Work

Automating COVID-19 epidemiological situation reports based on multiple data sources, the Netherlands, 2020 to 2023

Year: 2024

Type: article

Abstract: Background: During the COVID-19 pandemic, the National Institute for Public Health and the Environment in the Netherlands designed a pipeline of scripts to automate and streamline the production of epidemiological situation reports (epi-sitrep). The pipeline was applied for the Automation of Data Import, Summarization and Communication (A-DISC).ObjectiveThis paper elucidates the A-DISC pipeline and provides a customizable scripts template that may be useful for other countries willing to automate their infectious disease surveillance processes.Methods:The A-DISC was scripted using the open-source statistical software R. It is organized in four modules: Prepare, Process data, Produce report and Communicate. The Prepare scripts set the working environment (e.g. load packages). The (data-specific) Process data scripts import, validate, verify, transform, save, analyze and summarize data as tables and figures and store these data summaries. The Produce report scripts gather summaries from multiple data sources and integrate them into a RMarkdown document – the epi-sitrep. The Communicate scripts send e-mails to stakeholders with the epi-sitrep.Results:As of March 2023, up to ten data sources were automatically summarized into tables and figures by A-DISC. These data summaries were featured in routine extensive COVID-19 epi-sitreps, shared as open data, plotted on RIVM’s website and submitted to TESSy. Discussion:In the face of an unprecedented high number of cases being reported, as during the COVID-19 pandemic, the A-DISC was essential to produce frequent and comprehensive epi-sitreps. A-DISC’s modular and intuitive structure allowed the integration of data sources of varying complexities, encouraged collaboration among people with various R-scripting capabilities and improved data governance.ConclusionThe A-DISC pipeline is an open-source, robust and customizable tool for automating epi-sitreps based on multiple data sources.

Source: Computer Methods and Programs in Biomedicine

DOI: 10.1016/j.cmpb.2024.108436