MockVisitOccurrence()

[ilovemane]

No description provided.

[catalamarti]

all records of concepts (in observation) and cohorts must have a visit record in visit occurrence

[edward-burn]

another +1 for this :)

[catalamarti]

visitOccurrence <- purrr::map_df(allClinicalTables, \(x) {
  personIdentifier <- getPersonIdentifier(x) # omopgenerics::getPersonIdentifier()
  startDate <- getStartDate(x) # check if PatientProfiles::startDateColumn()
  cdm[[x]] |>
    dplyr::select(
      "person_id" = dplyr::all_of(personIdentifier),
      "visit_start_date" = dplyr::all_of(startDate)
    ) |>
    dplyr::mutate("visit_end_date" = .data$visit_start_date) |>
    dplyr::distinct()
}) |>
  dplyr::distinct() |>
  dplyr::mutate(visit_corrence_id = dplyr::row_number())

for (x in allClinicalTables) {
  personIdentifier <- getPersonIdentifier(x)
  startDate <- getStartDate(x)
  cdm[[x]] <- cdm[[x]] |>
    dplyr::select(!"visit_corrence_id") |>
    dplyr::inner_join(
      visitOccurrence |>
        dplyr::select(
          !!personIdentifier := "person_id",
          !!startDate := "visit_start_date",
          "visit_corrence_id"
        ), 
      by = c(personIdentifier, startDate)
    )
}

# populate extra columns for visit_occurrence table