tests/testthat/test-independent-testing-tlf_ae_specific.R

In Merck/metalite.ae: Adverse Events Analysis Using 'metalite'

meta <- meta_ae_example()
outdata <- prepare_ae_specific(meta,
  population = "apat",
  observation = "wk12",
  parameter = "rel"
)


test_that("rtf output: events, dur, n, and prop w/o total", {
  path_rtf <- file.path(tempdir(), "ednp_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  tbl <- outdata |>
    extend_ae_specific_events() |>
    extend_ae_specific_duration(duration_var = "ADURN") |>
    format_ae_specific(
      display = c("events_avg", "dur", "n", "prop"),
      mock = TRUE
    ) |>
    tlf_ae_specific(
      meddra_version = "24.0",
      source = "Source:  [CDISCpilot: adam-adsl; adae]",
      analysis = "ae_specific",
      path_outdata = path_rdata,
      path_outtable = path_rtf
    )

  testthat::expect_snapshot_file(path_rtf)
})

test_that("rtf output: events, dur, n, and prop w/ total", {
  path_rtf <- file.path(tempdir(), "ednpt_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  tbl <- outdata |>
    extend_ae_specific_events() |>
    extend_ae_specific_duration(duration_var = "ADURN") |>
    format_ae_specific(
      display = c("events_avg", "dur", "n", "prop", "total"),
      mock = TRUE
    ) |>
    tlf_ae_specific(
      meddra_version = "24.0",
      source = "Source:  [CDISCpilot: adam-adsl; adae]",
      analysis = "ae_specific",
      path_outdata = path_rdata,
      path_outtable = path_rtf
    )

  testthat::expect_snapshot_file(path_rtf)
})


test_that("rtf output: diff, events, dur, n, and prop w/o total", {
  path_rtf <- file.path(tempdir(), "diednp_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  tbl <- outdata |>
    extend_ae_specific_inference() |>
    extend_ae_specific_events() |>
    extend_ae_specific_duration(duration_var = "ADURN") |>
    format_ae_specific(display = c(
      "events_avg", "dur", "n", "prop",
      "diff", "diff_p", "diff_ci"
    ), mock = TRUE) |>
    tlf_ae_specific(
      meddra_version = "24.0",
      source = "Source:  [CDISCpilot: adam-adsl; adae]",
      analysis = "ae_specific",
      path_outdata = path_rdata,
      path_outtable = path_rtf
    )

  testthat::expect_snapshot_file(path_rtf)
})

test_that("rtf output: diff, events, dur, n, and prop w/ total", {
  path_rtf <- file.path(tempdir(), "diednpt_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  tbl <- outdata |>
    extend_ae_specific_inference() |>
    extend_ae_specific_events() |>
    extend_ae_specific_duration(duration_var = "ADURN") |>
    format_ae_specific(display = c(
      "events_avg", "dur", "n", "prop", "total",
      "diff", "diff_p", "diff_ci"
    ), mock = TRUE) |>
    tlf_ae_specific(
      meddra_version = "24.0",
      source = "Source:  [CDISCpilot: adam-adsl; adae]",
      analysis = "ae_specific",
      col_rel_width = c(5, rep(c(1, 2, 3, 3), 4), 1, 2, 3, 1, 2, 3),
      path_outdata = path_rdata,
      path_outtable = path_rtf
    )

  testthat::expect_snapshot_file(path_rtf)
})


test_that("rtf output: events, dur, n, and prop w/ total", {
  path_rtf <- file.path(tempdir(), "incprop_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  tbl <- outdata |>
    extend_ae_specific_events() |>
    extend_ae_specific_duration(duration_var = "ADURN") |>
    format_ae_specific(
      display = c("events_avg", "events_count", "dur", "n", "prop", "total"),
      filter_method = "percent",
      filter_criteria = 2,
      mock = TRUE
    ) |>
    tlf_ae_specific(
      meddra_version = "24.0",
      source = "Source:  [CDISCpilot: adam-adsl; adae]",
      analysis = "ae_specific",
      path_outdata = path_rdata,
      path_outtable = path_rtf
    )

  testthat::expect_snapshot_file(path_rtf)
})

#
# test_that("rtf output: diff, n, and prop w/ total", {
#   path_rtf <- file.path(tempdir(), "dinpt_ae0specific1.rtf")
#   path_rdata <- tempfile(fileext = '.Rdata')
#
#   tbl <- outdata |>
#     extend_ae_specific_inference() |>
#     format_ae_specific(display = c("n", "prop", "total",
#       "diff", "diff_p", "diff_ci")) |>
#     tlf_ae_specific(
#       meddra_version = "24.0",
#       source = "Source:  [CDISCpilot: adam-adsl; adae]",
#       path_outdata =  path_rdata,
#       path_outtable =  path_rtf
#     )
#
#   testthat::expect_snapshot_file(path_rtf)
# })
#
# test_that("rtf output: diff, n, and prop w/o total", {
#   path_rtf <- file.path(tempdir(), "dinp_ae0specific1.rtf")
#   path_rdata <- tempfile(fileext = '.Rdata')
#
#   tbl <- outdata |>
#     extend_ae_specific_inference() |>
#     format_ae_specific(display = c("n", "prop", "total",
#       "diff", "diff_p", "diff_ci")) |>
#     tlf_ae_specific(
#       meddra_version = "24.0",
#       source = "Source:  [CDISCpilot: adam-adsl; adae]",
#       path_outdata =  path_rdata,
#       path_outtable =  path_rtf
#     )
#
#   testthat::expect_snapshot_file(path_rtf)
# })

test_that("relative width 'works'", {
  path_rtf <- file.path(tempdir(), "dinp_ae0specific1.rtf")
  path_rdata <- tempfile(fileext = ".Rdata")

  expect_error(
    {
      tbl <- outdata |>
        format_ae_specific(display = c("n", "prop"), mock = TRUE) |>
        tlf_ae_specific(
          meddra_version = "24.0",
          source = "Source:  [CDISCpilot: adam-adsl; adae]",
          analysis = "ae_specific",
          path_outdata = path_rdata,
          path_outtable = path_rtf,
          col_rel_width = c(rep(1, 8))
        )
    },
    regexp = "col_rel_width must have the same length"
  )

  expect_message(
    {
      tbl <- outdata |>
        format_ae_specific(display = c("n", "prop"), mock = TRUE) |>
        tlf_ae_specific(
          meddra_version = "24.0",
          source = "Source:  [CDISCpilot: adam-adsl; adae]",
          analysis = "ae_specific",
          path_outdata = path_rdata,
          path_outtable = path_rtf,
          col_rel_width = c(rep(1, 7))
        )
    },
    regexp = "The outdata is saved"
  )
})