CohortSubsetDefinition: Cohort Subset Definition

In anthonysena/CohortGenerator: Cohort Generation for the OMOP Common Data Model

Cohort Subset Definition

Description

Set of subset definitions

Active bindings

targetOutputPairs

list of pairs of integers - (targetCohortId, outputCohortId)

subsetOperators

list of subset operations

name

name of definition

subsetCohortNameTemplate

template string for formatting resulting cohort names

operatorNameConcatString

string used when concatenating operator names together

definitionId

numeric definition id

identifierExpression

expression that can be evaluated from

Methods

Public methods

• CohortSubsetDefinition$new()

• CohortSubsetDefinition$toList()

• CohortSubsetDefinition$toJSON()

• CohortSubsetDefinition$addSubsetOperator()

• CohortSubsetDefinition$getSubsetQuery()

• CohortSubsetDefinition$getSubsetCohortName()

• CohortSubsetDefinition$setTargetOutputPairs()

• CohortSubsetDefinition$getJsonFileName()

• CohortSubsetDefinition$clone()

---

Method new()

Usage

CohortSubsetDefinition$new(definition = NULL)

Arguments

definition

json or list representation of object to List

---

Method toList()

List representation of object to JSON

Usage

CohortSubsetDefinition$toList()

---

Method toJSON()

json serialized representation of object add Subset Operator

Usage

CohortSubsetDefinition$toJSON()

---

Method addSubsetOperator()

add subset to class - checks if equivalent id is present Will throw an error if a matching ID is found but reference object is different

Usage

CohortSubsetDefinition$addSubsetOperator(subsetOperator)

Arguments

subsetOperator

a SubsetOperator instance

overwrite

if a subset operator of the same ID is present, replace it with a new definition get query for a given target output pair

---

Method getSubsetQuery()

Returns vector of join, logic, having statements returned by subset operations

Usage

CohortSubsetDefinition$getSubsetQuery(targetOutputPair)

Arguments

targetOutputPair

Target output pair Get name of an output cohort

---

Method getSubsetCohortName()

Usage

CohortSubsetDefinition$getSubsetCohortName(
  cohortDefinitionSet,
  targetOutputPair
)

Arguments

cohortDefinitionSet

Cohort definition set containing base names

targetOutputPair

Target output pair Set the targetOutputPairs to be added to a cohort definition set

---

Method setTargetOutputPairs()

Usage

CohortSubsetDefinition$setTargetOutputPairs(targetIds)

Arguments

targetIds

list of cohort ids to apply subsetting operations to Get json file name for subset definition in folder

---

Method getJsonFileName()

Usage

CohortSubsetDefinition$getJsonFileName(
  subsetJsonFolder = "inst/cohort_subset_definitions/"
)

Arguments

subsetJsonFolder

path to folder to place file

---

Method clone()

The objects of this class are cloneable with this method.

Usage

CohortSubsetDefinition$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

anthonysena/CohortGenerator documentation built on June 14, 2025, 5:48 a.m.