CohortGenerator

1.1.1

Cohort Generation for the OMOP Common Data Model

1packages depend

9.2Kdownloads / year

94.6%test coverage

13/13checks pass

Overview

About

Maintained by Anthony SenaFirst published 2024-09-1510 releasesCRAN page ↗GitHub ↗

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).

Install

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

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.

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

Health

CRAN checks

13OK

Slowest check: 7.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.76

94.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-22
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-06
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-04
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 227 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 99%
Return-value docs: 41%
References docs: 0%

Downloads

9.2K

CRAN downloads in the past year

Rank #6,776 · ~25/day · ~769/mo

Releases R versions

Daily download trend is not available in this view yet.

49130 days

1.5K90 days

9.2K1 year

Compare downloads with other packages →

Also on253 r2u

Repository

GitHub ↗ ohdsi/cohortgenerator

15Stars

15Forks

20Open issues

3Open PRs

23Releases

198Commits

8Contributors

hades

198 commits · Last activity 2026-07-10 · +7.1% stars, 30d

Stars over time

2025-04-02 · 142026-07-07 · 14

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/ohdsi/cohortgenerator on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

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

TreatmentPatterns

Code & Tests

Code Composition

R 12,269 (71%)Rd 3,844 (22%)Vignettes 1,018 (6%)Other 31 (0%)

Code characteristics

Object systems

R611

Cyclomatic complexity: 2.0 median / 15 max
Test cases: 158 / 0.76 per code line

Test coverage

Line coverage

95%

Expression

94.3%

Tests / Examples

94.6% / – ex

Functions

97 59 exported

Complexity

3.6 avg / 15 max

Call network

97 nodes / 150 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

97 functions

Function	Cyclo	Coverage
addUnionCohortDefinition exp	1	0%
createLimitSubset exp	1	0%
createUnionCohortTemplate exp	1	0%
loadTemplateFromJson	1	0%
saveCohortTemplateDefinitions	1	0%
loadTemplateDefinitionsFolder	2	63%

People & History

People (6)

Maintainer (1)

Anthony Sena

Author, Maintainer

Authors (5)

Anthony Sena

Author, Maintainer

Freddy Avila Cruz

Author · added in 0.12.0

Jamie Gilbert

Author

Gowtham Rao

Author

Martijn Schuemie

Author

Observational Health Data Science and Informatics

Package Timeline

10 releases. Pick two to compare their code metrics. R releases are shown for context.

1.1.1Latest
2026-07-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.0
2026-03-03 · diff ↗
1.0.2
2026-02-10 · diff ↗
1.0.1
2025-11-17 · diff ↗
1.0.0
2025-11-12 · diff ↗
0.12.2
2025-09-11 · diff ↗
0.12.1
2025-09-05 · diff ↗
0.12.0
2025-07-31 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.11.2
2024-09-30 · diff ↗
0.11.1
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
Installed size: not tracked yet
With dependencies: not tracked yet

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