CohortConstructor (version 0.6.1)

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:

• Cohort entries will not overlap. Overlapping records will be combined based on the overlap argument.

• Cohort entries will not go out of observation. 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",
  overlap = "merge",
  table = NULL,
  useRecordsBeforeObservation = FALSE,
  useSourceFields = FALSE,
  subsetCohort = NULL,
  subsetCohortId = NULL
)

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 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".

overlap

How to deal with overlapping records. In all cases cohort start will be set as the earliest start date. If "merge", cohort end will be the latest end date. If "extend", cohort end date will be set by adding together the total days from each of the overlapping records.

table

Name of OMOP tables to search for records of the concepts provided. If NULL, each concept will be search at the assigned domain in the concept table.

useRecordsBeforeObservation

If FALSE, only records in observation will be used. If TRUE, records before the start of observation period will be considered, with cohort start date set as the start date of the individuals next observation period (as cohort records must be within observation).

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 character refering to 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 subsetCohort table to include. If none are provided, all cohorts from the subsetCohort are included.

Examples

# \donttest{
library(CohortConstructor)
cdm <- mockCohortConstructor()

cdm$cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 444074), name = "cohort")

cdm$cohort |>
  attrition()

# Create a cohort based on a concept set. The cohort exit is set to the event start date.
# If two records overlap, the cohort end date is set as the sum of the duration of
# all overlapping records. Only individuals included in the existing `cohort` will be considered.

conceptSet <- list(
  "nitrogen" = c(35604434, 35604439),
  "potassium" = c(40741270, 42899580, 44081436)
)

cdm$study_cohort <- conceptCohort(cdm = cdm,
                                  conceptSet = conceptSet,
                                  name = "study_cohort",
                                  exit = "event_start_date",
                                  overlap = "extend",
                                  subsetCohort = "cohort")

cdm$study_cohort |>
  attrition()
# }