tests/testthat/test-derive_var_trtemfl.R
In pharmaverse/admiral: ADaM in R Asset Library
expected <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~TRTEMFL, ~TRTEM2FL, ~TRTEM3FL, # nolint
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", NA, NA, NA,
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", NA, NA, NA,
# starting before treatment and ending during treatment
"1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3", NA, "Y", "Y",
"1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1", NA, NA, NA,
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4", "Y", "Y", "Y",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "Y", "Y", "Y",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "Y", "Y", NA,
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "Y", NA, NA,
# missing dates
"1", "", "", "3", "4", "Y", "Y", "Y",
"1", "2021-12-30T09:00", "", "3", "4", NA, "Y", "Y",
"1", "2021-12-30T11:00", "", "3", "3", NA, NA, NA,
"1", "", "2022-01-04T09:00", "3", "4", "Y", "Y", "Y",
"1", "", "2021-12-24T19:00", "3", "4", NA, NA, NA,
"1", "", "2022-06-04T09:00", "3", "4", "Y", "Y", "Y",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", NA, NA, NA,
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", NA, NA, NA,
"2", "2021-12-06T18:00", "", "1", "2", NA, NA, NA
) %>%
mutate(
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", lubridate::ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", lubridate::ymd_hm("2022-04-30T11:30"), ymd_hms(""))
)
adae <- select(expected, -starts_with("TRTEM"))
expected2 <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID, ~TRTEMFL, ~TRTEM2FL,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", NA, NA,
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1", NA, NA,
# starting before treatment and ending during treatment
"1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2", NA, NA,
"1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2", NA, NA,
"1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2", "Y", "Y",
"1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2", "Y", "Y",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3", "Y", "Y",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4", "Y", "Y",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4", "Y", "Y",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4", NA, NA,
# missing dates
"1", "", "", "3", "4", "5", "Y", "Y",
"1", "2021-12-30T09:00", "", "3", "4", "5", NA, NA,
"1", "2021-12-30T11:00", "", "3", "3", "5", NA, NA,
"1", "", "2022-01-04T09:00", "3", "4", "5", "Y", "Y",
"1", "", "2021-12-24T19:00", "3", "4", "5", NA, NA,
"1", "", "2022-06-04T09:00", "3", "4", "5", "Y", "Y",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", "1", NA, NA,
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", NA, NA,
"2", "2021-12-06T18:00", "", "1", "2", "3", NA, NA
) %>%
mutate(
STUDYID = "ABC12345",
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID != "2", lubridate::ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID != "2", lubridate::ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
adae2 <- select(expected2, -starts_with("TRTEM"))
## Test 1: end_window and worsening parameters not specfied ----
test_that("derive_var_trtemfl Test 1: end_window and worsening parameters not specfied", {
expect_dfs_equal(
base = select(expected, -TRTEM2FL, -TRTEM3FL),
comp = derive_var_trtemfl(adae),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 2: with end_window and worsening ----
test_that("derive_var_trtemfl Test 2: with end_window and worsening", {
expect_dfs_equal(
base = select(expected, -TRTEMFL, -TRTEM3FL),
comp = derive_var_trtemfl(
adae,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
initial_intensity = AEITOXGR,
intensity = AETOXGR
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 3: with end_window and worsening within grouping variable----
test_that("derive_var_trtemfl Test 3: with end_window and worsening within grouping variable", {
expect_dfs_equal(
base = select(expected2, -TRTEM2FL),
comp = derive_var_trtemfl(
adae2,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 10,
intensity = AETOXGR,
group_var = AEGRPID
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 4: considering trt end time without grouping variable----
test_that("derive_var_trtemfl Test 4: considering trt end time", {
expect_dfs_equal(
base = select(expected, -TRTEMFL, -TRTEM2FL),
comp = derive_var_trtemfl(
adae,
new_var = TRTEM3FL,
trt_end_date = TRTEDTM,
end_window = 10,
ignore_time_for_trt_end = FALSE,
initial_intensity = AEITOXGR,
intensity = AETOXGR
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 5: considering trt end time with grouping variable----
test_that("derive_var_trtemfl Test 5: considering trt end time", {
expect_dfs_equal(
base = select(expected2, -TRTEMFL),
comp = derive_var_trtemfl(
adae2,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
ignore_time_for_trt_end = FALSE,
intensity = AETOXGR,
group_var = AEGRPID
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 6: error if `end_window` without `trt_end_date` ----
test_that("derive_var_trtemfl Test 6: error if `end_window` without `trt_end_date`", {
expect_snapshot(
derive_var_trtemfl(
adae,
end_window = 10
),
error = TRUE
)
})
## Test 7: error if `initial_intensity` without `intensity` ----
test_that("derive_var_trtemfl Test 7: error if `initial_intensity` without `intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae,
initial_intensity = AEITOXGR
),
error = TRUE
)
})
## Test 8: error if `intensity` without `initial_intensity` ----
test_that("derive_var_trtemfl Test 8: error if `intensity` without `initial_intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae,
intensity = AETOXGR
),
error = TRUE
)
})
## Test 9: error if `intensity` without `initial_intensity` ----
test_that("derive_var_trtemfl Test 9: error if `intensity` without `initial_intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae2,
intensity = AETOXGR
),
error = TRUE
)
})
## Test 10: warning if both `initial_intensity` and `group_var` are specified ----
test_that("derive_var_trtemfl Test 10: error if `intensity` without `initial_intensity`", {
expect_warning(
derive_var_trtemfl(
adae2,
initial_intensity = AETOXGR,
group_var = AEGRPID
),
"`initial_intensity` argument is ignored when `group_var` is specified"
)
})
## Test 11: error if `group_var` specified without `subject_keys` ----
test_that("derive_var_trtemfl Test 11: error if `group_var` specified without `subject_keys`", {
expect_snapshot(
derive_var_trtemfl(
adae2,
group_var = AEGRPID,
subject_keys = NULL
),
error = TRUE
)
})
# nolint start
## Test 12: Checking test cases from PHUSE White Paper on Treatment Emergent AEs ----
test_that("derive_var_trtemfl Test 12: Checking test cases from PHUSE White Paper on Treatment Emergent AEs", {
adae_phuse <- tribble(
~USUBJID, ~TRTSDTM, ~TRTEDTM, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~TRTEMFL,
# Patient 1: Pre-treatment AE
"1", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
# Patient 2: On-treatment AE
"2", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 3: Pre-treatment AE, then on-treatment AE at same intensity
"3", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"3", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 4: Pre-treatment AE, then on-treatment AE at worsened intensity
"4", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"4", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "3", "Y",
# Patient 5: Pre-treatment AE, then on-treatment AE at improved intensity
"5", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"5", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "1", "Y",
# Patient 6: AE starting pre-treatment and continuing on-treatment, then second AE at same intensity
"6", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"6", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 7: AE starting pre-treatment and continuing on-treatment, then second AE at worsened intensity
"7", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"7", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "3", "Y",
# Patient 8: AE starting pre-treatment and continuing on-treatment, then second AE at improved intensity
"8", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"8", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "1", "Y",
# Patient 9: AE starting pre-treatment and continuing on-treatment, and no change in intensity
"9", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
# Patient 10: AE starting pre-treatment and continuing on-treatment, and worsening intensity
"10", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "4", "Y",
# Patient 11: AE starting pre-treatment and continuing on-treatment, and improving intensity
"11", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "1", NA_character_,
# Patient 12: AE starting pre-treatment, worsening, then improving
"12", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "3", "2", NA_character_,
# Patient 13: AE starting pre-treatment, improving, then worsening
"13", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "1", "2", "Y",
) %>%
mutate(
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = lubridate::ymd_hm(TRTSDTM),
TRTEDTM = lubridate::ymd_hm(TRTEDTM),
)
# nolint end
expect_dfs_equal(
base = adae_phuse,
comp = derive_var_trtemfl(
select(adae_phuse, -TRTEMFL),
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 0,
initial_intensity = AEITOXGR,
intensity = AETOXGR,
subject_keys = exprs(USUBJID)
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
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expected <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~TRTEMFL, ~TRTEM2FL, ~TRTEM3FL, # nolint
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", NA, NA, NA,
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", NA, NA, NA,
# starting before treatment and ending during treatment
"1", "2021-12-30T20:00", "2022-01-14T11:00", "1", "3", NA, "Y", "Y",
"1", "2021-12-31T20:15", "2022-01-01T01:23", "1", "1", NA, NA, NA,
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "3", "4", "Y", "Y", "Y",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "Y", "Y", "Y",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "Y", "Y", NA,
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "Y", NA, NA,
# missing dates
"1", "", "", "3", "4", "Y", "Y", "Y",
"1", "2021-12-30T09:00", "", "3", "4", NA, "Y", "Y",
"1", "2021-12-30T11:00", "", "3", "3", NA, NA, NA,
"1", "", "2022-01-04T09:00", "3", "4", "Y", "Y", "Y",
"1", "", "2021-12-24T19:00", "3", "4", NA, NA, NA,
"1", "", "2022-06-04T09:00", "3", "4", "Y", "Y", "Y",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", NA, NA, NA,
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", NA, NA, NA,
"2", "2021-12-06T18:00", "", "1", "2", NA, NA, NA
) %>%
mutate(
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID == "1", lubridate::ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID == "1", lubridate::ymd_hm("2022-04-30T11:30"), ymd_hms(""))
)
adae <- select(expected, -starts_with("TRTEM"))
expected2 <- tribble(
~USUBJID, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~AEGRPID, ~TRTEMFL, ~TRTEM2FL,
# before treatment
"1", "2021-12-13T20:15", "2021-12-15T12:45", "1", "1", "1", NA, NA,
"1", "2021-12-14T20:15", "2021-12-14T22:00", "1", "3", "1", NA, NA,
# starting before treatment and ending during treatment
"1", "2021-12-30T20:15", "2022-01-14T01:23", "3", "3", "2", NA, NA,
"1", "2022-01-05T20:00", "2022-06-01T11:00", "3", "1", "2", NA, NA,
"1", "2022-01-10T20:15", "2022-01-11T01:23", "3", "2", "2", "Y", "Y",
"1", "2022-01-13T20:15", "2022-03-01T01:23", "3", "1", "2", "Y", "Y",
# starting during treatment
"1", "2022-01-01T12:00", "2022-01-02T23:25", "4", "4", "3", "Y", "Y",
# after treatment
"1", "2022-05-10T11:00", "2022-05-10T13:05", "2", "2", "4", "Y", "Y",
"1", "2022-05-10T12:00", "2022-05-10T13:05", "2", "2", "4", "Y", "Y",
"1", "2022-05-11T11:00", "2022-05-11T13:05", "2", "2", "4", NA, NA,
# missing dates
"1", "", "", "3", "4", "5", "Y", "Y",
"1", "2021-12-30T09:00", "", "3", "4", "5", NA, NA,
"1", "2021-12-30T11:00", "", "3", "3", "5", NA, NA,
"1", "", "2022-01-04T09:00", "3", "4", "5", "Y", "Y",
"1", "", "2021-12-24T19:00", "3", "4", "5", NA, NA,
"1", "", "2022-06-04T09:00", "3", "4", "5", "Y", "Y",
# without treatment
"2", "", "2021-12-03T12:00", "1", "2", "1", NA, NA,
"2", "2021-12-01T12:00", "2021-12-03T12:00", "1", "2", "2", NA, NA,
"2", "2021-12-06T18:00", "", "1", "2", "3", NA, NA
) %>%
mutate(
STUDYID = "ABC12345",
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = if_else(USUBJID != "2", lubridate::ymd_hm("2022-01-01T01:01"), ymd_hms("")),
TRTEDTM = if_else(USUBJID != "2", lubridate::ymd_hm("2022-04-30T23:59"), ymd_hms(""))
)
adae2 <- select(expected2, -starts_with("TRTEM"))
## Test 1: end_window and worsening parameters not specfied ----
test_that("derive_var_trtemfl Test 1: end_window and worsening parameters not specfied", {
expect_dfs_equal(
base = select(expected, -TRTEM2FL, -TRTEM3FL),
comp = derive_var_trtemfl(adae),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 2: with end_window and worsening ----
test_that("derive_var_trtemfl Test 2: with end_window and worsening", {
expect_dfs_equal(
base = select(expected, -TRTEMFL, -TRTEM3FL),
comp = derive_var_trtemfl(
adae,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
initial_intensity = AEITOXGR,
intensity = AETOXGR
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 3: with end_window and worsening within grouping variable----
test_that("derive_var_trtemfl Test 3: with end_window and worsening within grouping variable", {
expect_dfs_equal(
base = select(expected2, -TRTEM2FL),
comp = derive_var_trtemfl(
adae2,
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 10,
intensity = AETOXGR,
group_var = AEGRPID
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 4: considering trt end time without grouping variable----
test_that("derive_var_trtemfl Test 4: considering trt end time", {
expect_dfs_equal(
base = select(expected, -TRTEMFL, -TRTEM2FL),
comp = derive_var_trtemfl(
adae,
new_var = TRTEM3FL,
trt_end_date = TRTEDTM,
end_window = 10,
ignore_time_for_trt_end = FALSE,
initial_intensity = AEITOXGR,
intensity = AETOXGR
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 5: considering trt end time with grouping variable----
test_that("derive_var_trtemfl Test 5: considering trt end time", {
expect_dfs_equal(
base = select(expected2, -TRTEMFL),
comp = derive_var_trtemfl(
adae2,
new_var = TRTEM2FL,
trt_end_date = TRTEDTM,
end_window = 10,
ignore_time_for_trt_end = FALSE,
intensity = AETOXGR,
group_var = AEGRPID
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
## Test 6: error if `end_window` without `trt_end_date` ----
test_that("derive_var_trtemfl Test 6: error if `end_window` without `trt_end_date`", {
expect_snapshot(
derive_var_trtemfl(
adae,
end_window = 10
),
error = TRUE
)
})
## Test 7: error if `initial_intensity` without `intensity` ----
test_that("derive_var_trtemfl Test 7: error if `initial_intensity` without `intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae,
initial_intensity = AEITOXGR
),
error = TRUE
)
})
## Test 8: error if `intensity` without `initial_intensity` ----
test_that("derive_var_trtemfl Test 8: error if `intensity` without `initial_intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae,
intensity = AETOXGR
),
error = TRUE
)
})
## Test 9: error if `intensity` without `initial_intensity` ----
test_that("derive_var_trtemfl Test 9: error if `intensity` without `initial_intensity`", {
expect_snapshot(
derive_var_trtemfl(
adae2,
intensity = AETOXGR
),
error = TRUE
)
})
## Test 10: warning if both `initial_intensity` and `group_var` are specified ----
test_that("derive_var_trtemfl Test 10: error if `intensity` without `initial_intensity`", {
expect_warning(
derive_var_trtemfl(
adae2,
initial_intensity = AETOXGR,
group_var = AEGRPID
),
"`initial_intensity` argument is ignored when `group_var` is specified"
)
})
## Test 11: error if `group_var` specified without `subject_keys` ----
test_that("derive_var_trtemfl Test 11: error if `group_var` specified without `subject_keys`", {
expect_snapshot(
derive_var_trtemfl(
adae2,
group_var = AEGRPID,
subject_keys = NULL
),
error = TRUE
)
})
# nolint start
## Test 12: Checking test cases from PHUSE White Paper on Treatment Emergent AEs ----
test_that("derive_var_trtemfl Test 12: Checking test cases from PHUSE White Paper on Treatment Emergent AEs", {
adae_phuse <- tribble(
~USUBJID, ~TRTSDTM, ~TRTEDTM, ~ASTDTM, ~AENDTM, ~AEITOXGR, ~AETOXGR, ~TRTEMFL,
# Patient 1: Pre-treatment AE
"1", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
# Patient 2: On-treatment AE
"2", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 3: Pre-treatment AE, then on-treatment AE at same intensity
"3", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"3", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 4: Pre-treatment AE, then on-treatment AE at worsened intensity
"4", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"4", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "3", "Y",
# Patient 5: Pre-treatment AE, then on-treatment AE at improved intensity
"5", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-20T00:00", "2020-12-21T00:00", "2", "2", NA_character_,
"5", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "1", "Y",
# Patient 6: AE starting pre-treatment and continuing on-treatment, then second AE at same intensity
"6", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"6", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "2", "Y",
# Patient 7: AE starting pre-treatment and continuing on-treatment, then second AE at worsened intensity
"7", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"7", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "3", "Y",
# Patient 8: AE starting pre-treatment and continuing on-treatment, then second AE at improved intensity
"8", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
"8", "2021-01-01T00:01", "2021-12-31T23:59", "2021-12-20T00:00", "2021-12-21T00:00", "2", "1", "Y",
# Patient 9: AE starting pre-treatment and continuing on-treatment, and no change in intensity
"9", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "2", NA_character_,
# Patient 10: AE starting pre-treatment and continuing on-treatment, and worsening intensity
"10", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "4", "Y",
# Patient 11: AE starting pre-treatment and continuing on-treatment, and improving intensity
"11", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "2", "1", NA_character_,
# Patient 12: AE starting pre-treatment, worsening, then improving
"12", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "3", "2", NA_character_,
# Patient 13: AE starting pre-treatment, improving, then worsening
"13", "2021-01-01T00:01", "2021-12-31T23:59", "2020-12-23T00:00", "2021-01-21T00:00", "1", "2", "Y",
) %>%
mutate(
ASTDTM = lubridate::ymd_hm(ASTDTM),
AENDTM = lubridate::ymd_hm(AENDTM),
TRTSDTM = lubridate::ymd_hm(TRTSDTM),
TRTEDTM = lubridate::ymd_hm(TRTEDTM),
)
# nolint end
expect_dfs_equal(
base = adae_phuse,
comp = derive_var_trtemfl(
select(adae_phuse, -TRTEMFL),
new_var = TRTEMFL,
trt_end_date = TRTEDTM,
end_window = 0,
initial_intensity = AEITOXGR,
intensity = AETOXGR,
subject_keys = exprs(USUBJID)
),
keys = c("USUBJID", "ASTDTM", "AENDTM")
)
})
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