ampel-leipzig / sbcdata

Laboratory Diagnostics from Septic and Non-septic Patients Used in the AMPEL Project

sbcdata

Installation

You can install the released version of sbcdata from directly from github:

# install.packages("remotes")
remotes::install_github("ampel-leipzig/sbcdata")

About the data

The data were collected as part of the AMPEL project (Analysis and Reporting System for the Improvement of Patient Safety through Real-Time Integration of Laboratory Findings). They include administration data, sepsis labels based on ICD10 codes and laboratory diagnostics from patients admitted to the University Hospital Leipzig between Januar 2014 and December 2021 and to the University Hospital Greifswald between Januar 2015 and December 2020, respectively. Additionally it provides functions to generate a similar dataset from MIMIC-IV Johnson et al. 2021.

License

The datasets are available under the CC-BY license.

Citation

To cite the sbcdata package, please use:

Applying Machine Learning to Blood Count Data Predicts Sepsis with ICU Admission. D. Steinbach, P. C. Ahrens, M. Schmidt, M. Federbusch, L. Heuft, Ch. Lübbert, M. Nauck, M. Gründling, B. Isermann, S. Gibb, Th. Kaiser 2024. Clinical Chemistry. DOI: 10.1093/clinchem/hvae001.

sbcdata's Issues

Import CRP and PCT from MIMIC-IV

@Steinbach-D could you please look for the itemid of CRP and PCT in MIMIC-IV so we could add them here:
https://github.com/ampel-leipzig/ampelsepsisdata/blob/6f13eba054ad36ad1500414924e106066e7e99f7/R/import_mimic.R#L41-L50

Additionally we need to extend the renaming statement:
https://github.com/ampel-leipzig/ampelsepsisdata/blob/6f13eba054ad36ad1500414924e106066e7e99f7/R/import_mimic.R#L64-L67

(we have to remove the following lines afterwards):
https://github.com/ampel-leipzig/ampelsepsisdata/blob/6f13eba054ad36ad1500414924e106066e7e99f7/R/import_mimic.R#L68-L69