Package {CirceR}

Type: Package
Title: Construct Cohort Inclusion and Restriction Criteria Expressions
Version: 1.4.0
Date: 2026-11-01
Maintainer: Chris Knoll <cknoll@ohdsi.org>
Description: Wraps the 'CIRCE' (https://github.com/ohdsi/circe-be) 'Java' library allowing cohort definition expressions to be edited and converted to 'Markdown' or 'SQL'.
License: Apache License 2.0
URL: https://ohdsi.github.io/CirceR/, https://github.com/OHDSI/CirceR/
BugReports: https://github.com/OHDSI/CirceR/issues/
SystemRequirements: Java (>= 8)
Depends: R (≥ 3.5.0)
Imports: rJava, RJSONIO
Suggests: testthat, knitr, rmarkdown, reticulate
NeedsCompilation: no
Language: en-US
Encoding: UTF-8
Config/roxygen2/version: 8.0.0
Packaged: 2026-11-02 15:14:27 UTC; cknoll1
Author: Chris Knoll [aut, cre], Martijn Schuemie [aut]
Repository: CRAN
Date/Publication: 2026-11-02 15:50:02 UTC

CirceR: Construct Cohort Inclusion and Restriction Criteria Expressions

Description

Wraps the 'CIRCE' (https://github.com/ohdsi/circe-be) 'Java' library allowing cohort definition expressions to be edited and converted to 'Markdown' or 'SQL'.

Author(s)

Maintainer: Chris Knoll cknoll@ohdsi.org

Authors:

See Also

Useful links:

Get the backend implementation

Description

Get the backend implementation

Usage

.get_backend()

Value

An object with class 'circe_backend_python' or 'circe_backend_java'.

Build cohort SQL

Description

Generates the OMOP CDM Sql to generate the cohort expression

Usage

buildCohortQuery(expression, options)

Arguments

expression

result of cohortExpressionFromJson containing the cohort expression.

options

The options built using createGenerateOptions()

Value

A character vector containing the OHDSI Sql for the cohort expression

Build conceptset SQL

Description

Generates the OMOP CDM Sql to resolve the concept set expression

Usage

buildConceptSetQuery(conceptSetJSON)

Arguments

conceptSetJSON

a string containing the JSON for the conceptset expression.

Value

A character vector containing the OHDSI Sql for the conceptset expression

An example cohort definition

Description

An example cohort definition

Usage

data(cohortDefinitionJson)

Format

A character vector containing a JSON string

Details

An example cohort expression in JSON format

Render read JSON into a CohortExpression instance

Description

Reads a String (json) and deserializes it into a org.ohdsi.circe.cohortdefinition.CohortExpression

Usage

cohortExpressionFromJson(expressionJson)

Arguments

expressionJson

A character vector containing the cohort expression.

Value

A java instance of org.ohdsi.circe.cohortdefinition.CohortExpression.

Render cohort print-friendly

Description

Generates a print-friendly (human-readable) representation of the cohort definition. This can for example be used in a study protocol.

Usage

cohortPrintFriendly(expression)

Arguments

expression

A character vector or result of cohortExpressionFromJson containing the cohort expression.

Value

A character vector containing the markdown.

Render read JSON into a ConceptSetExpression instance

Description

Reads a String (json) and deserializes it into a org.ohdsi.circe.vocabulary.CohortExpression

Usage

conceptSetExpressionFromJson(expressionJson)

Arguments

expressionJson

A character vector containing the cohort expression.

Value

A java instance of org.ohdsi.circe.cohortdefinition.CohortExpression.

An example concept set

Description

An example concept set

Usage

data(conceptSetJson)

Format

A character vector containing a JSON string

Details

An example concept set in JSON format

An example concept set list

Description

An example concept set list

Usage

data(conceptSetListJson)

Format

A character vector containing a JSON string

Details

An example concept set list in JSON format

Render conceptSet array for print-friendly

Description

Generates a print-friendly (human-readable) representation of an array of concept sets. This can for example be used in a study protocol.

Usage

conceptSetListPrintFriendly(conceptSetList)

Arguments

conceptSetList

A ConceptSet[] (from cohortExpression.conceptSets), a JSON string, or a list from RJSONIO::fromJson

Value

A character vector containing the markdown.

Render conceptSet array for print-friendly

Description

Generates a print-friendly (human-readable) representation of a single concept set. This can for example be used in a study protocol.

Usage

conceptSetPrintFriendly(conceptSet)

Arguments

conceptSet

A ConceptSet (from cohortExpression.conceptSets[i]), a JSON string, or a list from RJSONIO::fromJson

Value

A character vector containing the markdown.

Create Generation Options

Description

Creates the generation options object for use in generateSql()

Usage

createGenerateOptions(
  cohortIdFieldName,
  cohortId,
  cdmSchema,
  targetTable,
  resultSchema,
  vocabularySchema,
  generateStats
)

Arguments

cohortIdFieldName

The field that contains the cohortId in the cohort table.

cohortId

The generated cohort ID.

cdmSchema

The value of the CDM schema.

targetTable

the cohort table name.

resultSchema

the schema the cohort table belongs to.

vocabularySchema

the schema of the vocabulary tables (defaults to cdmSchema)

generateStats

a boolean representing if the query should include inclusion rule statistics calculation

Value

A jObj that can be passed to generateSql().

Enables the Python backend

Description

Sets the CIRCER_BACKEND environment variable to 'python'.

Usage

enablePythonBackend()

Ensures the Java backend is available

Description

Ensures the Java backend is available

Usage

ensureJavaBackend()

Ensures the Python backend is available

Description

Ensures the Python backend is available

Usage

ensurePythonBackend()

Value

The 'circe' module (from the ohdsi-circepy package).

Checks if the Python backend is enabled

Description

Checks if the Python backend is enabled

Usage

usePythonBackend()

Value

TRUE if CIRCER_BACKEND environment variable is set to 'python', FALSE otherwise.