conceptCohort {CohortConstructor} | R Documentation |
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,
exit = "event_end_date",
useSourceFields = FALSE,
subsetCohort = NULL,
subsetCohortId = NULL
)
Arguments
cdm |
A cdm reference. |
conceptSet |
A conceptSet, which can either be a codelist or a conceptSetExpression. |
name |
Name of the new cohort table created in the cdm object. |
exit |
How the cohort end date is defined. Can be either "event_end_date" or "event_start_date". |
useSourceFields |
If TRUE, the source concept_id fields will also be used when identifying relevant clinical records. If FALSE, only the standard concept_id fields will be used. |
subsetCohort |
A cohort table containing individuals for whom cohorts will be generated. Only individuals in this table will appear in the generated cohort. |
subsetCohortId |
Optional. Specifies cohort IDs from the |
Value
A cohort table
Examples
library(CohortConstructor)
cdm <- mockCohortConstructor(conditionOccurrence = TRUE)
cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = "cohort")
cohort |> attrition()