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test-derive_blfl.R
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242 lines (212 loc) · 6.14 KB
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dm <- tibble::tribble(
~USUBJID, ~RFSTDTC, ~RFXSTDTC,
"test_study-375", "2020-09-28T10:10", "2020-09-28T10:10",
"test_study-376", "2020-09-21T11:00", "2020-09-21T11:00",
"test_study-377", NA, NA,
"test_study-378", "2020-01-20T10:00", "2020-01-20T10:00",
"test_study-379", NA, NA
)
sdtm_in <-
tibble::tribble(
~DOMAIN, ~oak_id, ~raw_source, ~patient_number, ~USUBJID, ~VSDTC, ~VSTESTCD, ~VSORRES, ~VSSTAT, ~VISIT, ~VSTPT,
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-01T13:31", "DIABP", "90", NA, "SCREENING", "PRE-DOSE",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T11:20", "DIABP", "90", NA, "SCREENING", "30 DAY POST-DOSE",
"VS", 1L, "VTLS1", 375L, "test_study-375", "2020-09-28T10:10", "PULSE", "ND", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 2L, "VTLS1", 375L, "test_study-375", "2020-10-01T13:31", "PULSE", "85", NA, "SCREENING", "30 DAY POST-DOSE",
"VS", 1L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:10", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 2L, "VTLS2", 375L, "test_study-375", "2020-09-28T10:05", "SYSBP", "120", NA, "SCREENING", "28 DAY POST-DOSE",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "DIABP", "75", NA, "SCREENING", "PRE-DOSE",
"VS", 1L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", NA, "NOT DONE", "SCREENING", "PRE-DOSE", # nolint
"VS", 2L, "VTLS1", 376L, "test_study-376", "2020-09-20", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
"VS", 2L, "VTLS1", 378L, "test_study-378", "2020-01-20T10:00", "PULSE", "110", NA, "SCREENING", "PRE-DOSE",
"VS", 3L, "VTLS1", 378L, "test_study-378", "2020-01-21T11:00", "PULSE", "105", NA, "SCREENING", "1 DAY POST-DOSE"
)
d <- list(sdtm_in = sdtm_in, dm = dm)
test_that("derive_blfl example works", {
observed_output <- derive_blfl(
sdtm_in = d$sdtm_in,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC",
baseline_visits = c("SCREENING"),
baseline_timepoints = c("PRE-DOSE")
)
observed_output
expect_snapshot_value(observed_output, style = "json2")
})
test_that("derive_blfl sdmt_in validations work", {
sdmt_in_no_domain <-
d$sdtm_in |>
dplyr::select(-DOMAIN)
expect_snapshot_error(derive_blfl(
sdtm_in = sdmt_in_no_domain,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
sdmt_in_no_id_vars <-
d$sdtm_in |>
dplyr::select(-sdtm.oak::oak_id_vars())
expect_snapshot_error(derive_blfl(
sdtm_in = sdmt_in_no_id_vars,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
sdmt_in_no_vs_vars <-
d$sdtm_in |>
dplyr::select(-c(
"VSORRES",
"VSSTAT",
"VSTESTCD",
"VSDTC"
))
expect_snapshot_error(derive_blfl(
sdtm_in = sdmt_in_no_vs_vars,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
sdmt_in_no_iso <- d$sdtm_in |>
dplyr::mutate(VSDTC = "DUMMY")
expect_snapshot_error(derive_blfl(
sdtm_in = sdmt_in_no_iso,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
})
test_that("derive_blfl dm_domain validations work", {
dm_no_vars <-
d$dm |>
dplyr::select(-c(RFXSTDTC, USUBJID))
expect_snapshot_error(derive_blfl(
sdtm_in = d$sdtm_in,
dm_domain = dm_no_vars,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
})
test_that("derive_blfl tgt_var and ref_var validations work", {
expect_snapshot_error(derive_blfl(
sdtm_in = d$sdtm_in,
dm_domain = d$dm,
tgt_var = list("bad"),
ref_var = "RFXSTDTC"
))
expect_snapshot_error(derive_blfl(
sdtm_in = d$sdtm_in,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = d$dm
))
expect_snapshot_error(derive_blfl(
sdtm_in = d$sdtm_in,
dm_domain = d$dm,
tgt_var = "DMLOBXFL",
ref_var = "RFXSTDTC"
))
})
test_that("derive_blfl DOMAIN validation works", {
sdtm_in_bad_domain <-
d$sdtm_in |>
dplyr::mutate(DOMAIN = 4L)
expect_snapshot_error(derive_blfl(
sdtm_in = sdtm_in_bad_domain,
dm_domain = d$dm,
tgt_var = "VSLOBXFL",
ref_var = "RFXSTDTC"
))
})
test_that("`dtc_datepart`: basic usage", {
expect_identical(
dtc_datepart(
c(NA, "", "2021", "2021-12", "2021-12-25", "2021-12-25T12:00:00")
),
c(NA, NA, NA, NA, "2021-12-25", "2021-12-25")
)
## Prevent partial or missing dates from being set to NA
expect_identical(
dtc_datepart(
c(NA, "", "2021", "2021-12", "2021-12-25", "2021-12-25T12:00:00"),
partial_as_na = FALSE
),
c(NA, "", "2021", "2021-12", "2021-12-25", "2021-12-25")
)
})
test_that("`dtc_timepart`: basic usage", {
# Partial or missing times set to NA and seconds ignored by default
expect_identical(dtc_timepart(
c(
NA,
"",
"2021-12-25",
"2021-12-25T12",
"2021-12-25T12:30",
"2021-12-25T12:30:59"
)
), c(NA, NA, NA, NA, "12:30", "12:30"))
# Prevent partial or missing times from being set to NA
expect_identical(
dtc_timepart(
c(
NA,
"",
"2021-12-25",
"2021-12-25T12",
"2021-12-25T12:30",
"2021-12-25T12:30:59"
),
partial_as_na = FALSE
),
c(NA, "", "", "12", "12:30", "12:30")
)
# Do not ignore seconds, partial or missing times set to NA
expect_identical(
dtc_timepart(
c(
NA,
"",
"2021-12-25",
"2021-12-25T12",
"2021-12-25T12:30",
"2021-12-25T12:30:59"
),
ignore_seconds = FALSE
),
c(NA, NA, NA, NA, NA, "12:30:59")
)
# Do not ignore seconds and prevent partial or missing times from being set to NA
expect_identical(
dtc_timepart(
c(
NA,
"",
"2021-12-25",
"2021-12-25T12",
"2021-12-25T12:30",
"2021-12-25T12:30:59"
),
partial_as_na = FALSE,
ignore_seconds = FALSE
),
c(NA, "", "", "12", "12:30", "12:30:59")
)
})
test_that("`is_iso8601`: basic usage", {
dtc_var <- c(
NA,
"",
"2021-12-25",
"2021-12-25T12",
"2021-12-25T12:30",
"2021-12-25T12:30:59"
)
expect_true(is_iso8601(dtc_var))
dtc_var <- c(
NA,
"DUMMY",
"2021-12-25"
)
expect_false(is_iso8601(dtc_var))
})