R Observatory: Metrics for PatientProfiles version 1.6.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PatientProfiles

1.6.1Package record

Identify Characteristics of Patients in the OMOP Common Data Model

12packages dependsuggested by 6

17.3Kdownloads / year

96.5%test coverage

13/13flavors OK

Overview

About

Maintained by Martí CatalàCRAN page ↗GitHub ↗Website ↗Issues ↗

Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.

Changes in 1.6.1

Fix na_matches = "na" performance by @catalamarti in #880

From NEWS.md in the release

Install

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

install.packages("PatientProfiles", 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("darwin-eu/PatientProfiles")

Development version from darwin-eu/PatientProfiles. 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-patientprofiles

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-PatientProfiles

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-PatientProfiles

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: 11.9 min · r-devel-linux-x86_64-debian-clang

Status changes

OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.1

READMEYes · 505 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.6.1Citation fileNoWebsiteYes · pkgdown

Help pages: 109 (53 internal)includes a package overview page
Examples that run: 0%52 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 93%
Documented parameters: 95%
Return-value docs: 96%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

17.3K

CRAN downloads in the past year

Rank #2,946 · ~47/day · ~1.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.8K30 days

4.6K90 days

17.3K1 year

Compare downloads with other packages →

Also on540 r2u5 autocran

How downloads are counted

Repository

darwin-eu/patientprofiles ↗Organization: darwin-eu

2Stars

3Forks

0Open issues

0Open PRs

12Releases

1,461Commits

14Commit identities

License file reads as Apache-2.0 · 1,461 commits · Last activity 2026-09-22

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 160
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-14 · 22026-07-07 · 2

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/darwin-eu/patientprofiles on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-09-22 · The repository has a site deploy workflow

pkgdown site last built 2026-09-22

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

34 external dependencies (excludes base and recommended)

Installing PatientProfiles adds 27 packages (14 with compiled code, 21 MB of source tarballs). Heaviest: stringi 11 MB, vctrs 1.0 MB, dplyr 902 KB.

Depends (1)

R >= 4.1.0

Imports (9)

cli clock dplyr lifecycle omopgenerics purrr rlang stringr tidyr

LinkingTo (0)

none

Suggests (25)

bit64 CDMConnector CodelistGenerator CohortConstructor covr DBI dbplyr DT duckdb ggplot2 glue gt here Hmisc knitr odbc omock patchwork rmarkdown RPostgres scales spelling testthat (>= 3.1.5)tictoc withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

12direct

2indirect

Imports 12

Suggested by 6

Show all 18 packagesHide all 18 packages

Depends, Imports or LinkingTo, most downloaded first

CodelistGenerator CohortConstructor CohortCharacteristics DrugUtilisation OmopSketch IncidencePrevalence CohortSurvival PhenotypeR MeasurementDiagnostics OmopConstructor OmopIndices CohortSymmetry

Suggests, most downloaded first

visOmopResults omock CohortContrast CohortCosts CohortUtilisation OmopViewer

How these are counted

Code & Tests

People & History

People (8)

Martí Català

Author, Maintainer · added in 1.4.2

Author

Author

Author

Author

Author

Contributor · added in 1.0.0

Xintong Li

Contributor

Maintainer since 0.1.0 (2023)

Listed in earlier versions (1)

Marti Catala

no longer listed · 0.1.0 to 1.4.1

Releases (30)

Pick two releases to compare their code metrics.

1.6.1Latest
record
2026-08-21 · current release · diff ↗
1.6.0
record
2026-07-25 · diff ↗ ·
added 4 exports
addCohortEventDate, addCohortEventDays, addConceptEventDate, addConceptEventDays
R
R 4.6.0 released · 2026-04-24
1.5.0
record
2026-02-24 · diff ↗ ·
added 3 exports
addBirthday, addBirthdayQuery, addCohortIntersectField
1.4.5
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2026-01-21 · diff ↗
1.4.4
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2025-10-29 · diff ↗
1.4.3
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2025-10-01 · diff ↗
1.4.2
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2025-07-09 · diff ↗
1.4.1
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2025-06-27 · diff ↗
1.4.0
record
2025-05-30 · diff ↗ ·
added 1 export
addConceptName
R
R 4.5.0 released · 2025-04-11
1.3.1
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2025-03-05 · diff ↗
1.3.0
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2025-02-26 · diff ↗ ·
added 4 exports
addConceptIntersectField, benchmarkPatientProfiles, filterCohortId, filterInObservation
1.2.3
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2024-12-12 · diff ↗
1.2.2
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2024-11-28 · diff ↗ ·
removed 1 export
%>%
1.2.1
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2024-10-25 · diff ↗

Show 18 earlier eventsHide 18 earlier events

1.2.0
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2024-09-12 · diff ↗ ·
added 2 exports
addObservationPeriodId, addObservationPeriodIdQuery
1.1.1
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2024-07-28 · diff ↗
1.1.0
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2024-06-11 · diff ↗ ·
added 7 exports
addAgeQuery, addDateOfBirthQuery, addDemographicsQuery, addFutureObservationQuery, addInObservationQuery, addPriorObservationQuery, addSexQuery
1.0.0
record
2024-05-16 · diff ↗ ·
removed 33 exports
addCohortIntersect, addConceptIntersect, addIntersect, addLargeScaleCharacteristics, addTableIntersect, assertNameStyle, availableFunctions, formatCharacteristics, gtCharacteristics, gtResult, optionsTableCharacteristics, optionsTableCohortOverlap, optionsTableCohortTiming, plotCharacteristics, plotCohortIntersect, plotCohortOverlap, plotCohortTiming, plotDemographics, plotLargeScaleCharacteristics, summariseCharacteristics, summariseCohortCounts, summariseCohortIntersect, summariseCohortOverlap, summariseCohortTiming, summariseConceptIntersect, summariseDemographics, summariseLargeScaleCharacteristics, tableCharacteristics, tableCohortIntersect, tableCohortOverlap and 3 more

added 1 export
mockDisconnect
R
R 4.4.0 released · 2024-04-24
0.8.0
record
2024-04-11 · diff ↗ ·
added 4 exports
addDeathDate, addDeathDays, addDeathFlag, summariseCohortCounts
0.7.0
record
2024-03-28 · diff ↗ ·
removed 2 exports
detectVariables, tidyCharacteristics

added 23 exports
assertNameStyle, availableEstimates, optionsTableCharacteristics, optionsTableCohortOverlap, optionsTableCohortTiming, plotCharacteristics, plotCohortIntersect, plotCohortOverlap, plotCohortTiming, plotDemographics, plotLargeScaleCharacteristics, settings, summariseCohortIntersect, summariseCohortOverlap, summariseCohortTiming, summariseConceptIntersect, summariseDemographics, tableCharacteristics, tableCohortIntersect, tableCohortOverlap, tableCohortTiming, tableDemographics, tableLargeScaleCharacteristics
0.6.2
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2024-03-05 · diff ↗
0.6.1
record
2024-02-22 · diff ↗ ·
added 1 export
suppress
0.6.0
record
2024-02-08 · diff ↗ ·
removed 6 exports
addAttributes, getConceptName, getEndName, getSourceConceptName, getStartName, suppressCounts

added 12 exports
addTableIntersect, addTableIntersectCount, addTableIntersectDate, addTableIntersectDays, addTableIntersectField, addTableIntersectFlag, endDateColumn, formatCharacteristics, sourceConceptIdColumn, standardConceptIdColumn, startDateColumn, tidyCharacteristics
0.5.1
record
2023-11-21 · diff ↗
0.5.0
record
2023-11-13 · diff ↗ ·
added 1 export
addLargeScaleCharacteristics
0.4.0
record
2023-10-06 · diff ↗ ·
added 10 exports
addConceptIntersect, addConceptIntersectCount, addConceptIntersectDate, addConceptIntersectDays, addConceptIntersectFlag, getSourceConceptName, gtCharacteristics, gtResult, summariseLargeScaleCharacteristics, suppressCounts
0.3.1
record
2023-08-25 · diff ↗
0.3.0
record
2023-07-18 · diff ↗ ·
removed 1 export
addPriorHistory

added 3 exports
addCdmName, addCohortName, addPriorObservation
0.2.0
record
2023-06-14 · diff ↗ ·
added 12 exports
addAttributes, addCategories, addDateOfBirth, addIntersect, availableFunctions, detectVariables, getConceptName, getEndName, getStartName, summariseCharacteristics, summariseResult, variableTypes
0.1.0
record
2023-05-02
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-05-02
Total releases: 30 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1.0
Download size: 951 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PatientProfiles")

Format

Català, M., Burn, E., Chen, X., Du, M., Guo, Y., Li, X., Lopez-Guell, K., & Mercade-Besora, N. (2026). PatientProfiles: Identify Characteristics of Patients in the OMOP Common Data Model (Version 1.6.1) [Computer software]. https://doi.org/10.32614/CRAN.package.PatientProfiles

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 PatientProfiles version 1.6.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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