R Observatory: Metrics for phoenix version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phoenix

1.1.3Package record

The Phoenix Pediatric Sepsis and Septic Shock Criteria

0packages depend

2.5Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Peter DeWittCRAN page ↗GitHub ↗Website ↗Issues ↗

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) doi:10.1001/jama.2024.0196 (Drs. Sanchez-Pinto and Bennett contributed equally to this manuscript; Dr. DeWitt and Mr. Russell contributed equally to the manuscript), "International Consensus Criteria for Pediatric Sepsis and Septic Shock" by Schlapbach, Watson, Sorce, Argent, et al. (2024) doi:10.1001/jama.2024.0179 (Drs Schlapbach, Watson, Sorce, and Argent contributed equally) and the application note "phoenix: an R package and Python module for calculating the Phoenix pediatric sepsis score and criteria" by DeWitt, Russell, Rebull, Sanchez-Pinto, and Bennett (2024) doi:10.1093/jamiaopen/ooae066.

Changes in 1.1.3

Spelling and grammar fixes in the documentation for the R, python, and sql.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phoenix", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("CU-DBMI-Peds/phoenix")

Development version from CU-DBMI-Peds/phoenix. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phoenix

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phoenix

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phoenix

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMEYes · 498 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.3Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 13 (1 internal)includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 85%

Vignettes (1)

The Phoenix Sepsis Criteria

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #20,809 · ~7/day · ~211/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

64290 days

2.5K1 year

Compare downloads with other packages →

Also on81 r2u3 autocran

How downloads are counted

Repository

cu-dbmi-peds/phoenix ↗Organization: CU-DBMI-Peds

6Stars

3Forks

2Open issues

0Open PRs

0Releases

277Commits

3Commit identities

pediatricphoenixsepsisseptic-shockpythonrsql

277 commits · Last activity 2026-09-01 · Default branch at 1.1.3.9000, ahead of CRAN 1.1.3 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 10
Median days to close, 50 most recently updated closed PRs: 1

Issues over time

2026-07-14 · 42026-07-21 · 2

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/cu-dbmi-peds/phoenix on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-01 · The repository has a site deploy workflow

pkgdown site last built 2026-09-01

Coverage (1)

Coverage reporting

Reproducibility and dev environment (2)

data-raw/Makefile

Show all practicesHide 1 practice

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing phoenix adds no packages beyond those that come with R.

Depends (1)

R >= 3.5.0

Imports (0)

none

LinkingTo (0)

none

Suggests (5)

knitr ggplot2 qwraps2 reticulate rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Peter DeWitt

Author, Maintainer since 1.0.0 (2024)

Tell Bennett

Contributor

Meg Rebull

Contributor

Seth Russell

Contributor

L. Nelson Sanchez-Pinto

Contributor

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
record
2025-10-22 · current release · diff ↗
1.1.2
record
2025-05-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.1
record
2024-07-08 · diff ↗
1.1.0
record
2024-05-03 · diff ↗ ·
added 1 export
map
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2024-03-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-03-12
Total releases: 5 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.4 KB / 1 file
Download size: 228 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("phoenix")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1001/jama.2024.0196, 10.1001/jama.2024.0179, 10.1093/jamiaopen/ooae066.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phoenix version 1.1.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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