Run cohort-level diagnostics

Runs phenotypeR diagnostics on the cohort. The diganotics include: * Age groups and sex summarised. * A summary of visits of everyone in the cohort using visit_occurrence table. * A summary of age and sex density of the cohort. * Attritions of the cohorts. * Overlap between cohorts (if more than one cohort is being used).

Usage

cohortDiagnostics(cohort)

Arguments

cohort

Cohort table in a cdm reference

Value

A summarised result

Examples

# \donttest{
  cdm_local <- omock::mockCdmReference() |>
   omock::mockPerson(nPerson = 100) |>
   omock::mockObservationPeriod() |>
   omock::mockConditionOccurrence() |>
   omock::mockDrugExposure() |>
   omock::mockObservation() |>
   omock::mockMeasurement() |>
   omock::mockCohort(name = "my_cohort")
   cdm_local$visit_occurrence <- dplyr::tibble(
    person_id = 1L,
    visit_occurrence_id = 1L,
    visit_concept_id = 1L,
    visit_start_date = as.Date("2000-01-01"),
    visit_end_date = as.Date("2000-01-01"),
    visit_type_concept_id = 1L
    )
    cdm_local$procedure_occurrence <- dplyr::tibble(
      person_id = 1L,
      procedure_occurrence_id = 1L,
      procedure_concept_id = 1L,
      procedure_date = as.Date("2000-01-01"),
      procedure_type_concept_id = 1L
      )
 db <- DBI::dbConnect(duckdb::duckdb())
 cdm <- CDMConnector::copyCdmTo(con = db,
                                cdm = cdm_local,
                                schema ="main",
                                overwrite = TRUE)

 cdm$my_cohort |> cohortDiagnostics()
#> • Getting cohort summary
#> ℹ adding demographics columns
#> ℹ adding tableIntersectCount 1/1
#> ℹ summarising data
#> ✔ summariseCharacteristics finished!
#> • Getting age density
#> • Getting cohort attrition
#> # A tibble: 2,307 × 13
#>    result_id cdm_name      group_name  group_level strata_name strata_level
#>        <int> <chr>         <chr>       <chr>       <chr>       <chr>       
#>  1         1 mock database cohort_name cohort_1    overall     overall     
#>  2         1 mock database cohort_name cohort_1    overall     overall     
#>  3         1 mock database cohort_name cohort_1    overall     overall     
#>  4         1 mock database cohort_name cohort_1    overall     overall     
#>  5         1 mock database cohort_name cohort_1    overall     overall     
#>  6         1 mock database cohort_name cohort_1    overall     overall     
#>  7         1 mock database cohort_name cohort_1    overall     overall     
#>  8         1 mock database cohort_name cohort_1    overall     overall     
#>  9         1 mock database cohort_name cohort_1    overall     overall     
#> 10         1 mock database cohort_name cohort_1    overall     overall     
#> # ℹ 2,297 more rows
#> # ℹ 7 more variables: variable_name <chr>, variable_level <chr>,
#> #   estimate_name <chr>, estimate_type <chr>, estimate_value <chr>,
#> #   additional_name <chr>, additional_level <chr>
 CDMConnector::cdmDisconnect(cdm = cdm)
# }