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

Le résumé fourni par la source

• During the COVID-19 pandemic, we developed a modular pipeline of scripts to automate the production of epidemiological situation reports. • The pipeline was scripted using the open-source statistical software R. • The modular design of the pipeline enables the integration of novel data, while keeping independency in the scripts between the multiple data sources. • The intuitive design of the pipeline facilitates the collaboration of epidemiologists with various programming skills. • We share a template of our pipeline that can be easily customizable to automate other disease surveillance processes. During the COVID-19 pandemic, the National Institute for Public Health and the Environment in the Netherlands developed a pipeline of scripts to automate and streamline the production of epidemiological situation reports (epi‑sitrep). The pipeline was developed for the Automation of Data Import, Summarization, and Communication (hereafter called the A-DISC pipeline). This paper describes the A-DISC pipeline and provides a customizable scripts template that may be useful for other countries wanting to automate their infectious disease surveillance processes. The A-DISC pipeline was developed 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. 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, sent to stakeholders and submitted to European Centre for Disease Prevention and Control via the European Surveillance System -TESSy [ 38 ]. In the face of an unprecedented high number of cases being reported during the COVID-19 pandemic, the A-DISC pipeline was essential to produce frequent and comprehensive epi‑sitreps. A-DISC's modular and intuitive structure allowed for the integration of data sources of varying complexities, encouraged collaboration among people with various R-scripting capabilities, and improved data lineage. The A-DISC pipeline remains under active development and is currently being used in modified form for the automatization and professionalization of various other disease surveillance processes at the RIVM, with high acceptance from the participant epidemiologists. The A-DISC pipeline is an open-source, robust, and customizable tool for automating epi‑sitreps based on multiple data sources.

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