CohortConstructor (version 0.2.2)

conceptCohort: Create cohorts based on a concept set

Description

conceptCohort() creates a cohort table from patient records from the clinical tables in the OMOP CDM.

The following tables are currently supported for creating concept cohorts:

• condition_occurrence

• device_exposure

• drug_exposure

• measurement

• observation

• procedure_occurrence

• visit_occurrence

Cohort duration is based on record start and end (e.g. condition_start_date and condition_end_date for records coming from the condition_occurrence tables). So that the resulting table satisfies the requirements of an OMOP CDM cohort table:

• Overlapping records are collapsed into a single cohort entry.

• If a record starts outside of an observation period it will be silently ignored.

• If a record ends outside of an observation period it will be trimmed so as to end at the preceding observation period end date.

Usage

conceptCohort(cdm, conceptSet, name)

Value

A cohort table

Arguments

cdm

A cdm reference.

conceptSet

A conceptSet, which can either be a codelist or a conceptSetExpression.

name

Name of the cohort in the cdm object.

Examples

# \donttest{
library(CohortConstructor)

cdm <- mockCohortConstructor(conditionOccurrence = TRUE)

cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = "cohort")

cohort |> attrition()
# }