This repository contains files for implementing the Sepsis-3 definition in the freely-accessible Amsterdam University Medical Centers Database. The folder sepsis3_gigabyte contains code accompanying our manuscript published in the journal Gigabyte. The folder sepsis3_epidemiology contains complementary code for a forthcoming manuscript describing sepsis epidemiology in AmsterdamUMCdb.
You must first have access to AmsterdamUMCdb, including the data. Further instructions for this can be found on the Amsterdam Medical Data Science website or AmsterdamUMCdb GitHub. To run code in this repository, refer to the README file in either of the folders sepsis3_gigabyte or sepsis3_epidemiology.
The database is primarily in Dutch. It is generally easier to work with itemids rather than the (Dutch) item names, in any table. The database contains a lookup dictionary of all terms, instructions for installing the amsterdamumcdb package that contains this is given here. It may be worth familiarising yourself with some common terms (e.g. Neurochirurgie = Neurosurgery, Vaatchirurgie = Vascular Surgery) ahead of time.
We encourage other researchers (or anyone interested in this code from a data or clinical perspective) to submit an issue on this repository if they would like to report or fix any bugs or to contribute improvements.