dm <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03",
"TEST01", "PAT04"
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSCAT, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", "PROTOCOL MILESTONE", "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01", # nolint
"TEST01", "PAT01", "PROTOCOL MILESTONE", "RANDOMIZATION", "RANDOMIZED", "2021-04-11",
"TEST01", "PAT01", "DISPOSITION EVENT", "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", "OTHER EVENT", "DEATH", "DEATH", "2022-02-01",
"TEST01", "PAT02", "PROTOCOL MILESTONE", "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02", # nolint
"TEST01", "PAT02", "PROTOCOL MILESTONE", "RANDOMIZATION", "RANDOMIZED", "2021-04-11",
"TEST01", "PAT02", "DISPOSITION EVENT", "COMPLETED", NA_character_, "2021-12-01",
"TEST01", "PAT02", "OTHER EVENT", "DEATH", "DEATH", "2022-04",
"TEST01", "PAT03", "PROTOCOL MILESTONE", "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02", # nolint
"TEST01", "PAT03", "PROTOCOL MILESTONE", "RANDOMIZATION", "RANDOMIZED", "2021-04-11",
"TEST01", "PAT03", "DISPOSITION EVENT", "PROGRESSIVE DISEASE", "DISEASE PROGRESSION", "2021-05-01", # nolint
"TEST01", "PAT03", "OTHER EVENT", "DEATH", "DEATH", "2022-04",
"TEST01", "PAT04", "PROTOCOL MILESTONE", "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02", # nolint
"TEST01", "PAT04", "PROTOCOL MILESTONE", "RANDOMIZATION", "RANDOMIZED", "2021-04-11"
)
test_that("Derive DCSREAS using default mapping", {
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DCSREAS,
"TEST01", "PAT01", "ADVERSE EVENT",
"TEST01", "PAT02", NA_character_,
"TEST01", "PAT03", "PROGRESSIVE DISEASE",
"TEST01", "PAT04", NA_character_
)
actual_output <- derive_vars_disposition_reason(
dataset = dm,
dataset_ds = ds,
new_var = DCSREAS,
reason_var = DSDECOD,
filter_ds = DSCAT == "DISPOSITION EVENT"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID")
)
})
test_that("Derive DCTREAS, DCTREASP using a study specific mapping", {
format_dctreas <- function(x, y = NULL) {
out <- if (is.null(y)) x else y
case_when(
x %notin% c("COMPLETED", "SCREEN FAILURE") & !is.na(x) ~ out,
TRUE ~ NA_character_
)
}
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DCTREAS, ~DCTREASP,
"TEST01", "PAT01", "ADVERSE EVENT", "ADVERSE EVENT",
"TEST01", "PAT02", NA_character_, NA_character_,
"TEST01", "PAT03", "PROGRESSIVE DISEASE", "DISEASE PROGRESSION",
"TEST01", "PAT04", NA_character_, NA_character_
)
actual_output <- derive_vars_disposition_reason(
dataset = dm,
dataset_ds = ds,
new_var = DCTREAS,
reason_var = DSDECOD,
new_var_spe = DCTREASP,
reason_var_spe = DSTERM,
format_new_var = format_dctreas,
filter_ds = DSCAT == "DISPOSITION EVENT"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID")
)
})
test_that("derive_vars_disposition_reason checks new_var_spe and reason_var_spe", {
expect_error(
derive_vars_disposition_reason(
dataset = dm,
dataset_ds = ds,
new_var = DCSREAS,
new_var_spe = DCTREASP,
reason_var = DSDECOD,
filter_ds = DSCAT == "DISPOSITION EVENT"
),
regexp = paste(
"^`new_var_spe` is specified as .* but `reason_var_spe` is NULL.",
"Please specify `reason_var_spe` together with `new_var_spe`."
)
)
})
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