tests/testthat/test-tableMeasurementValueAsNumeric.R

In MeasurementDiagnostics: Diagnostics for Lists of Codes Based on Measurements

test_that("table works", {
  cdm <- testMockCdm()
  cdm <- copyCdm(cdm)

  # Summarise measurement use ----
  result <- summariseMeasurementUse(cdm = cdm,
                                    codes = list("test_codelist" = c(3001467L, 45875977L)))
  # Table types
  expect_no_error(x <- tableMeasurementValueAsNumber(result,
                                                      type = "gt",
                                                      header = c(visOmopResults::strataColumns(result)),
                                                      groupColumn = c("codelist_name"),
                                                      hide = c("variable_name", "variable_level", "domain_id"),
                                                      .options = list()))
  expect_true("gt_tbl" %in% class(x))
  expect_true(all(c("Codelist name", "CDM name", "Concept name", "Concept ID", "Source concept name", "Source concept ID", "Unit concept name", "Unit concept ID", "Estimate name", "Estimate value") %in% colnames(x$`_data`)))

  expect_no_error(x <- tableMeasurementValueAsNumber(result, type = "flextable"))
  expect_true("flextable" %in% class(x))

  expect_no_error(x <- tableMeasurementValueAsNumber(result, type = "tibble"))
  expect_true(all(class(x) %in% c("tbl_df", "tbl", "data.frame")))


  # Different package versions
  x <- result |>
    omopgenerics::newSummarisedResult(
      "settings" = omopgenerics::settings(result) |>
        dplyr::mutate("package_version" = "0.0.0")
    )
  expect_message(tableMeasurementSummary(x))

  # Empty output message
  expect_warning(x <- tableMeasurementSummary(
    result = omopgenerics::emptySummarisedResult(), type = "gt"
  ))

  # Summarise cohort measurement use ----
  result <- summariseCohortMeasurementUse(cohort = cdm$my_cohort, bySex = TRUE,
                                          codes = list("test_codelist" = c(3001467L, 45875977L)))
  expect_no_error(x <- tableMeasurementValueAsNumber(result))

  expect_true(all(
    c('Codelist name', 'CDM name', 'Concept name', 'Concept ID', "Domain ID", 'Unit concept name',
      'Unit concept ID', 'Estimate name', '[header_name]Sex\n[header_level]overall',
      '[header_name]Sex\n[header_level]Male') %in%
      colnames(x$`_data`)))

  expect_no_error(x <- tableMeasurementValueAsNumber(result, settingsColumn = "timing"))

  result <- result |> dplyr::filter(variable_name != "number records")
  expect_no_error(x <- tableMeasurementValueAsNumber(result, settingsColumn = "timing"))

  dropCreatedTables(cdm = cdm)
})