R Observatory: Metrics for PheValuator version 2.2.18

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PheValuator

2.2.18Package record

Rapid Phenotype Evaluation

0packages depend

–downloads / year

0.0%test coverage

7/7flavors OK

Overview

About

Maintained by William J. O'BrienCRAN page ↗GitHub ↗Website ↗Issues ↗

Evaluates phenotype algorithms by developing a diagnostic prediction model using a set of noisy positives and noisy negatives. It can then apply the model to a large cohort to create a set of subjects each with a predicted probability for the health outcome of interest. This cohort can then be used to evaluate phenotype algorithms through the calculation of the necessary performance characteristics - sensitivity, specificity, and positive and negative predictive value. Based on work by Swerdel (2022) doi:10.1016/j.jbi.2022.104177 and Swerdel (2019) doi:10.1016/j.jbi.2019.103258.

Changes in 2.2.18

Changes:

1. CRAN submission

From NEWS.md in the release

Install

R (CRAN)pak (dev)Fedora (COPR)

install.packages("PheValuator", 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/PheValuator")

Development version from OHDSI/PheValuator. Installs pak first if it is not already available.

# 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-PheValuator

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

7OK

CRAN check page ↗

Slowest check: 3.2 min · r-release-macos-x86_64

Status changes

OK7 OK2026-10-25

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.18

READMEYes · 849 wordsVignettesYes · 1 · dynamicNEWSYes · 0% structured · mentions 2.2.18Citation fileNoWebsiteYes

Help pages: 12 (1 internal)includes a package overview page
Examples that run: 45%5 run in a plain check · 5 never run · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Evaluating Phenotype Algorithms

How these are measured

Downloads

PheValuator Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

How downloads are counted

Repository

ohdsi/phevaluator ↗Organization: OHDSI

22Stars

6Forks

12Open issues

3Open PRs

26Releases

420Commits

5Commit identities

420 commits · Last activity 2026-06-03

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

Repository github.com/ohdsi/phevaluator is linked, but repository-practices checks have not run for it yet.

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing PheValuator adds 61 packages (35 with compiled code, 49 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 7.9 MB, RSQLite 4.2 MB.

Depends (1)

R >= 4.1.1

Imports (8)

DatabaseConnector PatientLevelPrediction FeatureExtraction SqlRender dplyr (>= 0.7.8)methodsParallelLogger tibble

LinkingTo (0)

none

Suggests (11)

knitr rmarkdown shiny shinydashboard DT htmltools qpdf testthat Eunomia withr CohortGenerator

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

William J. O'Brien

Author, Maintainer since 2.2.18 (2026)

Martijn Schuemie

Author

Joel Swerdel

Author

Releases (1)

Submitted 2.2.19, in newbies since 2026-10-22 21:24 UTC, as of the 2026-10-25 16:57 UTC queue snapshot. See the queue →

2.2.18Latest
record
2026-10-24 · current release ·
12 days in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-12 18:25 to 2026-10-24 06:43 UTC, in 66 readings. It was also listed earlier, first on 2026-10-03 21:57 UTC, and left the queue for more than a day before this stay.
R
R 4.6.0 released · 2026-04-24

Across CRAN, the median accepted release of the past year spent 26 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-10-24
Total releases: 1 / 1 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 4.1.1
Download size: 398 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PheValuator")

Format

O'Brien, W. J., Schuemie, M., & Swerdel, J. (2026). PheValuator: Rapid Phenotype Evaluation (Version 2.2.18) [Computer software]. https://doi.org/10.32614/CRAN.package.PheValuator

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 PheValuator version 2.2.18 [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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