cohortDiagnostics {PhenotypeR}R Documentation

Run cohort-level diagnostics

Description

Runs phenotypeR diagnostics on the cohort. The diganostics 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


cdm_local <- omock::mockCdmReference() |>
  omock::mockPerson(nPerson = 100) |>
  omock::mockObservationPeriod() |>
  omock::mockConditionOccurrence() |>
  omock::mockDrugExposure() |>
  omock::mockObservation() |>
  omock::mockMeasurement() |>
  omock::mockVisitOccurrence() |>
  omock::mockProcedureOccurrence() |>
  omock::mockCohort(name = "my_cohort")
 db <- DBI::dbConnect(duckdb::duckdb())
 cdm <- CDMConnector::copyCdmTo(con = db,
                                cdm = cdm_local,
                                schema ="main",
                                overwrite = TRUE)

 cdm$my_cohort |> cohortDiagnostics()
 CDMConnector::cdmDisconnect(cdm = cdm)


[Package PhenotypeR version 0.1.0 Index]