R Observatory: Metrics for PhenotypeR version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PhenotypeR

0.5.0Package record

Assess Study Cohorts Using a Common Data Model

0packages dependsuggested by 1

7.3Kdownloads / year

60.1%test coverage

13/13flavors OK

Overview

About

Maintained by Edward BurnCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 1.8 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 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 449 wordsVignettesYes · 4 · evaluation depends on the environmentNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 30 (12 internal)includes a package overview page
Examples that run: 0%11 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 58%
Documented parameters: 99%
Return-value docs: 95%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

7.3K

CRAN downloads in the past year

Rank #4,050 · ~20/day · ~607/mo

Releases R versions

Daily download trend is not available in this view yet.

75430 days

2.2K90 days

7.3K1 year

Compare downloads with other packages →

Also on142 r2u13 autocran

How downloads are counted

Repository

ohdsi/phenotyper ↗Organization: OHDSI

10Stars

1Forks

61Open issues

3Open PRs

14Releases

1,150Commits

7Commit identities

License file reads as Apache-2.0 · 1,150 commits · Last activity 2026-10-16 · +11.1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 21
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-14 · 72026-10-19 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/ohdsi/phenotyper on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-02 · The repository has a site deploy workflow

pkgdown site last built 2026-08-02

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

59 external dependencies (excludes base and recommended)

Installing PhenotypeR adds 53 packages (25 with compiled code, 44 MB of source tarballs). Heaviest: stringi 11 MB, CDMConnector 4.0 MB, CodelistGenerator 3.1 MB.

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

Suggested by 1

Suggests, most downloaded first

OmopIndices

How these are counted

Code & Tests

People & History

People (6)

Edward Burn

Author, Maintainer since 0.1.0 (2024)

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

Releases (15)

Pick two releases to compare their code metrics.

0.5.0Latest
record
2026-05-27 · current release · diff ↗ ·
removed 1 export
getClinicalDescription

added 7 exports
clinicalDescriptionSpecification, dataSourceDescriptionSpecification, draftClinicalDescription, importClinicalDescription, importDatabaseDescription, shinyClinicalDescriptions, shinyDataSourceDescriptions
R
R 4.6.0 released · 2026-04-24
0.4.0
record
2026-04-16 · diff ↗ ·
added 3 exports
downloadClinicalDescriptionTemplate, downloadDatabaseDescriptionTemplate, getClinicalDescription
0.3.4
record
2026-03-25 · diff ↗
0.3.3
record
2026-02-23 · diff ↗
0.3.2
record
2026-02-08 · diff ↗ ·
removed 1 export
%>%
0.3.1
record
2026-01-28 · diff ↗
0.3.0
record
2026-01-12 · diff ↗ ·
removed 1 export
mockPhenotypeR
0.2.0
record
2025-07-31 · diff ↗ ·
added 2 exports
getCohortExpectations, tableCohortExpectations
0.1.6
record
2025-06-22 · diff ↗ ·
removed 1 export
matchedDiagnostics
0.1.5
record
2025-05-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.4
record
2025-03-28 · diff ↗
0.1.3
record
2025-02-17 · diff ↗
0.1.2
record
2025-02-05 · diff ↗
0.1.1
record
2025-01-17 · diff ↗ ·
added 1 export
mockPhenotypeR

Show 2 earlier eventsHide 2 earlier events

0.1.0
record
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: 1.9 MB

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 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 PhenotypeR version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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