tests/testthat/test-period_dataset.R
In Roche-GSK/admiral: ADaM in R Asset Library
# create_period_dataset ----
## Test 1: periods ----
test_that("create_period_dataset Test 1: periods", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)
),
keys = c("USUBJID", "APERIOD")
)
})
## Test 2: phases ----
test_that("create_period_dataset Test 2: phases", {
adsl <- tibble::tribble(
~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
"2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA
) %>%
mutate(
dplyr::across(matches("PH\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE,
"1", 1, "2021-01-04", "2021-02-06", "TREATMENT",
"1", 2, "2021-02-07", "2021-03-07", "FUP",
"2", 1, "2021-02-02", "2021-03-02", "TREATMENT"
) %>%
mutate(
STUDYID = "xyz",
APHASEN = as.integer(APHASEN),
dplyr::across(matches("PH[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw)
),
keys = c("USUBJID", "APHASEN")
)
})
## Test 3: subperiods ----
test_that("create_period_dataset Test 3: subperiods", {
adsl <- tibble::tribble(
~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT,
"1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("PH\\d\\dS\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT,
"1", 1, 1, "2021-01-04", "2021-01-19",
"1", 1, 2, "2021-01-20", "2021-02-06",
"1", 2, 1, "2021-02-07", "2021-03-07",
"2", 1, 1, "2021-02-02", "2021-03-02",
"2", 2, 1, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
ASPER = as.integer(ASPER),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT)
),
keys = c("USUBJID", "APERIOD", "ASPER")
)
})
## Test 4: error if no period/phase variable on RHS ----
test_that("create_period_dataset Test 4: error if no period/phase variable on RHS", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(USUBJ = USUBJID)
),
error = TRUE
)
})
## Test 5: error if different type of RHSs ----
test_that("create_period_dataset Test 5: error if different type of RHSs", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, ASPRSDT = PxxSwSDT)
),
error = TRUE
)
})
## Test 6: error if RHS variable not in input dataset ----
test_that("create_period_dataset Test 6: error if RHS variable not in input dataset", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(PHSDT = PHwSDT)
),
error = TRUE
)
})
# derive_vars_period ----
## Test 7: periods ----
test_that("derive_vars_period Test 7: periods", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT)
),
keys = c("USUBJID")
)
})
## Test 8: phases ----
test_that("derive_vars_period Test 8: phases", {
expected <- tibble::tribble(
~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
"2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA
) %>%
mutate(
dplyr::across(matches("PH\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
phase_ref <- tibble::tribble(
~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE,
"1", 1, "2021-01-04", "2021-02-06", "TREATMENT",
"1", 2, "2021-02-07", "2021-03-07", "FUP",
"2", 1, "2021-02-02", "2021-03-02", "TREATMENT"
) %>%
mutate(
STUDYID = "xyz",
APHASEN = as.integer(APHASEN),
dplyr::across(matches("PH[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = phase_ref,
new_vars = exprs(PHwSDT = PHSDT, PHwEDT = PHEDT, APHASEw = APHASE)
),
keys = c("USUBJID")
)
})
## Test 9: subperiods ----
test_that("derive_vars_period Test 9: subperiods", {
expected <- tibble::tribble(
~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT,
"1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("PH\\d\\dS\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
subperiod_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT,
"1", 1, 1, "2021-01-04", "2021-01-19",
"1", 1, 2, "2021-01-20", "2021-02-06",
"1", 2, 1, "2021-02-07", "2021-03-07",
"2", 1, 1, "2021-02-02", "2021-03-02",
"2", 2, 1, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
ASPER = as.integer(ASPER),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = subperiod_ref,
new_vars = exprs(PxxSwSDT = ASPRSDT, PxxSwEDT = ASPREDT)
),
keys = c("USUBJID")
)
})
## Test 10: error if no period/phase variable on LHS ----
test_that("derive_vars_period Test 10: error if no period/phase variable on LHS", {
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_snapshot(
derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(USUBJ = USUBJID)
),
error = TRUE
)
})
## Test 11: error if different type of LHSs ----
test_that("derive_vars_period Test 11: error if different type of LHSs", {
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_snapshot(
derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, PxxSwSDT = ASPRSDT)
),
error = TRUE
)
})
## Test 12: DT and DTM columns exist, pulls only one unique col ----
test_that("create_period_dataset Test 12: DT and DTM columns exist, pulls only one unique col", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01SDTM, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-01-04T12:00:00", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-02-02T12:00:00", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT\\b"), ymd),
dplyr::across(matches("AP\\d\\d[ES]DTM"), ymd_hms),
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)
),
keys = c("USUBJID", "APERIOD")
)
})
## Test 13: Periods derived even when some variables in dataset_ref are unused ----
test_that("derive_vars_period Test 13: periods", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT,
"1", "2021-01-04", "2021-02-06",
"2", "2021-02-02", "2021-03-02"
) %>%
mutate(
across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, ~APERSDTM, ~APEREDTM,
"1", 1, "2021-01-04", "2021-02-06", "2021-01-04 10:01:02", "2021-02-06 14:03:04",
"2", 1, "2021-02-02", "2021-03-02", "2021-02-02 04:11:34", "2021-03-02 16:55:59"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
APERSDT = ymd(APERSDT),
APEREDT = ymd(APEREDT),
APERSDTM = ymd_hms(APERSDTM),
APEREDTM = ymd_hms(APEREDTM)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT)
),
keys = c("USUBJID")
)
})
## Test 14: periods variable derived when only one variable needed ----
test_that("derive_vars_period Test 14: periods variable derived when only one variable needed", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT,
"1", "2021-01-04",
"2", "2021-02-02",
) %>%
mutate(
across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, ~APERSDTM, ~APEREDTM,
"1", 1, "2021-01-04", "2021-02-06", "2021-01-04 10:01:02", "2021-02-06 14:03:04",
"2", 1, "2021-02-02", "2021-03-02", "2021-02-02 04:11:34", "2021-03-02 16:55:59"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
APERSDT = ymd(APERSDT),
APEREDT = ymd(APEREDT),
APERSDTM = ymd_hms(APERSDTM),
APEREDTM = ymd_hms(APEREDTM)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT)
),
keys = c("USUBJID")
)
})
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# create_period_dataset ----
## Test 1: periods ----
test_that("create_period_dataset Test 1: periods", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)
),
keys = c("USUBJID", "APERIOD")
)
})
## Test 2: phases ----
test_that("create_period_dataset Test 2: phases", {
adsl <- tibble::tribble(
~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
"2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA
) %>%
mutate(
dplyr::across(matches("PH\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE,
"1", 1, "2021-01-04", "2021-02-06", "TREATMENT",
"1", 2, "2021-02-07", "2021-03-07", "FUP",
"2", 1, "2021-02-02", "2021-03-02", "TREATMENT"
) %>%
mutate(
STUDYID = "xyz",
APHASEN = as.integer(APHASEN),
dplyr::across(matches("PH[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(PHSDT = PHwSDT, PHEDT = PHwEDT, APHASE = APHASEw)
),
keys = c("USUBJID", "APHASEN")
)
})
## Test 3: subperiods ----
test_that("create_period_dataset Test 3: subperiods", {
adsl <- tibble::tribble(
~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT,
"1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("PH\\d\\dS\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT,
"1", 1, 1, "2021-01-04", "2021-01-19",
"1", 1, 2, "2021-01-20", "2021-02-06",
"1", 2, 1, "2021-02-07", "2021-03-07",
"2", 1, 1, "2021-02-02", "2021-03-02",
"2", 2, 1, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
ASPER = as.integer(ASPER),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(ASPRSDT = PxxSwSDT, ASPREDT = PxxSwEDT)
),
keys = c("USUBJID", "APERIOD", "ASPER")
)
})
## Test 4: error if no period/phase variable on RHS ----
test_that("create_period_dataset Test 4: error if no period/phase variable on RHS", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(USUBJ = USUBJID)
),
error = TRUE
)
})
## Test 5: error if different type of RHSs ----
test_that("create_period_dataset Test 5: error if different type of RHSs", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, ASPRSDT = PxxSwSDT)
),
error = TRUE
)
})
## Test 6: error if RHS variable not in input dataset ----
test_that("create_period_dataset Test 6: error if RHS variable not in input dataset", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
expect_snapshot(
create_period_dataset(
adsl,
new_vars = exprs(PHSDT = PHwSDT)
),
error = TRUE
)
})
# derive_vars_period ----
## Test 7: periods ----
test_that("derive_vars_period Test 7: periods", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT)
),
keys = c("USUBJID")
)
})
## Test 8: phases ----
test_that("derive_vars_period Test 8: phases", {
expected <- tibble::tribble(
~USUBJID, ~PH1SDT, ~PH1EDT, ~PH2SDT, ~PH2EDT, ~APHASE1, ~APHASE2,
"1", "2021-01-04", "2021-02-06", "2021-02-07", "2021-03-07", "TREATMENT", "FUP",
"2", "2021-02-02", "2021-03-02", NA, NA, "TREATMENT", NA
) %>%
mutate(
dplyr::across(matches("PH\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
phase_ref <- tibble::tribble(
~USUBJID, ~APHASEN, ~PHSDT, ~PHEDT, ~APHASE,
"1", 1, "2021-01-04", "2021-02-06", "TREATMENT",
"1", 2, "2021-02-07", "2021-03-07", "FUP",
"2", 1, "2021-02-02", "2021-03-02", "TREATMENT"
) %>%
mutate(
STUDYID = "xyz",
APHASEN = as.integer(APHASEN),
dplyr::across(matches("PH[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = phase_ref,
new_vars = exprs(PHwSDT = PHSDT, PHwEDT = PHEDT, APHASEw = APHASE)
),
keys = c("USUBJID")
)
})
## Test 9: subperiods ----
test_that("derive_vars_period Test 9: subperiods", {
expected <- tibble::tribble(
~USUBJID, ~P01S1SDT, ~P01S1EDT, ~P01S2SDT, ~P01S2EDT, ~P02S1SDT, ~P02S1EDT,
"1", "2021-01-04", "2021-01-19", "2021-01-20", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-03-02", NA, NA, "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("PH\\d\\dS\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
subperiod_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~ASPER, ~ASPRSDT, ~ASPREDT,
"1", 1, 1, "2021-01-04", "2021-01-19",
"1", 1, 2, "2021-01-20", "2021-02-06",
"1", 2, 1, "2021-02-07", "2021-03-07",
"2", 1, 1, "2021-02-02", "2021-03-02",
"2", 2, 1, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
ASPER = as.integer(ASPER),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = subperiod_ref,
new_vars = exprs(PxxSwSDT = ASPRSDT, PxxSwEDT = ASPREDT)
),
keys = c("USUBJID")
)
})
## Test 10: error if no period/phase variable on LHS ----
test_that("derive_vars_period Test 10: error if no period/phase variable on LHS", {
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_snapshot(
derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(USUBJ = USUBJID)
),
error = TRUE
)
})
## Test 11: error if different type of LHSs ----
test_that("derive_vars_period Test 11: error if different type of LHSs", {
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
adsl <- tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_snapshot(
derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, PxxSwSDT = ASPRSDT)
),
error = TRUE
)
})
## Test 12: DT and DTM columns exist, pulls only one unique col ----
test_that("create_period_dataset Test 12: DT and DTM columns exist, pulls only one unique col", {
adsl <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01SDTM, ~AP01EDT, ~AP02SDT, ~AP02EDT,
"1", "2021-01-04", "2021-01-04T12:00:00", "2021-02-06", "2021-02-07", "2021-03-07",
"2", "2021-02-02", "2021-02-02T12:00:00", "2021-03-02", "2021-03-03", "2021-04-01"
) %>%
mutate(
dplyr::across(matches("AP\\d\\d[ES]DT\\b"), ymd),
dplyr::across(matches("AP\\d\\d[ES]DTM"), ymd_hms),
) %>%
mutate(
STUDYID = "xyz"
)
expected <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT,
"1", 1, "2021-01-04", "2021-02-06",
"1", 2, "2021-02-07", "2021-03-07",
"2", 1, "2021-02-02", "2021-03-02",
"2", 2, "2021-03-03", "2021-04-01"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
dplyr::across(matches("APER[ES]DT"), ymd)
)
expect_dfs_equal(
base = expected,
compare = create_period_dataset(
adsl,
new_vars = exprs(APERSDT = APxxSDT, APEREDT = APxxEDT)
),
keys = c("USUBJID", "APERIOD")
)
})
## Test 13: Periods derived even when some variables in dataset_ref are unused ----
test_that("derive_vars_period Test 13: periods", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT, ~AP01EDT,
"1", "2021-01-04", "2021-02-06",
"2", "2021-02-02", "2021-03-02"
) %>%
mutate(
across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, ~APERSDTM, ~APEREDTM,
"1", 1, "2021-01-04", "2021-02-06", "2021-01-04 10:01:02", "2021-02-06 14:03:04",
"2", 1, "2021-02-02", "2021-03-02", "2021-02-02 04:11:34", "2021-03-02 16:55:59"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
APERSDT = ymd(APERSDT),
APEREDT = ymd(APEREDT),
APERSDTM = ymd_hms(APERSDTM),
APEREDTM = ymd_hms(APEREDTM)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT, APxxEDT = APEREDT)
),
keys = c("USUBJID")
)
})
## Test 14: periods variable derived when only one variable needed ----
test_that("derive_vars_period Test 14: periods variable derived when only one variable needed", {
expected <- tibble::tribble(
~USUBJID, ~AP01SDT,
"1", "2021-01-04",
"2", "2021-02-02",
) %>%
mutate(
across(matches("AP\\d\\d[ES]DT"), ymd)
) %>%
mutate(
STUDYID = "xyz"
)
period_ref <- tibble::tribble(
~USUBJID, ~APERIOD, ~APERSDT, ~APEREDT, ~APERSDTM, ~APEREDTM,
"1", 1, "2021-01-04", "2021-02-06", "2021-01-04 10:01:02", "2021-02-06 14:03:04",
"2", 1, "2021-02-02", "2021-03-02", "2021-02-02 04:11:34", "2021-03-02 16:55:59"
) %>%
mutate(
STUDYID = "xyz",
APERIOD = as.integer(APERIOD),
APERSDT = ymd(APERSDT),
APEREDT = ymd(APEREDT),
APERSDTM = ymd_hms(APERSDTM),
APEREDTM = ymd_hms(APEREDTM)
)
adsl <- tibble::tibble(STUDYID = "xyz", USUBJID = c("1", "2"))
expect_dfs_equal(
base = expected,
compare = derive_vars_period(
adsl,
dataset_ref = period_ref,
new_vars = exprs(APxxSDT = APERSDT)
),
keys = c("USUBJID")
)
})
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