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)
-
"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 has been implemented as an
- R package
- python module
- SQL queries
The repository has been built with R as the primary and default language.
This package is not yet on CRAN - it will be soon!
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.
The package comes with an example data set call sepsis. To get the Phoenix
score and determine sepsis (score ≥ 2) and septic shock (score ≥ 2 and
cardiovascular dysfunction, just call the phoenix function:
library(phoenix)
phoenix_scores <-
phoenix(
# respiratory
pf_ratio = pao2 / fio2,
sf_ratio = ifelse(spo2 <= 97, spo2 / fio2, NA_real_),
imv = vent,
other_respiratory_support = as.integer(fio2 > 0.21),
# cardiovascular
vasoactives = dobutamine + dopamine + epinephrine +
milrinone + norepinephrine + vasopressin,
lactate = lactate,
age = age,
map = dbp + (sbp - dbp)/3,
# coagulation
platelets = platelets,
inr = inr,
d_dimer = d_dimer,
fibrinogen = fibrinogen,
# neurologic
gcs = gcs_total,
fixed_pupils = as.integer(pupil == "both-fixed"),
data = sepsis
)
str(phoenix_scores)
#> 'data.frame': 20 obs. of 7 variables:
#> $ phoenix_respiratory_score : int 0 3 3 0 0 3 3 0 3 3 ...
#> $ phoenix_cardiovascular_score: int 2 2 1 0 0 1 4 0 3 0 ...
#> $ phoenix_coagulation_score : int 1 1 2 1 0 2 2 1 1 0 ...
#> $ phoenix_neurologic_score : int 0 1 0 0 0 1 0 0 1 1 ...
#> $ phoenix_sepsis_score : int 3 7 6 1 0 7 9 1 8 4 ...
#> $ phoenix_sepsis : int 1 1 1 0 0 1 1 0 1 1 ...
#> $ phoenix_septic_shock : int 1 1 1 0 0 1 1 0 1 0 ...
# 'data.frame': 20 obs. of 7 variables:
# $ phoenix_respiratory_score : int 0 3 3 0 0 3 3 0 3 3 ...
# $ phoenix_cardiovascular_score: int 2 2 1 0 0 1 4 0 3 0 ...
# $ phoenix_coagulation_score : int 1 1 2 1 0 2 2 1 1 0 ...
# $ phoenix_neurologic_score : int 0 1 0 0 0 1 0 0 1 1 ...
# $ phoenix_sepsis_score : int 3 7 6 1 0 7 9 1 8 4 ...
# $ phoenix_sepsis : int 1 1 1 0 0 1 1 0 1 1 ...
# $ phoenix_septic_shock : int 1 1 1 0 0 1 1 0 1 0 ...The subdirectory python provided a module and example use. It is our goal to
make this python code more robust and distribute it via PyPI soon.
You can read the article The Phoenix Septic Criteria in python for details and examples of using the python code as is.
import numpy as np
import pandas as pd
import python.phoenix as phx
sepsis = pd.read_csv("./python/sepsis.csv")
phx.phoenix(
pf_ratio = sepsis["pao2"] / sepsis["fio2"],
sf_ratio = sepsis["spo2"] / sepsis["fio2"],
imv = sepsis["vent"],
other_respiratory_support = (sepsis["fio2"] > 0.21).astype(int).to_numpy(),
vasoactives = sepsis["dobutamine"] + sepsis["dopamine"] + sepsis["epinephrine"] + sepsis["milrinone"] + sepsis["norepinephrine"] + sepsis["vasopressin"],
lactate = sepsis["lactate"],
age = sepsis["age"],
map = sepsis["dbp"] + (sepsis["sbp"] - sepsis["dbp"]) / 3,
platelets = sepsis['platelets'],
inr = sepsis['inr'],
d_dimer = sepsis['d_dimer'],
fibrinogen = sepsis['fibrinogen'],
gcs = sepsis["gcs_total"],
fixed_pupils = (sepsis["pupil"] == "both-fixed").astype(int),
)
#> phoenix_respiratory_score phoenix_cardiovascular_score phoenix_coagulation_score phoenix_neurologic_score phoenix_sepsis_score phoenix_sepsis phoenix_septic_shock
#> 0 3 2 1 0 6 1 1
#> 1 3 2 1 1 7 1 1
#> 2 3 1 2 0 6 1 1
#> 3 0 0 1 0 1 0 0
#> 4 0 0 0 0 0 0 0
#> 5 3 1 2 1 7 1 1
#> 6 3 4 2 0 9 1 1
#> 7 0 0 1 0 1 0 0
#> 8 3 3 1 1 8 1 1
#> 9 3 0 0 1 4 1 0
#> 10 3 3 1 2 9 1 1
#> 11 1 0 0 0 1 0 0
#> 12 0 0 0 0 0 0 0
#> 13 2 2 1 0 5 1 1
#> 14 3 3 2 0 8 1 1
#> 15 0 2 1 0 3 1 1
#> 16 2 2 1 0 5 1 1
#> 17 3 2 2 0 7 1 1
#> 18 2 2 0 0 4 1 1
#> 19 0 1 1 0 2 1 1Read 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.