R Observatory: Metrics for PhenotypeR version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PhenotypeR

0.5.0

Assess Study Cohorts Using a Common Data Model

0packages depend

6.1Kdownloads / year

60.1%test coverage

13/13checks pass

Overview

About

Maintained by Edward BurnFirst published 2024-12-0615 releasesCRAN page ↗GitHub ↗

Phenotype study cohorts in data mapped to the Observational Medical Outcomes Partnership Common Data Model. Diagnostics are run at the database, code list, cohort, and population level to assess whether study cohorts are ready for research.

Install

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

install.packages("PhenotypeR", 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("OHDSI/PhenotypeR")

Development version from OHDSI/PhenotypeR. 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-phenotyper

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-PhenotypeR

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-PhenotypeR

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

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.38

60.1%

Coverage · measured lines

100%

Documentation · exports

16

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 449 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 95%
References docs: 0%

Downloads

6.1K

CRAN downloads in the past year

Rank #3,762 · ~17/day · ~509/mo

Releases R versions

Daily download trend is not available in this view yet.

62930 days

2.5K90 days

6.1K1 year

Compare downloads with other packages →

Also on205 r2u15 autocran

Repository

GitHub ↗ ohdsi/phenotyper

7Stars

1Forks

58Open issues

2Open PRs

14Releases

1,146Commits

7Contributors

License Apache-2.0 · 1,146 commits · Last activity 2026-08-02

Issues over time

2026-07-14 · 572026-07-23 · 58

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ohdsi/phenotyper on 2026-08-09.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

59 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (16)

cli clock CodelistGenerator CohortCharacteristics CohortConstructor dplyr DrugUtilisation IncidencePrevalence (>= 1.2.0)MeasurementDiagnostics omopgenerics (>= 1.2.0)OmopSketch PatientProfiles purrr readr rlang vctrs

LinkingTo (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Edward Burn

Author, Maintainer

Authors (6)

Edward Burn

Author, Maintainer

Marta Alcalde-Herraiz

Author

Martí Català

Author · added in 0.3.2

Xihang Chen

Author

Nuria Mercade-Besora

Author · added in 0.2.0

Albert Prats-Uribe

Author

Listed in earlier versions (1)

Marti Catala

no longer listed · 0.1.0 to 0.3.1

Package Timeline

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

0.5.0Latest
2026-05-27 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.4.0
2026-04-17 · diff ↗
0.3.4
2026-03-25 · diff ↗
0.3.3
2026-02-23 · diff ↗
0.3.2
2026-02-08 · diff ↗
0.3.1
2026-01-28 · diff ↗
0.3.0
2026-01-12 · diff ↗
0.2.0
2025-07-31 · diff ↗
0.1.6
2025-06-22 · diff ↗
0.1.5
2025-05-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.4
2025-03-28 · diff ↗
0.1.3
2025-02-17 · diff ↗
0.1.2
2025-02-05 · diff ↗
0.1.1
2025-01-17 · diff ↗

Show 2 earlier events

0.1.0
2024-12-06
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-12-06
Total releases: 15 / 2 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1.0
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PhenotypeR")

Format

Burn, E., Alcalde-Herraiz, M., Català, M., Chen, X., Mercade-Besora, N., & Prats-Uribe, A. (2026). PhenotypeR: Assess Study Cohorts Using a Common Data Model (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PhenotypeR

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 PhenotypeR version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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