tests/testthat/test-tableCohortOverlap.R

In CohortCharacteristics: Summarise and Visualise Characteristics of Patients in the OMOP CDM

test_that("tableCohortOverlap", {
  skip_on_cran()
  person <- dplyr::tibble(
    person_id = 1:20L,
    gender_concept_id = sample(c(8532L, 8507L), size = 20, replace = T),
    year_of_birth = sample(1950:2000L, size = 20, replace = TRUE),
    month_of_birth = sample(1:12L, size = 20, replace = TRUE),
    day_of_birth = sample(1:28L, size = 20, replace = TRUE),
    race_concept_id = 0L,
    ethnicity_concept_id = 0L
  )

  table <- dplyr::tibble(
    cohort_definition_id = c(rep(1L, 15), rep(2L, 10), rep(3L, 15), rep(4L, 5)),
    subject_id = c(
      20, 5, 10, 12, 4, 15, 2, 1, 5, 10, 5, 8, 13, 4, 10,
      6, 18, 5, 1, 20, 14, 13, 8, 17, 3,
      16, 15, 20, 17, 3, 14, 6, 11, 8, 7, 20, 19, 5, 2, 18,
      5, 12, 3, 14, 13
    ) |>
      as.integer(),
    cohort_start_date = as.Date(c(
      rep("2000-01-01", 5), rep("2010-09-05", 5), rep("2006-05-01", 5),
      rep("2003-03-31", 5), rep("2008-07-02", 5), rep("2000-01-01", 5),
      rep("2012-09-05", 5), rep("1996-05-01", 5), rep("1989-03-31", 5)
    )),
    cohort_end_date = as.Date(c(
      rep("2000-01-01", 5), rep("2010-09-05", 5), rep("2006-05-01", 5),
      rep("2003-03-31", 5), rep("2008-07-02", 5), rep("2000-01-01", 5),
      rep("2012-09-05", 5), rep("1996-05-01", 5), rep("1989-03-31", 5)
    ))
  )

  obs <- dplyr::tibble(
    observation_period_id = 1:20L,
    person_id = 1:20L,
    observation_period_start_date = as.Date("1930-01-01"),
    observation_period_end_date = as.Date("2025-01-01"),
    period_type_concept_id = 0L
  )

  cdm <- mockCohortCharacteristics(
    con = connection(), writeSchema = writeSchema(), person = person,
    observation_period = obs, table = table
  )

  overlap <- summariseCohortOverlap(cdm$table)

  gtResult1 <- tableCohortOverlap(overlap)
  expect_true("gt_tbl" %in% class(gtResult1))

  fxResult1 <- tableCohortOverlap(
    overlap,
    type = "flextable", header = "cohort_name"
  )
  expect_true("flextable" %in% class(fxResult1))

  cdm$table <- cdm$table |>
    PatientProfiles::addAge(ageGroup = list(c(0, 40), c(41, 100))) |>
    PatientProfiles::addSex() |>
    dplyr::compute(name = "table", temporary = FALSE) |>
    omopgenerics::newCohortTable()

  overlap3 <- summariseCohortOverlap(
    cdm$table,
    strata = list("age_group", c("age_group", "sex"))
  )
  tibbleResult1 <- tableCohortOverlap(overlap3, type = "tibble")
  expect_true(all(c("tbl_df", "tbl", "data.frame") %in% class(tibbleResult1)))

  gtResult2 <- tableCohortOverlap(overlap3, type = "gt")
  expect_true("gt_tbl" %in% class(gtResult2))

  mockDisconnect(cdm)
})