R Observatory: Metrics for CodelistGenerator version 4.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CodelistGenerator

4.1.0Package record

Identify Relevant Clinical Codes and Evaluate Their Use

4packages dependsuggested by 7

15.3Kdownloads / year

86.8%test coverage

13/13flavors OK

Overview

About

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

Generate a candidate code list for the Observational Medical Outcomes Partnership (OMOP) common data model based on string matching. For a given search strategy, a candidate code list will be returned.

Install

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

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

Development version from darwin-eu/CodelistGenerator. 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-codelistgenerator

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-CodelistGenerator

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-CodelistGenerator

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: 24.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK11 OK, 2 FAILURE2026-08-05
NOTE10 OK, 1 NOTE, 2 FAILURE2026-08-03
ERROR9 OK, 1 NOTE, 1 ERROR, 2 FAILURE2026-08-02

Show 10 earlier changesHide 10 earlier changes

NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
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
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.1.0

READMEYes · 242 wordsVignettesYes · 9 · evaluation depends on the environmentNEWSYes · 100% structured · does not mention 4.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 99 (36 internal)includes a package overview page
Examples that run: 0%54 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run
Exported functions with examples: 92%
Documented parameters: 98%
Return-value docs: 98%
Help pages citing references: 0%

Vignettes (9)

a01_GettingOmopCdmVocabularies HTML
a02_ExploreCDMvocabulary HTML
a03_TypesOfCodelist HTML
a04_GenerateCandidateCodelist HTML
a05_GenerateVocabularyBasedCodelist HTML
a06_ImportExport HTML
a08_ManipulateCodelists HTML
a09_RunCodelistDiagnostics HTML
a10_CodelistGeneratorBenchmark HTML

How these are measured

Downloads

15.3K

CRAN downloads in the past year

Rank #3,056 · ~42/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

2K30 days

4.2K90 days

15.3K1 year

Compare downloads with other packages →

Also on400 r2u17 autocran

How downloads are counted

Repository

darwin-eu/codelistgenerator ↗Organization: darwin-eu

18Stars

9Forks

14Open issues

0Open PRs

25Releases

460Commits

9Commit identities

460 commits · Last activity 2026-08-01 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 92
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-16 · 162026-07-07 · 18

How these are measured

PracticesBeta

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

Checks run against github.com/darwin-eu/codelistgenerator on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (2)

Contributing guideIssue templates

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-08-01 · The repository has a site deploy workflow

pkgdown site last built 2026-08-01

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

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

32 external dependencies (excludes base and recommended)

Installing CodelistGenerator adds 28 packages (14 with compiled code, 22 MB of source tarballs). Heaviest: stringi 11 MB, vctrs 1.0 MB, PatientProfiles 951 KB.

Depends (1)

R >= 4.1

Imports (14)

cli clock DBI dplyr glue lifecycle omopgenerics PatientProfiles purrr rlang stringi stringr tidyr vctrs

LinkingTo (0)

none

Suggests (18)

omock covr duckdb CDMConnector visOmopResults CohortConstructor jsonlite knitr rmarkdown testthat RPostgres odbc openxlsx spelling tibble gt flextable tictoc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

4indirect

Imports 4

Suggested by 7

Depends, Imports or LinkingTo, most downloaded first

CohortConstructor DrugUtilisation PhenotypeR CohortSymmetry

Suggests, most downloaded first

PatientProfiles CohortCharacteristics OmopSketch CohortSurvival MeasurementDiagnostics OmopIndices OmopViewer

How these are counted

Code & Tests

Datasets

People & History

People (7)

Edward Burn

Author, Maintainer since 1.0.0 (2023)

Marta Alcalde-Herraiz

Author · added in 3.4.1

Martí Català

Author · added in 4.0.0

Xihang Chen

Author · added in 3.0

Mike Du

Author · added in 3.1.0

Nuria Mercade-Besora

Author · added in 3.2.0

Danielle Newby

Author · added in 3.1.0

Listed in earlier versions (1)

Marti Catala

no longer listed · 1.6.0 to 3.5.0

Releases (29)

Pick two releases to compare their code metrics.

4.1.0Latest
record
2026-08-01 · current release · diff ↗ ·
added 3 exports
emptyCodeSearch, exportCodeSearch, importCodeSearch
R
R 4.6.0 released · 2026-04-24
4.0.2
record
2026-01-19 · diff ↗
4.0.1
record
2026-01-08 · diff ↗
4.0.0
record
2025-12-17 · diff ↗ ·
removed 16 exports
availableICD10, availableIngredients, buildAchillesTables, codesInUse, getConceptClassId, getDomains, getDoseForm, getDoseUnit, getICD10StandardCodes, getRelationshipId, getRouteCategories, getVocabVersion, getVocabularies, sourceCodesInUse, summariseUnmappedCodes, tableUnmappedCodes

added 33 exports
addConcepts, asCodelist, asCodelistWithDetails, asConceptSetExpression, associatedConceptClassIds, associatedDomains, associatedDoseForms, associatedDoseUnits, associatedDrugIngredients, associatedRelationshipIds, associatedRouteCategories, associatedVocabularies, availableConceptClassIds, availableDomains, availableDoseForms, availableDoseUnits, availableDrugIngredients, availableRelationshipIds, availableRouteCategories, availableVocabularies, benchmarkCodelistGenerator, excludeConcepts, intersectCodelists, searchStrategy, stratifyByBrand, stratifyByDomain, stratifyByDoseForm, stratifyByVocabulary, subsetOnDoseForm, subsetOnIngredientRange and 3 more
R
R 4.5.0 released · 2025-04-11
3.5.0
record
2025-04-10 · diff ↗ ·
added 9 exports
buildAchillesTables, cohortCodelist, exportCodelist, exportConceptSetExpression, importCodelist, importConceptSetExpression, newCodelist, newCodelistWithDetails, newConceptSetExpression
3.4.1
record
2025-03-26 · diff ↗
3.4.0
record
2025-02-19 · diff ↗
3.3.2
record
2025-01-28 · diff ↗
3.3.1
record
2024-11-26 · diff ↗ ·
removed 1 export
%>%
3.3.0
record
2024-11-11 · diff ↗ ·
removed 1 export
restrictToCodesInUse

added 3 exports
subsetOnDomain, summariseUnmappedCodes, tableUnmappedCodes
3.2.1
record
2024-10-17 · diff ↗
3.2.0
record
2024-09-25 · diff ↗ ·
added 3 exports
availableATC, availableICD10, availableIngredients
3.1.0
record
2024-07-12 · diff ↗ ·
removed 2 exports
achillesCodeUse, findOrphanCodes

added 8 exports
getDoseUnit, getRouteCategories, stratifyByConcept, stratifyByDoseUnit, stratifyByRouteCategory, subsetOnDoseUnit, subsetOnRouteCategory, subsetToCodesInUse
3.0
record
2024-05-31 · diff ↗ ·
added 7 exports
getRelationshipId, summariseAchillesCodeUse, summariseOrphanCodes, tableAchillesCodeUse, tableCodeUse, tableCohortCodeUse, tableOrphanCodes

Show 20 earlier eventsHide 20 earlier events

R
R 4.4.0 released · 2024-04-24
2.2.3
record
2024-03-08 · diff ↗
2.2.2
record
2024-02-14 · diff ↗
2.2.1
record
2024-02-07 · diff ↗
unarchivedReturned to CRAN
2024-01-25
2.2.0
record
2024-01-25 · diff ↗ ·
added 5 exports
achillesCodeUse, codesInUse, findOrphanCodes, restrictToCodesInUse, sourceCodesInUse
archivedRemoved from CRAN
2024-01-14
issues were not corrected in time Does not use 'arrow' conditionally
2.1.1
record
2023-11-20 · diff ↗
2.1.0
record
2023-11-17 · diff ↗
2.0.0
record
2023-10-09 · diff ↗ ·
added 1 export
summariseCohortCodeUse
1.7.0
record
2023-08-16 · diff ↗ ·
added 1 export
codesFromCohort
1.6.0
record
2023-07-07 · diff ↗ ·
added 1 export
codesFromConceptSet
1.5.0
record
2023-06-13 · diff ↗
1.4.0
record
2023-06-06 · diff ↗ ·
added 1 export
summariseCodeUse
1.3.0
record
2023-05-31 · diff ↗ ·
added 1 export
getICD10StandardCodes
1.2.0
record
2023-05-04 · diff ↗ ·
added 2 exports
getATCCodes, getDrugIngredientCodes
R
R 4.3.0 released · 2023-04-21
1.1.0
record
2023-04-01 · diff ↗
1.0.0
record
2023-02-07
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-02-07
Total releases: 29 / 3 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.1
Bundled data: 2.4 KB / 1 file
Download size: 3.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CodelistGenerator")

Format

Burn, E., Alcalde-Herraiz, M., Català, M., Chen, X., Du, M., Mercade-Besora, N., & Newby, D. (2026). CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use (Version 4.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CodelistGenerator

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 CodelistGenerator version 4.1.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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