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Create cohorts based on a concept set

Source: R/conceptCohort.R
conceptCohort.Rd

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",
  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".

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.

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.

Value

A cohort table

Examples

# \donttest{
library(CohortConstructor)

cdm <- mockCohortConstructor(conditionOccurrence = TRUE)
#> Note: method with signature ‘DBIConnection#Id’ chosen for function ‘dbExistsTable’,
#>  target signature ‘duckdb_connection#Id’.
#>  "duckdb_connection#ANY" would also be valid

cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = "cohort")
#> Warning: ! `codelist` contains numeric values, they are casted to integers.
#> ✖ Domain NA (1 concept) excluded because it is not supported.
#> ℹ No cohort entries found, returning empty cohort table.

cohort |> attrition()
#> # A tibble: 1 × 7
#>   cohort_definition_id number_records number_subjects reason_id reason          
#>                  <int>          <int>           <int>     <int> <chr>           
#> 1                    1              0               0         1 Initial qualify…
#> # ℹ 2 more variables: excluded_records <int>, excluded_subjects <int>
# }