tests/testthat/test-set_limit_data_by.R

In atorus-research/Tplyr: A Traceability Focused Grammar of Clinical Data Summary

test_that("Descriptive statistics data limiting works properly", {
  t1 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_desc(AVAL, by = vars(PECAT, PARAM, AVISIT))
    )

  x1 <- build(t1)

  cnts1 <- dplyr::count(x1, row_label1, row_label2)
  expect_equal(cnts1$n, c(18, 18, 18, 18))

  t2 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_desc(AVAL, by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PARAM, AVISIT)
    )

  x2 <- build(t2)

  cnts2 <- dplyr::count(x2, row_label1, row_label2)
  expect_equal(cnts2$n, c(6, 18, 6, 18))


  t3 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_desc(AVAL, by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PECAT, PARAM, AVISIT)
    )

  x3 <- build(t3)

  cnts3 <- dplyr::count(x3, row_label1, row_label2)
  expect_equal(cnts3$n, c(6, 18, 18))
})


test_that("Shift layers can also handle data limiting", {

  t1 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_shift(vars(row=BASEC, column=AVALC), by = vars(PECAT, PARAM, AVISIT))
    )

  x1 <- build(t1)

  cnts1 <- dplyr::count(x1, row_label1, row_label2)
  expect_equal(cnts1$n, c(9, 9, 9, 9))

  t2 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_shift(vars(row=BASEC, column=AVALC), by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PARAM, AVISIT)
    )

  x2 <- build(t2)

  cnts2 <- dplyr::count(x2, row_label1, row_label2)
  expect_equal(cnts2$n, c(3, 9, 3, 9))

  t3 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_shift(vars(row=BASEC, column=AVALC), by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PECAT, PARAM, AVISIT)
    )

  x3 <- build(t3)

  cnts3 <- dplyr::count(x3, row_label1, row_label2)
  expect_equal(cnts3$n, c(3, 9, 9))

})


test_that("Count data limiting works properly", {

  t1 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_count(AVALC, by = vars(PECAT, PARAM, AVISIT))
    )

  x1 <- build(t1)

  cnts1 <- dplyr::count(x1, row_label1, row_label2)
  expect_equal(cnts1$n, c(9, 9, 9, 9))

  t2 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_count(AVALC, by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PARAM, AVISIT)
    )

  x2 <- build(t2)

  cnts2 <- dplyr::count(x2, row_label1, row_label2)
  expect_equal(cnts2$n, c(3, 9, 3, 9))

  t3 <- tplyr_table(tplyr_adpe, TRT01A) %>%
    add_layer(
      group_count(AVALC, by = vars(PECAT, PARAM, AVISIT)) %>%
        set_limit_data_by(PECAT, PARAM, AVISIT)
    )

  x3 <- build(t3)

  cnts3 <- dplyr::count(x3, row_label1, row_label2)
  expect_equal(cnts3$n, c(3, 9, 9))
})


test_that("Nested count layers limit data accurately", {

  t_ae1 <- tplyr_table(tplyr_adae, TRTA) %>%
    add_layer(
      group_count(vars(AEBODSYS, AEDECOD), by = vars(AESEV, AEOUT)) %>%
        set_limit_data_by(AEOUT, AEDECOD)
    )

  t_ae_df1 <- t_ae1 %>%
    build() %>% select(-starts_with('ord'))

  t_ae2 <- tplyr_table(tplyr_adae, TRTA) %>%
    add_layer(
      group_count(vars(AEBODSYS, AEDECOD), by = vars(AESEV, AEOUT)) %>%
        set_limit_data_by(AESEV, AEOUT, AEDECOD)
    )

  t_ae_df2 <- t_ae2 %>%
    build() %>% select(-starts_with('ord'))

  dropped_rows <- anti_join(
    t_ae_df1,
    t_ae_df2,
    by=names(t_ae_df1)
  )

  check <- c(dropped_rows$var1_Placebo, dropped_rows$`var1_Xanomeline High Dose`, dropped_rows$`var1_Xanomeline Low Dose`)
  expect_true(all(check == " 0 (  0.0%)"))
})