test_that("`target` is set to NA when ` start_date` < `ref_start_date`", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT,
"TEST01", "PAT01", as.Date("2021-01-01"), as.Date("2021-01-02")
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~ONTRTFL,
"TEST01", "PAT01", as.Date("2021-01-01"), as.Date("2021-01-02"), as.character(NA)
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to NA when `ref_start_date` is NA", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT,
"TEST01", "PAT01", as.Date("2021-01-01"), as.Date(NA)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~ONTRTFL,
"TEST01", "PAT01", as.Date("2021-01-01"), as.Date(NA), as.character(NA)
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to `Y` when ` start_date` is NA", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT,
"TEST01", "PAT01", as.Date(NA), as.Date("2020-01-01"),
"TEST01", "PAT02", as.Date(NA), as.Date(NA)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~ONTRTFL,
"TEST01", "PAT01", as.Date(NA), as.Date("2020-01-01"), "Y",
"TEST01", "PAT02", as.Date(NA), as.Date(NA), as.character(NA)
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to `Y` when ` start_date` >= `ref_start_date` and
`ref_end_date` and `filter_pre_timepoint` are not specified", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT,
"TEST01", "PAT01", as.Date("2020-01-01"), as.Date("2020-01-01"),
"TEST01", "PAT02", as.Date("2020-01-02"), as.Date("2020-01-01")
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~ONTRTFL,
"TEST01", "PAT01", as.Date("2020-01-01"), as.Date("2020-01-01"), "Y",
"TEST01", "PAT02", as.Date("2020-01-02"), as.Date("2020-01-01"), "Y"
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to 'Y' when `filter_pre_timepoint` is not 'PRE' and
` start_date` = `ref_start_date` and `ref_end_date` is not specified", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TPT,
"TEST01", "PAT01", as.Date("2020-01-01"), as.Date("2020-01-01"), "PRE",
"TEST01", "PAT02", as.Date("2020-01-01"), as.Date("2020-01-01"), "POST"
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TPT, ~ONTRTFL,
"TEST01", "PAT01", as.Date("2020-01-01"), as.Date("2020-01-01"), "PRE", NA,
"TEST01", "PAT02", as.Date("2020-01-01"), as.Date("2020-01-01"), "POST", "Y"
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT,
filter_pre_timepoint = TPT == "PRE"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to `Y` when ` start_date` >= `ref_start_date` and ` start_date` <=
`ref_end_date` and no `ref_end_window` is specified, otherwise NA", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT,
"TEST01", "PAT01", as.Date("2019-12-13"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT02", as.Date("2020-01-01"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT03", as.Date("2020-01-02"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT04", as.Date("2020-02-01"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT05", as.Date("2020-02-02"), as.Date("2020-01-01"), as.Date("2020-02-01")
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, ~ONTRTFL, # nolint
"TEST01", "PAT01", as.Date("2019-12-13"), as.Date("2020-01-01"), as.Date("2020-02-01"), NA,
"TEST01", "PAT02", as.Date("2020-01-01"), as.Date("2020-01-01"), as.Date("2020-02-01"), "Y",
"TEST01", "PAT03", as.Date("2020-01-02"), as.Date("2020-01-01"), as.Date("2020-02-01"), "Y",
"TEST01", "PAT04", as.Date("2020-02-01"), as.Date("2020-01-01"), as.Date("2020-02-01"), "Y",
"TEST01", "PAT05", as.Date("2020-02-02"), as.Date("2020-01-01"), as.Date("2020-02-01"), NA
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to `Y` when ` start_date` >= `ref_start_date` and ` start_date` <=
`ref_end_date` + `ref_end_window`", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT,
"TEST01", "PAT01", as.Date("2020-02-01"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT02", as.Date("2020-02-05"), as.Date("2020-01-01"), as.Date("2020-02-01"),
"TEST01", "PAT03", as.Date("2020-02-10"), as.Date("2020-01-01"), as.Date("2020-02-01")
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ADT, ~TRTSDT, ~TRTEDT, ~ONTRTFL, # nolint
"TEST01", "PAT01", as.Date("2020-02-01"), as.Date("2020-01-01"), as.Date("2020-02-01"), "Y",
"TEST01", "PAT02", as.Date("2020-02-05"), as.Date("2020-01-01"), as.Date("2020-02-01"), "Y",
"TEST01", "PAT03", as.Date("2020-02-10"), as.Date("2020-01-01"), as.Date("2020-02-01"), NA
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ADT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 5
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ADT")
)
})
test_that("`target` is set to NA when `end_date`<`ref_start_date`
regradless of start_date being NA", {
input <- tibble::tribble(
~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT,
"PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2019-03-15"),
"PAT01", NA, ymd("2020-01-01"), ymd("2020-03-01"), ymd("2019-03-15"),
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, ~ONTRTFL,
"PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2019-03-15"), NA_character_,
"PAT01", NA, ymd("2020-01-01"), ymd("2020-03-01"), ymd("2019-03-15"), NA_character_,
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 60
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("USUBJID", "ASTDT")
)
})
test_that("`target` is set to `Y` when `end_date`>`ref_start_date` when `start_date` is missing", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT,
"TEST01", "PAT01", NA, ymd("2020-01-01"), ymd("2020-03-01"), ymd("2021-03-15"),
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, ~ONTRTFL,
"TEST01", "PAT01", NA, ymd("2020-01-01"), ymd("2020-03-01"), ymd("2021-03-15"), "Y"
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 60
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ASTDT")
)
})
test_that("`target` is set to NA when `end_date` is missing and
`start_date` is before `ref_start_date` a la Roche", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA,
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, ~ONTRTFL,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, NA_character_,
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 60
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ASTDT")
)
})
test_that("`target` is set to Y when `end_date` is missing and
`start_date` is before `ref_start_date` a la GSK", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA,
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, ~ONTRTFL,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, "Y",
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 60,
span_period = "Y"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ASTDT")
)
})
test_that("`target` is set to Y when `end_date` is missing and
`start_date` is before `ref_start_date` a la GSK", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA,
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~TRTSDT, ~TRTEDT, ~AENDT, ~ONTRTFL,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), NA, "Y",
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTRTFL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = TRTSDT,
ref_end_date = TRTEDT,
ref_end_window = 60,
span_period = "Y"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ASTDT")
)
})
test_that("`target` is set to Y when `start_date` is before `ref_start_date` and
`end_date` is before `ref_end_date` for Period 01", {
input <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"), ymd("2020-03-01"), ymd("2020-03-15")
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~ASTDT, ~AP01SDT, ~AP01EDT, ~AENDT, ~ONTR01FL,
"TEST01", "PAT01", ymd("2019-04-30"), ymd("2020-01-01"),
ymd("2020-03-01"), ymd("2020-03-15"), "Y",
)
actual_output <- derive_var_ontrtfl(
input,
new_var = ONTR01FL,
start_date = ASTDT,
end_date = AENDT,
ref_start_date = AP01SDT,
ref_end_date = AP01EDT,
span_period = "Y"
)
expect_dfs_equal(
expected_output,
actual_output,
keys = c("STUDYID", "USUBJID", "ASTDT")
)
})
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