Function reference • Capr

All functions
`age()`	Age attribute for a query
`ageAtEnd()`	Age at era end attribute (for era and period domains)
`ageAtStart()`	Age at era start attribute (for era and period domains)
`as.data.frame(<ConceptSet>)`	Coerce a concept set expression to a dataframe
`as.json()`	Coerce Capr object to json
`atLeast()`	Require at least N occurrences of a query within a window
`atMost()`	Require at most N occurrences of a query within a window
`male()` `female()` `raceConcepts()` `ethnicityConcepts()`	Add male attribute to a query
`attrition()`	Define cohort inclusion/exclusion rules (attrition)
`bt()`	Between operator
`CensoringCriteria-class`	An S4 class identifying a censoring criteria for the cohort
`censoringEvents()`	Constructor for a set of censoring events
`cohort()`	Build a cohort definition
`compile(<Cohort>)` `compile(<ConceptSet>)`	Compile a Capr cohort to json
`compile()`	Compile a Capr object to json
`Concept-class`	An S4 class for a single OMOP Concept
`conceptAttribute-class`	An S4 class for a concept attribute
`ConceptSet-class`	An S4 class for ConceptSetExpresion
`conceptSetAttribute-class`	An S4 class for a concept set attribute that holds a reference to a concept set ID
`ConceptSetItem-class`	An S4 class for ConceptSetItem
`conditionEra()`	Query the condition era domain
`conditionOccurrence()`	Query the condition occurrence domain
`conditionSourceConcept()`	Add a condition source concept attribute
`conditionStatus()`	Add a condition status attribute
`conditionStatusCS()`	Condition status filter via concept set — ConditionOccurrence
`conditionType()`	Add a condition type attribute to determine the provenance of the record
`conditionTypeCS()`	ConditionType filter via concept set (ConceptSetSelection)
`conditionTypeExclude()`	ConditionTypeExclude query attribute
`continuousObservation()`	A function to construct the observationWindow
`Criteria-class`	An S4 for a criteria
`cs()` `exclude()` `mapped()` `descendants()`	Create a concept set
`dateAdjustment()`	Shift the start and/or end date of a query event
`dateAdjustmentAttribute-class`	An S4 class for a date adjustment attribute
`daysOfSupply()`	Function to create days supply attribute
`death()`	Query the death domain
`deathType()`	Add a death type attribute to determine the provenance of the record
`deathTypeCS()`	DeathType filter via concept set (ConceptSetSelection)
`deathTypeExclude()`	DeathTypeExclude query attribute
`detectUnsupportedKeys()`	Detect domain keys not in the supported set and emit skipOrStop for each (non-null/non-empty). Prevents silent semantic drift when new Circe fields appear.
`deviceExposure()`	Query the device exposure domain
`deviceType()`	Add a device type attribute to determine the provenance of the record
`deviceTypeCS()`	DeviceType filter via concept set (ConceptSetSelection)
`deviceTypeExclude()`	DeviceTypeExclude query attribute
`doseEra()`	Query the dose era domain
`doseUnit()`	Dose unit attribute for drug exposure
`doseUnitCS()`	Dose unit filter via concept set — DrugExposure
`doseValue()`	Dose value attribute for DoseEra
`drugEra()`	Query the drug era domain
`drugExit()`	Function to create an exit based on exit based on the end of a continuous drug exposure
`drugExposure()`	Query the drug exposure domain
`DrugExposureExit-class`	An S4 class for a cohort exit based on continuous exposure persistence.
`drugQuantity()`	Function to create quantity attribute
`drugRefills()`	Function to create refills attribute
`drugSourceConcept()`	Add a drug source concept attribute
`drugType()`	Add a drug type attribute to determine the provenance of the record
`drugTypeCS()`	DrugType filter via concept set (ConceptSetSelection)
`drugTypeExclude()`	DrugTypeExclude query attribute
`duringInterval()`	Function that creates an eventAperture an opening where an event can occur relative to the index event
`endDate()`	Function that creates a end date attribute
`Endpoint-class`	An S4 class for an Endpoint
`entry()`	Create a cohort entry definition
`eq()`	Equal to operator
`==`(<ConceptSet>,<ConceptSet>)	FUnction checks if two concept set class objects are equivalent
`era()`	Define cohort era collapse settings
`eraLength()`	Era length attribute for DrugEra
`ethnicityCS()`	Ethnicity filter via concept set (ConceptSetSelection, for demographic criteria)
`EventAperture-class`	An S4 class for Aperture
`eventEnds()`	Function creates an event window where the event ends
`eventStarts()`	Function creates an event window where the event starts
`EventWindow-class`	An S4 class for a Window
`exactly()`	Require exactly N occurrences of a query within a window
`exit()`	Define cohort exit strategy
`firstOccurrence()`	Add first occurrence attribute
`FixedDurationExit-class`	An S4 class for a cohort exit based on fixed duration persistence.
`fixedExit()`	Function to create an exit based on exit based on the end of a continuous drug exposure
`genderConcepts()`	Add gender attribute with one or more concept IDs (e.g. both sexes)
`genderCS()`	Gender filter via concept set (ConceptSetSelection, for demographic criteria)
`getConceptDescendants()`	Get all descendants of one or more standard concepts
`getConceptInfo()`	Look up concept details by concept ID
`getConceptSetCall()`	Create the Capr code to build a concept set
`getConceptSetDetails()`	Fill in Concept Set details using a vocab
`Group-class`	An S4 class for a group
`gt()`	Greater than operator
`gte()`	Greater than or equal to operator
`insertCaprCode()`	Insert decompiled Capr code into the current document (RStudio only)
`jsonToCapr()`	Decompile Atlas/Circe cohort JSON to Capr R code
`jsonToCaprFile()`	Write decompiled Capr R code to a file
`keyValueAttribute-class`	Attribute that serializes to a single key-value pair in query JSON. Used for boolean query options like ConditionTypeExclude. Has a `name` slot (same as key) so compile/collectGuid work.
`logicAttribute-class`	An S4 class for a logical attribute
`lotNumber()`	Lot number attribute for DrugExposure
`lt()`	Less than operator
`lte()`	Less than or equal to operator
`makeCohortSet()`	Make a cohort dataframe for cohort generator
`mapSourceToStandard()`	Map source (non-standard) codes to their standard OMOP concepts
`measurement()`	Query the measurement domain
`measurementOperator()`	Measurement operator attribute (e.g. equal to, less than)
`measurementOperatorCS()`	Measurement operator filter via concept set
`measurementSourceConcept()`	Add a measurement source concept attribute
`measurementType()`	Add a measurement type attribute to determine the provenance of the record
`measurementTypeCS()`	MeasurementType filter via concept set (ConceptSetSelection)
`measurementTypeExclude()`	MeasurementTypeExclude query attribute
`measurementUnit()`	Unit attribute for a query
`nbt()`	Not between operator
`nestedAttribute-class`	An S4 class for a nested attribute
`nestedWithAll()`	Construct a nested group where all criteria and groups must be satisfied
`nestedWithAny()`	Function to construct a nested group where any criteria and groups may be satisfied
`nestedWithAtLeast()`	Function to construct a nested group where at least some of the criteria or groups must be satisfied
`nestedWithAtMost()`	Function to construct a nested group where at most some of the criteria or groups must be satisfied
`observation()`	Query the observation domain
`ObservationExit-class`	An S4 class for a cohort exit based on end of continuous observation.
`observationExit()`	Function to create an exit based on continuous observation
`observationPeriod()`	Query the observation period domain
`observationPeriodType()`	Add a observation period type attribute to determine the provenance of the record
`observationQualifier()`	Observation qualifier attribute
`observationQualifierCS()`	Observation qualifier filter via concept set
`observationSourceConcept()`	Add a observation source concept attribute
`observationType()`	Add an observation type attribute to determine the provenance of the record
`observationTypeCS()`	ObservationType filter via concept set (ConceptSetSelection)
`observationTypeExclude()`	ObservationTypeExclude query attribute
`ObservationWindow-class`	An S4 class for an ObservationWindow
`Occurrence-class`	An S4 class for an occurrence.
`occurrenceCount()`	Occurrence count attribute for ConditionEra
`opAttributeCharacter-class`	An S4 class for a op attribute that is a character
`opAttributeDate-class`	An S4 class for a op attribute that is a date
`opAttributeInteger-class`	An S4 class for a op attribute that is an integer
`opAttributeNumeric-class`	An S4 class for a op attribute that is a numeric
`opAttributeSuper-class`	An S4 super class for other opAttribute objects to inherit.
`payerConcept()`	Payer concept attribute for PayerPlanPeriod
`payerPlanPeriod()`	Query the payer plan period domain (CDM >= 5.3)
`payerSourceConcept()`	Payer source concept attribute for PayerPlanPeriod
`periodLength()`	Period length attribute — ObservationPeriod, PayerPlanPeriod
`periodTypeCS()`	ObservationPeriod period type filter via concept set (ConceptSetSelection)
`placeOfService()`	Place of service attribute for visit occurrence
`placeOfServiceCS()`	Place of service filter via concept set — VisitOccurrence, VisitDetail
`planConcept()`	Plan concept attribute for PayerPlanPeriod
`planSourceConcept()`	Plan source concept attribute for PayerPlanPeriod
`procedure()`	Query the procedure occurrence domain
`procedureModifier()`	Procedure modifier attribute
`procedureModifierCS()`	Procedure modifier filter via concept set
`procedureSourceConcept()`	Add a procedure source concept attribute
`procedureType()`	Add a procedure type attribute to determine the provenance of the record
`procedureTypeCS()`	ProcedureType filter via concept set (ConceptSetSelection)
`procedureTypeExclude()`	ProcedureTypeExclude query attribute
`providerSpecialtyConcepts()`	Add provider specialty filter to a visit (round-trip from Atlas JSON)
`providerSpecialtyCS()`	Provider specialty filter via concept set — multiple domains
`quantityValue()`	Quantity attribute — ProcedureOccurrence, DeviceExposure, Specimen
`Query-class`	An S4 class for a Circe Query
`raceCS()`	Race filter via concept set (ConceptSetSelection, for demographic criteria)
`rangeHigh()`	Function to create rangeHigh attribute
`rangeHighRatio()`	Range high ratio attribute for Measurement
`rangeLow()`	Function to create rangeLow attribute
`rankedSearchConcepts()`	Ranked vocabulary search with dialect-specific similarity scoring
`readConceptSet()`	Read a concept set json or csv into R
`routeConcept()`	Route concept attribute for drug exposure
`routeConceptCS()`	Route concept filter via concept set — DrugExposure
`searchConcepts()`	Search the OMOP vocabulary by keyword
`specimen()`	Query the specimen domain
`specimenAnatomicSite()`	Specimen anatomic site attribute
`specimenAnatomicSiteCS()`	Specimen anatomic site filter via concept set
`specimenDiseaseStatus()`	Specimen disease status attribute
`specimenDiseaseStatusCS()`	Specimen disease status filter via concept set
`specimenSourceId()`	Filter by specimen source ID text — Specimen
`specimenType()`	Add a specimen type attribute to determine the provenance of the record
`specimenTypeCS()`	SpecimenType filter via concept set (ConceptSetSelection)
`specimenTypeExclude()`	SpecimenTypeExclude query attribute
`sponsorConcept()`	Sponsor concept attribute for PayerPlanPeriod
`sponsorSourceConcept()`	Sponsor source concept attribute for PayerPlanPeriod
`startDate()`	Function that creates a start date attribute
`stopReason()`	Filter by stop reason text — ConditionOccurrence or DrugExposure
`stopReasonConcept()`	Stop reason concept attribute for PayerPlanPeriod
`stopReasonSourceConcept()`	Stop reason source concept attribute for PayerPlanPeriod
`stringContains()`	String contains operator
`stringEndsWith()`	String ends with operator
`stringNotContains()`	String does not contain operator
`stringNotEndsWith()`	String does not end with operator
`stringNotStartsWith()`	String does not start with operator
`stringStartsWith()`	String starts with operator
`summary()`	Summarise a Capr object
`toCirce()`	Function to coerce cohort to circe
`toCohortJson()`	Convert a Capr cohort to JSON
`toConceptSetJson()`	Convert a Capr concept set to JSON
`uniqueDeviceId()`	Filter by unique device ID text — DeviceExposure
`unitCS()`	Unit filter via concept set — Measurement, Observation, DoseEra, Specimen
`valueAsConcept()`	Add a value as concept attribute
`valueAsConceptSet()`	ValueAsConcept attribute from a concept set (for round-trip without DB)
`valueAsNumber()`	Function to create valueAsNumber attribute
`valueAsString()`	Attribute for Observation value_as_string filter (round-trip from Atlas ValueAsString)
`visit()`	Query the visit occurrence domain
`visitDetail()`	Query the visit detail domain
`visitDetailSourceConcept()`	Add a visit detail source concept attribute
`visitDetailTypeCS()`	Visit detail type filter via concept set — VisitDetail
`visitLength()`	Visit length attribute for VisitOccurrence
`visitSourceConcept()`	Add a visit source concept attribute
`visitType()`	Add a visit type attribute to determine the provenance of the record
`visitTypeCS()`	VisitType filter via concept set (ConceptSetSelection)
`visitTypeExclude()`	VisitTypeExclude query attribute
`visitTypeSet()`	Add a visit type attribute (filter by visit_concept_id) from a concept set
`withAll()`	Function to construct a group where all criteria and groups must be satisfied
`withAny()`	Function to construct a group where any criteria and groups may be satisfied
`withAtLeast()`	Function to construct a group where at least some of the criteria or groups must be satisfied
`withAtMost()`	Function to construct a group where at most some of the criteria or groups must be satisfied
`writeCohort()`	Write Cohort json file
`writeConceptSet()`	Save a concept set as a json file

Reference

All functions