R Observatory: Metrics for phers version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phers

1.0.5

Calculate Phenotype Risk Scores

0packages depend

2.7Kdownloads / year

82.9%test coverage

13/13checks pass

Overview

About

Maintained by Jake HugheyFirst published 2022-05-105 releasesCRAN page ↗GitHub ↗

Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 doi:10.1126/science.aal4043.

Install

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

install.packages("phers", 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("hugheylab/phers")

Development version from hugheylab/phers. 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-phers

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-phers

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-phers

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.32

82.9%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.7K

CRAN downloads in the past year

Rank #16,087 · ~7/day · ~222/mo

Releases R versions

Daily download trend is not available in this view yet.

16630 days

67690 days

2.7K1 year

Compare downloads with other packages →

Also on123 r2u25 autocran

Repository

GitHub ↗ hugheylab/phers

0Stars

0Forks

1Open issues

0Open PRs

0Releases

Last activity 2026-03-03

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/hugheylab/phers on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (6)

BEDMatrix checkmate data.table (>= 1.5.0)foreach iterators survival (>= 3.3.1)

LinkingTo (0)

none

Suggests (4)

doParallel knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Jake Hughey

Author, Maintainer

Authors (2)

Jake Hughey

Author, Maintainer

Layla Aref

Author

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.5Latest
2026-03-03 · current release · diff ↗
unarchivedReturned to CRAN
2026-03-03
archivedRemoved from CRAN
2026-01-31
issues were not corrected in time
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
1.0.2
2023-03-26 · diff ↗
1.0.0
2022-12-15 · diff ↗
0.0.3
2022-06-01 · diff ↗
0.0.2
2022-05-10
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-10
Total releases: 5 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5
Bundled data: 1.5 MB / 7 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phers")

Format

Hughey, J., & Aref, L. (2026). phers: Calculate Phenotype Risk Scores (Version 1.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.phers

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 phers version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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