R Observatory: Metrics for PheNorm version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheNorm

0.1.0Package record

Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data

0packages depend

2.4Kdownloads / year

78.5%test coverage

13/13flavors OK

Overview

About

Maintained by Clara-Lea BonzelCRAN page ↗GitHub ↗Issues ↗

The algorithm combines the most predictive variable, such as count of the main International Classification of Diseases (ICD) codes, and other Electronic Health Record (EHR) features (e.g. health utilization and processed clinical note data), to obtain a score for accurate risk prediction and disease classification. In particular, it normalizes the surrogate to resemble gaussian mixture and leverages the remaining features through random corruption denoising. Background and details about the method can be found at Yu et al. (2018) doi:10.1093/jamia/ocx111.

Install

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

install.packages("PheNorm", 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("celehs/PheNorm")

Development version from celehs/PheNorm. 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-phenorm

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-PheNorm

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-PheNorm

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: 2.4 min · r-oldrel-windows-x86_64

Status changes

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

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 260 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNo

Help pages: 1
Examples that run: 0%1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

my-vignette HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #22,682 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

21730 days

58690 days

2.4K1 year

Compare downloads with other packages →

Also on67 r2u3 autocran

How downloads are counted

Repository

celehs/phenorm ↗Account: celehs

5Stars

1Forks

2Open issues

0Open PRs

0Releases

24Commits

3Commit identities

24 commits · Last activity 2021-02-23 · Default branch at 0.1.1, ahead of CRAN 0.1.0 (checked 2026-10-22)

Responsiveness

not measured

Issues over time

2026-07-14 · 12026-09-19 · 2

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/celehs/phenorm on 2026-10-22.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2021-02-23

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

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

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Clara-Lea Bonzel

Author, Maintainer since 0.1.0 (2021)

Author

Author

Author

Author

Author

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1.0Latest
record
2021-01-07 · current release
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-07
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Download size: 8.9 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PheNorm")

Format

Bonzel, C., Cai, T., Castro, V., Hong, C., Liu, M., PARSE LTD, , & Yu, S. (2021). PheNorm: Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PheNorm

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 PheNorm version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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