R Observatory: Metrics for CohortIncidence version 4.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CohortIncidence

4.2.0Package record

Cohort Incidence Analysis for the OMOP Common Data Model

0packages dependsuggested by 1

863downloads / year

89.9%test coverage

13/13flavors OK

Overview

About

Maintained by Christopher KnollCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functionality for performing cohort incidence analyses against data stored in the OMOP Common Data Model (CDM). The package generates database-specific SQL, executes analyses across supported database platforms, and returns standardized incidence estimates using configurable time-at-risk, stratification, and cohort definitions. It is intended to support reproducible observational research within the OHDSI analytics framework.

Changes in 4.2.0

New Features

Two new options are available on the IncidenceDesign:

firstAtRisk: limits TARs to the first continuous TAR period
firstPostOutcome: Only uses outcomes that occur within clean window of TAR or later.

From NEWS.md in the release

Install

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

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

Development version from OHDSI/CohortIncidence. 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-cohortincidence

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-CohortIncidence

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-CohortIncidence

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: 3.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-10-18
ERROR11 OK, 2 ERROR2026-10-09
OK7 OK2026-08-26

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.2.0

READMEYes · 268 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 4.2.0Citation fileNoWebsiteYes · pkgdown

Help pages: 23 (1 internal)includes a package overview page
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

863

CRAN downloads in the past year

Rank #13,508 · ~2/day · ~72/mo

Releases R versions

Daily download trend is not available in this view yet.

35430 days

86390 days

8631 year

Compare downloads with other packages →

Also on31 r2u19 autocran

How downloads are counted

Repository

ohdsi/cohortincidence ↗Organization: OHDSI

6Stars

4Forks

7Open issues

0Open PRs

19Releases

90Commits

4Commit identities

90 commits · Last activity 2026-08-27

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 44
Median days to close, 50 most recently updated closed PRs: 0

Releases over time

2026-08-26 · 182026-08-28 · 19

How these are measured

PracticesBeta

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

Checks run against github.com/ohdsi/cohortincidence on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-08-27

pkgdown site last built 2026-08-20, before release 4.2.0 (2026-08-25)

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing CohortIncidence adds 43 packages (25 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, jsonlite 1.0 MB.

Depends (2)

R >= 3.2.2DatabaseConnector

Imports (5)

rlang rJava checkmate jsonlite SqlRender (>= 1.6.0)

LinkingTo (0)

none

Suggests (8)

testthat knitr rmarkdown withr readr Eunomia duckdb R6

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

Characterization

How these are counted

Code & Tests

People & History

People (1)

Christopher Knoll

Author, Maintainer since 4.2.0 (2026)

Releases (1)

4.2.0Latest
record
2026-08-25 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-08-25
Total releases: 1 / 1 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 3.2.2
Download size: 3.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CohortIncidence")

Format

Knoll, C. (2026). CohortIncidence: Cohort Incidence Analysis for the OMOP Common Data Model (Version 4.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CohortIncidence

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 CohortIncidence version 4.2.0 [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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