PheNorm

0.1.0

Unsupervised Gold-Standard Label Free Phenotyping Algorithm for EHR Data

0packages depend

2.6Kdownloads / year

78.5%test coverage

13/13checks pass

Overview

About

Maintained by Clara-Lea BonzelFirst published 2021-01-071 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 2.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.14

78.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 260 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #21,648 · ~7/day · ~219/mo

Releases R versions

Daily download trend is not available in this view yet.

16230 days

52290 days

2.6K1 year

Compare downloads with other packages →

Also on95 r2u

Repository

GitHub ↗ celehs/phenorm

5Stars

1Forks

1Open issues

0Open PRs

0Releases

24Commits

3Contributors

24 commits · Last activity 2021-02-23

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/celehs/phenorm on 2026-07-30.

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (7)

Maintainer (1)

Clara-Lea Bonzel

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author

Author

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-01-07
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Download size: 8.9 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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