R Observatory: Metrics for CohortGenerator version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CohortGenerator

1.1.1Package record

Cohort Generation for the OMOP Common Data Model

1packages dependsuggested by 2

7.9Kdownloads / year

94.6%test coverage

13/13flavors OK

Overview

About

Maintained by Anthony SenaCRAN page ↗GitHub ↗Website ↗Issues ↗

Generate cohorts and subsets using an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) Database. Cohorts are defined using 'CIRCE' (https://github.com/ohdsi/circe-be) or SQL compatible with 'SqlRender' (https://github.com/OHDSI/SqlRender).

Changes in 1.1.1

Bug Fixes

Prevents duplicate cohort IDs bin runCohortGeneration (#275)
Fix backwards compatiblity for v0.x cohort subset operator (#276)

From NEWS.md in the release

Install

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

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

Development version from OHDSI/CohortGenerator. 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-cohortgenerator

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-CohortGenerator

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-CohortGenerator

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: 7.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-10-18
ERROR11 OK, 2 ERROR2026-10-09
OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-22

Show 14 earlier changesHide 14 earlier changes

ERROR12 OK, 1 ERROR2026-08-20
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-22
ERROR12 OK, 1 ERROR2026-06-21
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
OK14 OK2026-04-06
ERROR13 OK, 1 ERROR2026-04-04
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 227 wordsVignettesYes · 4 · dynamicNEWSYes · 33% structured · mentions 1.1.1Citation fileNoWebsiteYes · pkgdown

Help pages: 69 (1 internal)includes a package overview page
Examples that run: 25%1 run in a plain check · 3 never run
Exported functions with examples: 6%
Documented parameters: 99%
Return-value docs: 41%
Help pages citing references: 0%

Vignettes (4)

How these are measured

Downloads

7.9K

CRAN downloads in the past year

Rank #3,877 · ~22/day · ~662/mo

Releases R versions

Daily download trend is not available in this view yet.

91830 days

2.4K90 days

7.9K1 year

Compare downloads with other packages →

Also on169 r2u12 autocran

How downloads are counted

Repository

ohdsi/cohortgenerator ↗Organization: OHDSI

15Stars

15Forks

21Open issues

4Open PRs

23Releases

198Commits

8Commit identities

hades

198 commits · Last activity 2026-07-10 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-04-02 · 142026-07-21 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/ohdsi/cohortgenerator on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-10 · The repository has a site deploy workflow

pkgdown site last built 2026-07-10

Coverage (1)

Coverage reporting

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Installing CohortGenerator adds 55 packages (32 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ResultModelManager 1.5 MB.

Depends (3)

R >= 4.1.0DatabaseConnector R6

Imports (13)

checkmate digest dplyr lubridatemethodsParallelLogger readr rlang jsonlite ResultModelManager SqlRender stringi tibble

LinkingTo (0)

none

Suggests (9)

CirceR duckdb Eunomia ggplot2 knitr rmarkdown testthat withr zip

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

SelfControlledCohort

Suggests, most downloaded first

TreatmentPatterns PheValuator

How these are counted

Code & Tests

Datasets

People & History

People (6)

Anthony Sena

Author, Maintainer since 0.11.1 (2024)

Freddy Avila Cruz

Author · added in 0.12.0

Jamie Gilbert

Author

Gowtham Rao

Author

Martijn Schuemie

Author

Observational Health Data Science and Informatics

Copyright holder

Releases (10)

Pick two releases to compare their code metrics.

1.1.1Latest
record
2026-07-10 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.0
record
2026-03-03 · diff ↗ ·
added 2 exports
computeCohortAttrition, exportCohortSubsetStatsTables
1.0.2
record
2026-02-10 · diff ↗
1.0.1
record
2025-11-17 · diff ↗
1.0.0
record
2025-11-12 · diff ↗ ·
removed 4 exports
getRequiredTasks, isTaskRequired, recordTasksDone, saveIncremental

added 21 exports
CohortTemplateDefinition, addCohortTemplateDefintion, addExcludeOnIndexSubsetDefinition, addIndicationSubsetDefinition, addRestrictionSubsetDefinition, addSqlCohortDefinition, addUnionCohortDefinition, createAtcCohortTemplateDefinition, createCohortSubsetOperator, createCohortTemplateDefintion, createDemographicSubsetOperator, createLimitSubsetOperator, createRxNormCohortTemplateDefinition, createSnomedCohortTemplateDefinition, createUnionCohortTemplate, getCohortValidationCounts, getExcludeOnIndexSubsetDefinitionIds, getIndicationSubsetDefinitionIds, getLastGeneratedCohortChecksums, getRestrictionSubsetDefinitionIds, getTemplateDefinitions
0.12.2
record
2025-09-11 · diff ↗
0.12.1
record
2025-09-05 · diff ↗
0.12.0
record
2025-07-31 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.11.2
record
2024-09-30 · diff ↗
0.11.1
record
2024-09-15
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-15
Total releases: 10 / 2 yrs
License: Apache License
Minimum R: ≥ 4.1.0
Bundled data: 0.7 KB / 2 files
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CohortGenerator")

Format

Sena, A., Observational Health Data Science and Informatics, Avila Cruz, F., Gilbert, J., Rao, G., & Schuemie, M. (2026). CohortGenerator: Cohort Generation for the OMOP Common Data Model (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.CohortGenerator

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 CohortGenerator version 1.1.1 [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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