phoenix: an R package and Python module for calculating the Phoenix pediatric sepsis score and criteria
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Published on: September 16, 2022
Peter E DeWitt1, Seth Russell1, Margaret N Rebull1
1Department of Biomedical Informatics, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
Insights
New R package and Python module help researchers consistently apply the Phoenix criteria for pediatric sepsis and septic shock using electronic health records (EHRs). These tools ensure accurate data analysis for improved clinical care and research.
Area of Science:
- Pediatric critical care medicine
- Clinical informatics
- Biostatistics
Background:
- The Phoenix criteria represent a significant advancement in defining pediatric sepsis and septic shock.
- Consistent application of these criteria is crucial for robust research and clinical practice.
- Electronic health records (EHRs) are vital data sources for sepsis research.
Purpose of the Study:
- To develop user-friendly tools for applying the Phoenix criteria to EHR data.
- To facilitate consistent and accurate analysis of pediatric sepsis data.
- To support a unified body of research across different institutions.
Main Methods:
- Development of the "phoenix" R package.
- Development of a "phoenix" Python module.
- Functions designed for intuitive application to EHR datasets.
Main Results:
- The R package and Python module enable derivation of key indicators, total scores, and sub-scores from EHR data.
- These tools ensure consistent and accurate implementation of the Phoenix criteria.
- The software is readily available for research use.
Conclusions:
- The "phoenix" R package and Python module are essential for researchers utilizing the Phoenix criteria.
- These tools promote standardized data analysis, enhancing the reliability of pediatric sepsis research.
- The availability of these free tools supports improved clinical care and research globally.
Objectives:
The publication of the Phoenix criteria for pediatric sepsis and septic shock initiates a new era in clinical care and research of pediatric sepsis. Tools to consistently and accurately apply the Phoenix criteria to electronic health records (EHRs) is one part of building a robust and internally consistent body of research across multiple research groups and datasets.
Materials And Methods:
We developed the phoenix R package and Python module to provide researchers with intuitive and simple functions to apply the Phoenix criteria to EHR data.
Results:
The phoenix R package and Python module enable researchers to apply the Phoenix criteria to EHR datasets and derive the relevant indicators, total scores, and sub-scores.
Discussion:
The transition to the Phoenix criteria marks a major change in the conceptual definition of pediatric sepsis. Applicable across differentially resourced settings, the Phoenix criteria should help improve clinical care and research.
Conclusion:
The phoenix R package and Python model are freely available on CRAN, PyPi, and GitHub. These tools enable the consistent and accurate application of the Phoenix criteria to EHR datasets.
