phoenix: Phoenix Sepsis and Phoenix-8 Sepsis Criteria

Implementation of the Phoenix and Phoenix-8 Sepsis Criteria as described in:

“Development and Validation of the Phoenix Criteria for Pediatric Sepsis and Septic Shock” by Sanchez-Pinto*, Bennett*, DeWitt**, Russell** et al. (2024)
- * Drs Sanchez-Pinto and Bennett contributed equally; ** Dr DeWitt and Mr Russell contributed equally.
“International Consensus Criteria for Pediatric Sepsis and Septic Shock” by Schlapbach, Watson, Sorce, et al. (2024).

The best overview for this package is the R vignette which you can view locally after installing the R package via

vignette("phoenix")

or you can read it online here

The Phoenix Criteria have been implemented in

an R package,
a Python module, and
example SQL queries.

The repository has been built with R as the primary and default language.

Citation

If you use this package in your work, please cite the Phoenix criteria by citing the two JAMA papers. Please cite this code base by citing the application note, and if using the R package, cite it explicitly as well.

Peter E DeWitt, Seth Russell, Margaret N Rebull, L Nelson Sanchez-Pinto, Tellen
D Bennett, phoenix: an R package and Python module for calculating the Phoenix
pediatric sepsis score and criteria, JAMIA Open, Volume 7, Issue 3, October
2024, ooae066, [doi:10.1093/jamiaopen/ooae066](doi:10.1093/jamiaopen/ooae066)

Bibtex formatted citations can be retrieved within R via

# Manuscripts
print(citation("phoenix"), bibtex = TRUE)

# R package
print(citation("phoenix", auto = TRUE), bibtex = TRUE)

Or in this repo from the file inst/CITATION

R

Install

From CRAN

Install the current release from the Comprehensive R Archive Network (CRAN). Within R call:

install.packages("phoenix", repos = "https://cran.rstudio.com")

Developmental

Install the development version of phoenix directly from github via the remotes package:

if (!("remotes" %in% rownames(installed.packages()))) {
  warning("installing remotes from https://cran.rstudio.com")
  install.packages("remotes", repo = "https://cran.rstudio.com")
}

remotes::install_github("cu-dbmi-peds/phoenix")

NOTE: If you are working on a Windows machine you will need to download and install Rtools.

Examples

Details on the Phoenix criteria and the use of the R package can be found in the manual for the package, the Get started on the website, or the vignette within R

vignette("phoenix")

Python

A python module is available on PyPi. You can install it via pip

pip install phoenix-sepsis

Examples

Read the article The Phoenix Septic Criteria in Python for details and examples of using the python code as is.

SQL

Read The Phoenix Sepsis Criteria in SQL article for details and examples of implementing the scoring rubrics in SQL. These examples are done in SQLite but will be easily translated into other SQL dialects.