Package: CohortIncidence 4.2.0

Christopher Knoll

CohortIncidence: Cohort Incidence Analysis for the OMOP Common Data Model

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.

Authors:Christopher Knoll [aut, cre]

CohortIncidence_4.2.0.tar.gz
CohortIncidence_4.2.0.zip(r-4.7-any)CohortIncidence_4.2.0.zip(r-4.6-any)CohortIncidence_4.2.0.zip(r-4.5-any)
CohortIncidence_4.2.0.tgz(r-4.6-any)CohortIncidence_4.2.0.tgz(r-4.5-any)
CohortIncidence_4.2.0.tar.gz(r-4.7-any)CohortIncidence_4.2.0.tar.gz(r-4.6-any)
CohortIncidence_4.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CohortIncidence/json (API)

# Install 'CohortIncidence' in R:
install.packages('CohortIncidence', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/cohortincidence/issues

Pkgdown/docs site:https://ohdsi.github.io

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

openjdk

6.15 score 6 stars 26 scripts 497 downloads 22 exports 43 dependencies

Last updated from:fc39a9d42c. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK199
source / vignettesOK209
linux-release-x86_64OK178
macos-release-arm64OK117
macos-oldrel-arm64OK178
windows-devel-x86_64OK110
windows-release-x86_64OK118
windows-oldrel-x86_64OK178
wasm-releaseOK169

Exports:buildOptionsbuildQueryCohortDefinitionCohortReferenceCohortSubgroupcreateCohortRefcreateCohortSubgroupcreateDateRangecreateIncidenceAnalysiscreateIncidenceDesigncreateOutcomeDefcreateStrataSettingscreateTimeAtRiskDefDateRangeexecuteAnalysisgetCleanupSqlgetResultsDdlIncidenceAnalysisIncidenceDesignOutcomeStrataSettingsTimeAtRisk

Dependencies:backportsbitbit64blobcheckmateclicliprcpp11crayonDatabaseConnectorDBIdbplyrdigestdplyrgenericsgluehmsjsonlitelifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6RcppreadrrJavarlangSqlRenderstringistringrtibbletidyrtidyselecttriebeardtzdburltoolsutf8vctrsvroomwithr

CohortIncidence Method Documentation
Background | Terminology | Example: Calcuating incidence from a single patient timeline | Step 1: Define TAR and Clean Windows | Step 2: Collapse TAR and Clean Windows | Step 3: Remove Immortal Time | Step 4: Calculate Incidence Rate and Proportion | Limiting follow up to first outcome | A Tabular Example
Rendered fromcohortincidence-method-documentation.Rmdusingknitr::rmarkdown

Last update: 2026-08-27
Started: 2024-10-04

Using CohortIncidence
Introduction | Installation instructions | Database Preparation | A simple example | Build the design | Using age, gender and start year strata | Using executeAnalysis() | Advanced Usage: Budling and Executing SQL manually | Build analysis SQL from design | Render SQL with paramaters and execute | Using Temp Tables
Rendered fromusing-cohortincidence.Rmdusingknitr::rmarkdown

Last update: 2026-08-27
Started: 2021-08-14