CohortGenerator (version 1.0.2)

addExcludeOnIndexSubsetDefinition: Add exclude on index subset definition

Description

The purpose of this subset recipe is to exclude all individuals if their index aligns with the specified exclusion cohort ids. If the index date of the exclusionCohortIds aligns with the targetCohortIds (or it lies within some relative window of the target cohort start date) then they will be excluded from the resulting sub population.

This may be used in situations where an outcome cohort may contain individuals treated for a target medication, complicating calculation of incidence rates.

Usage

addExcludeOnIndexSubsetDefinition(
  cohortDefinitionSet,
  subsetDefinitionName,
  subsetCohortNameTemplate = "@baseCohortName - @subsetDefinitionName",
  targetCohortIds,
  exclusionCohortIds,
  exclusionWindow = 0,
  subsetDefinitionId,
  cohortCombinationOperator = "any"
)

Arguments

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort

subsetDefinitionName

name of the subset definition (used in resulting cohort definitions)

subsetCohortNameTemplate

template string format for naming resulting cohorts

targetCohortIds

Set of integer cohort IDs. Must be within the cohort definition set.

exclusionCohortIds

cohort ids to exclude members of target from

exclusionWindow

Days Default is 0 (target index date). by changing this you can adjust the period around target index for which you would exclude members.

subsetDefinitionId

Unique integer Id of the subset definition

cohortCombinationOperator

Logic for multiple indication cohort IDs: any (default) or all.

Examples

if (FALSE) {
library(CohortGenerator)

initialSet <- getCohortDefinitionSet(
  settingsFileName = "testdata/name/Cohorts.csv",
  jsonFolder = "testdata/name/cohorts",
  sqlFolder = "testdata/name/sql/sql_server",
  cohortFileNameFormat = "%s",
  cohortFileNameValue = c("cohortName"),
  packageName = "CohortGenerator",
  verbose = FALSE
)

print(initialSet[, c("cohortId", "cohortName")])

# Subset cohorts 1 & 2 by an "indication" cohort 3:
res <- addExcludeOnIndexSubsetDefinition(
  cohortDefinitionSet = initialSet,
  targetCohortIds = c(1, 2),
  exclusionCohortIds = c(3),
  subsetDefinitionId = 20,
  subsetDefinitioName = "Exclude on index if in cohort 3"
)

print(res[, c("cohortId", "cohortName", "subsetParent", "subsetDefinitionId", "isSubset")])

# Get all subset definitions that were created using the addExcludeOnIndexSubsetDefinition:
subsetDefinitionId <- getExcludeOnIndexSubsetDefinitionIds(res)

# Filter the cohortDefinitionSet to those cohorts defined using an exclusion subset definition:
newCohorts <- res |>
  dplyr::filter(subsetDefinitionId == subsetDefinitionId) |>
  dplyr::select(cohortId, cohortName, subsetParent, isSubset)
print(newCohorts)
}