In OHDSI/Capr: Cohort Definition Application Programming

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE # for now...
)

library(Capr)

# Function to test that cohort compiles
assertCohortCompiles <- function(cohortDefinition) {
  sql <- CirceR::cohortExpressionFromJson(as.json(ch))
  sql <- CirceR::buildCohortQuery(sql, options = CirceR::createGenerateOptions(generateStats = TRUE))

  stopifnot(nchar(sql) > 1)
  invisible(NULL)
}

This vignette provides a number of example cohorts built with Capr from the OHDSI Phenotype Phebruary event.

Type 2 diabetes mellitus

Persons with new type 2 diabetes mellitus at first diagnosis

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/88/definition

# DRAFT version that uses observationPeriod Query type
# TODO implement observation period Query type
cs1 <- cs(descendants(443238, 201820, 442793), 
          descendants(exclude(195771, 201254, 435216, 761051, 4058243, 40484648)),
          name = "Type 2 diabetes mellitus (diabetes mellitus excluding T1DM and secondary)")

ch <- cohort(
  entry = conditionOccurrence(cs1),
  attrition = attrition(
    withAll(
          atLeast(1, 
            observationPeriod(), #function not currently in Capr
            duringInterval(eventStarts(-Inf, -365, "startDate"))
    )
    )
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

library(Capr)

cs0 <- cs(descendants(443238, 201820, 442793), 
          descendants(exclude(195771, 201254, 435216, 761051, 4058243, 40484648)),
          name = "Type 2 diabetes mellitus (diabetes mellitus excluding T1DM and secondary)")

ch <- cohort(
  entry = entry(
    conditionOccurrence(cs0),
    observationWindow = continuousObservation(priorDays = 365)
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

assertCohortCompiles(ch)

Persons with new type 2 diabetes and no prior T1DM or secondary diabetes

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/89/export

library(Capr)

cs0 <- cs(descendants(443238, 201820, 442793), 
          descendants(exclude(195771, 201254, 435216, 761051, 4058243, 40484648)),
          name = "Type 2 diabetes mellitus (diabetes mellitus excluding T1DM and secondary)")

cs1 <- cs(descendants(201254, 435216, 40484648),
          name = "Type 1 diabetes mellitus")

cs2 <- cs(descendants(195771),
          name = "Secondary diabetes mellitus")

ch <- cohort(
  entry = entry(
    conditionOccurrence(cs0),
    observationWindow = continuousObservation(priorDays = 365)
  ),
  attrition = attrition(
    't1d' = withAll(
    exactly(0, conditionOccurrence(cs1), duringInterval(eventStarts(-Inf, 0)))
    ),
    'secondaryDiabetes' = withAll(
    exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0)))
    )
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

assertCohortCompiles(ch)

Persons with new type 2 diabetes mellitus at first dx rx or lab

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/90

library(Capr)

cs0 <- cs(descendants(443238, 201820, 442793), 
          descendants(exclude(195771, 201254, 435216, 761051, 4058243, 40484648)),
          name = "Type 2 diabetes mellitus (diabetes mellitus excluding T1DM and secondary)")

cs1 <- cs(descendants(201254, 435216, 40484648),
          name = "Type 1 diabetes mellitus")

cs2 <- cs(descendants(195771),
          name = "Secondary diabetes mellitus")

cs3 <- cs(descendants(4184637, 37059902),
          name = "Hemoglobin A1c (HbA1c) measurements")

cs4 <- cs(descendants(21600744),
          name = "Drugs for diabetes except insulin")


ch <- cohort(
  entry = entry(
    conditionOccurrence(cs0),
    drugExposure(cs4),
    measurement(cs3, valueAsNumber(bt(6.5, 30)), unit("%")),
    measurement(cs3, valueAsNumber(bt(48, 99)), unit("mmol/mol")),
    observationWindow = continuousObservation(priorDays = 365)
  ),
  attrition = attrition(
    'no T1D' = withAll(
      exactly(0, conditionOccurrence(cs1), duringInterval(eventStarts(-Inf, 0)))
      ),
    'no secondary diabettes' = withAll(
      exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0)))
    )
  ),
  exit = exit(
    endStrategy = observationExit()
  )
)

assertCohortCompiles(ch)

Type 1 diabetes mellitus

Persons with new type 1 diabetes

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/92

cs0 <- cs(descendants(195771),
          name = "Type 1 diabetes mellitus")

ch <- cohort(
  entry = entry(
    conditionOccurrence(cs0),
    observationWindow = continuousObservation(priorDays = 365)
  )
)

assertCohortCompiles(ch)

Persons with new type 1 diabetes and no prior T2DM or secondary diabetes

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/91

cs0 <- cs(descendants(443238, 201820, 442793), 
          descendants(exclude(195771, 201254, 435216, 761051, 4058243, 40484648)),
          name = "Type 2 diabetes mellitus (diabetes mellitus excluding T1DM and secondary)")

cs1 <- cs(descendants(201254, 435216, 40484648),
          name = "Type 1 diabetes mellitus")

cs2 <- cs(descendants(195771),
          name = "Secondary diabetes mellitus")

ch <- cohort(
  entry = entry(
    conditionOccurrence(cs1),
    observationWindow = continuousObservation(priorDays = 365)
  ),
  attrition = attrition(
    "no prior T2DM" = withAll(exactly(0, conditionOccurrence(cs0), duringInterval(eventStarts(-Inf, 0)))),
    "no prior secondary T1DM" = withAll(exactly(0, conditionOccurrence(cs2), duringInterval(eventStarts(-Inf, 0))))
  )
)

assertCohortCompiles(ch)

Atrial Fibrillation

Persons with atrial fibrillation per Wharton et al 2021

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/93

cs0 <- cs(descendants(313217),
          name = "Atrial fibrillation")

ch <- cohort(conditionOccurrence(cs0))

assertCohortCompiles(ch)

Persons with atrial fibrillation per Subramanya et al 2021

https://atlas-phenotype.ohdsi.org/#/cohortdefinition/94

afib <- cs(descendants(313217),
           name = "Atrial fibrillation")

ip <- cs(descendants(262, 9201),
         name = "Inpatient or inpatient ER visit")

op <- cs(descendants(9202, 9203),
         name = "Outpatient or ER visit")

ch <- cohort(
  entry = entry(
    conditionOccurrence(
      conceptSet = afib,
      nestedWithAll(
        # an inpatient afib
        atLeast(
          x = 1, 
          aperture = duringInterval(eventStarts(-Inf, 0), eventEnds(0, Inf)),
          query = visit(conceptSet = ip)
        )
      )
    ), 
    conditionOccurrence(
      conceptSet = afib,
      nestedWithAll(
        # 2 afib in outpatient
        atLeast(
          x = 1,
          aperture = duringInterval(eventStarts(-Inf, 0), eventEnds(0, Inf)),
          query = visit(
            conceptSet = op, 
            nestedWithAll(
              atLeast(
                x = 1, 
                aperture = duringInterval(eventStarts(7, 365)),
                query = conditionOccurrence(
                  conceptSet = afib, 
                  nestedWithAll(
                    atLeast(
                      x = 1, 
                      aperture = duringInterval(eventStarts(-Inf, 0), eventEnds(0, Inf)),
                      query = visit(conceptSet = op)
                    )
                  )
                )
              )
            )
          )
        )
      )
    )

  )
)

# not compiling
assertCohortCompiles(ch)

OHDSI/Capr documentation built on Feb. 20, 2025, 4 a.m.