Automating the Dutch National Flu Surveillance for Pandemic Preparedness
summary
Automates the Dutch national influenza surveillance by replacing a weekly two‑hour manual Control+Enter job with a reproducible, modular pipeline built in R that mirrors a R targets-style DAG. Adds logging, version control, import/export adapters, and an internal R package Run_pipeline that executes steps, collects metadata and supports optional static checks and visualization. Deployed as a working MVP for influenza and expanded into 20 parallel pipelines; metadata storage is the next extension.
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chapters (9)
- 0:00Pandemic risks and automation
- 2:39COVID-19 to influenza surveillance
- 4:26Manual data processing problems
- 5:30Minimum viable disease tracking pipeline
- 8:44Modular pipeline design
- 10:12Scalable surveillance automation
- 11:38Pipeline with metadata and checks
- 13:01Current status and future plans
- 14:07Q&A
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