name: Estupiñán-Romero, Francisco
name: Van Goethem, Nina
name: Perola, Markus
name: Paajanen, Teemu
name: González-Galindo, Javier
name: Bernal-Delgado, Enrique
Publisher: name: Zenodo
Year: 2024
Subjects: COVID-19
Comparative effectiveness
International comparison
Causal inference
SARS-CoV-2

description: This publication corresponds to the local outputs and comparative analysis of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “SARS-CoV-2 Vaccine effectiveness in preventing SARS-CoV-2 infection.”

Research question: "How effective have the SARS-CoV-2 vaccination programmes been in preventing SARS-CoV-2 infections?”

Study design: An observational retrospective longitudinal (cohort) study using routinely collected population, health and care data from several countries/regions in Europe. We have designed the observational study to emulate a hypothetical Target Trial (TT) of the causal effect of SARS-CoV-2 vaccination programs in preventing SARS-CoV-2 infections.

A federated analysis approach was adopted, with the secured distributed deployment of the interoperable analytical pipeline by different Participant Nodes (i.e., institutions hosting or having access to the required individual-level data). A detailed description of the data processing procedures and the security measures within the Secured Processing Environments (SPE) of each of the Participant Nodes is provided in the published Data Management Plan (DMP). For more details on the methodological approach, see here. 

The local outputs correspond with the interactive reports of each main step of the analytical pipeline described in 'Methods analytical pipeline' and an Excel file used as input for the comparative analysis. They have been produced using real-world data from public health and the national health system in Aragon (Spain), Brussels and Wallonia (Belgium), and Finland. 

The scripts implementing the statistical analyses in the analytical pipeline are available on GitHub, with additional documentation supporting the development and implementation of the baseline use case. 

Files included in this publication: 



Local outputs produced by each Participant Node: 6 interactive HTML reports (Human-readable, interactive report) + 1 XLSX file (Human-readable, Excel)



Aragon v.1.0.0

Brussels-Wallonia v.1.0.0

Finland v.1.0.0 



Comparative analysis: 



SARS-CoV-2 vaccine effectiveness comparative analysis results v.1.0.0 - Interactive report (HTML file)

SARS-CoV-2 vaccine effectiveness comparative analysis execution script v.1.0.0 - Quarto RMarkdown script to execute the comparative analysis and produce the interactive report (QMD file)



Reproducible environment using renv:



renv/library - Library to contain packages used by the project

renv.lock - Lockfile

.Rprofile - Project R profile



RO-Crate



ro-crate-metadata.json - RO-Crate Metadata Document (Machine-readable JSON file)

ro-crate-preview.html - HTML preview (Human-readible HTML file)




Version 1.0.1 changelog



Reproducible environment created, R project converted to use renv


Version 1.0.2 changelog



Reproducible environment adjusted

Folder turned into an RO-Crate (addition RO-Crate Metadata and HTML preview)
description: The contents of this document are the sole responsibility of their authors. All rights reserved. Copying and distribution by any means is permitted provided that the authors are acknowledged, that no commercial use is made of the works and that no modifications are made (CC-BY INT 4.0.).