tests/testthat/test-derive_var_dthcaus.R
In Roche-GSK/admiral: ADaM in R Asset Library
## Test 1: deprecation message if function is called ----
test_that("derive_var_dthcaus Test 1: deprecation message if function is called", {
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
expect_snapshot({
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
})
})
## Test 2: error on invalid mode ----
test_that("derive_var_dthcaus Test 2: error on invalid mode", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expect_error(dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDTC,
mode = "blah",
dthcaus = AEDECOD
))
})
# derive_var_dthcaus ----
## Test 3: DTHCAUS is added from AE and DS ----
test_that("derive_var_dthcaus Test 3: DTHCAUS is added from AE and DS", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE",
"TEST01", "PAT02", NA,
"TEST01", "PAT03", "SUDDEN DEATH"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 4: `dthcaus` handles symbols and string literals correctly ----
test_that("derive_var_dthcaus Test 4: `dthcaus` handles symbols and string literals correctly", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT02", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = "Adverse Event"
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "Adverse Event",
"TEST01", "PAT02", "DEATH DUE TO PROGRESSION OF DISEASE"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 5: traceability variables are added from AE and DS ----
test_that("derive_var_dthcaus Test 5: traceability variables are added from AE and DS", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD,
set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM,
set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS, ~DTHDOM, ~DTHSEQ,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE", "DS", 4,
"TEST01", "PAT02", NA, NA, NA,
"TEST01", "PAT03", "SUDDEN DEATH", "AE", 12
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 6: DTHCAUS/traceabiity are added from 2 input datasets ----
test_that("derive_var_dthcaus Test 6: DTHCAUS/traceabiity are added from 2 input datasets", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 14, "SUDDEN DEATH", "FATAL", "2021-04-04",
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2021-02-03",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD,
set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM,
set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS, ~DTHDOM, ~DTHSEQ,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE", "DS", 4,
"TEST01", "PAT02", NA, NA, NA,
"TEST01", "PAT03", "SUDDEN DEATH", "AE", 12
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 7: DTHCAUS is added from AE and DS if filter is not specified ----
test_that("derive_var_dthcaus Test 7: DTHCAUS is added from AE and DS if filter is not specified", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
# test based on covr report - the case for unspecified filter has not been tested
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = NULL,
date = DSSTDT,
mode = "first",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "INFORMED CONSENT OBTAINED",
"TEST01", "PAT02", "INFORMED CONSENT OBTAINED",
"TEST01", "PAT03", "INFORMED CONSENT OBTAINED"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 8: error on a dthcaus_source object with invalid order ----
test_that("derive_var_dthcaus Test 8: error on a dthcaus_source object with invalid order", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expect_error(dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDTC,
order = c(AESEQ),
mode = "first",
dthcaus = AEDECOD
))
})
## Test 9: `dataset` is sorted using the `order` parameter ----
test_that("derive_var_dthcaus Test 9: `dataset` is sorted using the `order` parameter", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-02-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "DEATH", "DEATH DUE TO ADVERSE EVENT", "2022-02-02",
"TEST01", "PAT02", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-02"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = "Adverse Event"
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
order = exprs(DSSEQ),
mode = "last",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "Adverse Event",
"TEST01", "PAT02", "DEATH DUE TO PROGRESSION OF DISEASE"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 10: multiple observations from different sources ----
test_that("derive_var_dthcaus Test 10: multiple observations from different sources", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expected <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "SUDDEN DEATH",
"TEST01", "PAT02", NA_character_,
"TEST01", "PAT03", "DEATH DUE TO progression of disease"
)
adsl <- select(expected, -DTHCAUS)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2021-04-05",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "DEATH", "DEATH DUE TO progression of disease", "2021-04-07",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
# Derive `DTHCAUS` only - for on-study deaths only
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = convert_dtc_to_dt(AEDTHDTC),
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = DSTERM
)
actual <- adsl %>%
derive_var_dthcaus(src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID")
)
})
## Test 11: multiple observations with same date ----
test_that("derive_var_dthcaus Test 11: multiple observations with same date", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expected <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "SUDDEN DEATH",
"TEST01", "PAT02", NA_character_,
"TEST01", "PAT03", "DEATH DUE TO progression of disease"
)
adsl <- select(expected, -DTHCAUS)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-05"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2021-04-05",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "DEATH", "DEATH DUE TO progression of disease", "2021-04-07",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
# Derive `DTHCAUS` only - for on-study deaths only
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = convert_dtc_to_dt(AEDTHDTC),
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = DSTERM
)
actual <- adsl %>%
derive_var_dthcaus(src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID")
)
})
## Test 12: error if source dataset is not available ----
test_that("derive_var_dthcaus Test 12: error if source dataset is not available", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
expect_snapshot(
derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, dd = ds),
src_ae, src_ds
),
error = TRUE
)
})
Roche-GSK/admiral documentation built on April 14, 2025, 12:36 p.m.
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## Test 1: deprecation message if function is called ----
test_that("derive_var_dthcaus Test 1: deprecation message if function is called", {
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
expect_snapshot({
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
})
})
## Test 2: error on invalid mode ----
test_that("derive_var_dthcaus Test 2: error on invalid mode", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expect_error(dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDTC,
mode = "blah",
dthcaus = AEDECOD
))
})
# derive_var_dthcaus ----
## Test 3: DTHCAUS is added from AE and DS ----
test_that("derive_var_dthcaus Test 3: DTHCAUS is added from AE and DS", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE",
"TEST01", "PAT02", NA,
"TEST01", "PAT03", "SUDDEN DEATH"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 4: `dthcaus` handles symbols and string literals correctly ----
test_that("derive_var_dthcaus Test 4: `dthcaus` handles symbols and string literals correctly", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT02", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = "Adverse Event"
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "Adverse Event",
"TEST01", "PAT02", "DEATH DUE TO PROGRESSION OF DISEASE"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 5: traceability variables are added from AE and DS ----
test_that("derive_var_dthcaus Test 5: traceability variables are added from AE and DS", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD,
set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM,
set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS, ~DTHDOM, ~DTHSEQ,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE", "DS", 4,
"TEST01", "PAT02", NA, NA, NA,
"TEST01", "PAT03", "SUDDEN DEATH", "AE", 12
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 6: DTHCAUS/traceabiity are added from 2 input datasets ----
test_that("derive_var_dthcaus Test 6: DTHCAUS/traceabiity are added from 2 input datasets", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 14, "SUDDEN DEATH", "FATAL", "2021-04-04",
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2021-02-03",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD,
set_values_to = exprs(DTHDOM = "AE", DTHSEQ = AESEQ)
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
mode = "first",
dthcaus = DSTERM,
set_values_to = exprs(DTHDOM = "DS", DTHSEQ = DSSEQ)
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS, ~DTHDOM, ~DTHSEQ,
"TEST01", "PAT01", "DEATH DUE TO PROGRESSION OF DISEASE", "DS", 4,
"TEST01", "PAT02", NA, NA, NA,
"TEST01", "PAT03", "SUDDEN DEATH", "AE", 12
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 7: DTHCAUS is added from AE and DS if filter is not specified ----
test_that("derive_var_dthcaus Test 7: DTHCAUS is added from AE and DS if filter is not specified", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
# test based on covr report - the case for unspecified filter has not been tested
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = NULL,
date = DSSTDT,
mode = "first",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "INFORMED CONSENT OBTAINED",
"TEST01", "PAT02", "INFORMED CONSENT OBTAINED",
"TEST01", "PAT03", "INFORMED CONSENT OBTAINED"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 8: error on a dthcaus_source object with invalid order ----
test_that("derive_var_dthcaus Test 8: error on a dthcaus_source object with invalid order", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expect_error(dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDTC,
order = c(AESEQ),
mode = "first",
dthcaus = AEDECOD
))
})
## Test 9: `dataset` is sorted using the `order` parameter ----
test_that("derive_var_dthcaus Test 9: `dataset` is sorted using the `order` parameter", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-02-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "DEATH", "DEATH DUE TO ADVERSE EVENT", "2022-02-02",
"TEST01", "PAT02", 4, "DEATH", "DEATH DUE TO PROGRESSION OF DISEASE", "2022-02-02"
) %>%
mutate(
DSSTDT = ymd(DSSTDTC)
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = "Adverse Event"
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = DSSTDT,
order = exprs(DSSEQ),
mode = "last",
dthcaus = DSTERM
)
expected_output <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "Adverse Event",
"TEST01", "PAT02", "DEATH DUE TO PROGRESSION OF DISEASE"
)
actual_output <- derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, ds = ds),
src_ae, src_ds
)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 10: multiple observations from different sources ----
test_that("derive_var_dthcaus Test 10: multiple observations from different sources", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expected <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "SUDDEN DEATH",
"TEST01", "PAT02", NA_character_,
"TEST01", "PAT03", "DEATH DUE TO progression of disease"
)
adsl <- select(expected, -DTHCAUS)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2021-04-05",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "DEATH", "DEATH DUE TO progression of disease", "2021-04-07",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
# Derive `DTHCAUS` only - for on-study deaths only
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = convert_dtc_to_dt(AEDTHDTC),
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = DSTERM
)
actual <- adsl %>%
derive_var_dthcaus(src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID")
)
})
## Test 11: multiple observations with same date ----
test_that("derive_var_dthcaus Test 11: multiple observations with same date", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
expected <- tibble::tribble(
~STUDYID, ~USUBJID, ~DTHCAUS,
"TEST01", "PAT01", "SUDDEN DEATH",
"TEST01", "PAT02", NA_character_,
"TEST01", "PAT03", "DEATH DUE TO progression of disease"
)
adsl <- select(expected, -DTHCAUS)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT01", 12, "SUDDEN DEATH", "FATAL", "2021-04-05"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2021-04-05",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "DEATH", "DEATH DUE TO progression of disease", "2021-04-07",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
# Derive `DTHCAUS` only - for on-study deaths only
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = convert_dtc_to_dt(AEDTHDTC),
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = DSTERM
)
actual <- adsl %>%
derive_var_dthcaus(src_ae, src_ds, source_datasets = list(ae = ae, ds = ds))
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID")
)
})
## Test 12: error if source dataset is not available ----
test_that("derive_var_dthcaus Test 12: error if source dataset is not available", {
# Suppress lifecycle messages within the test environment
withr::local_options(list(lifecycle_verbosity = "quiet"))
adsl <- tibble::tribble(
~STUDYID, ~USUBJID,
"TEST01", "PAT01",
"TEST01", "PAT02",
"TEST01", "PAT03"
)
ae <- tibble::tribble(
~STUDYID, ~USUBJID, ~AESEQ, ~AEDECOD, ~AEOUT, ~AEDTHDTC,
"TEST01", "PAT03", 12, "SUDDEN DEATH", "FATAL", "2021-04-04"
) %>%
mutate(
AEDTHDT = ymd(AEDTHDTC)
)
ds <- tibble::tribble(
~STUDYID, ~USUBJID, ~DSSEQ, ~DSDECOD, ~DSTERM, ~DSSTDTC,
"TEST01", "PAT01", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-01",
"TEST01", "PAT01", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT01", 3, "ADVERSE EVENT", "ADVERSE EVENT", "2021-12-01",
"TEST01", "PAT01", 4, "DEATH", "DEATH DUE TO progression of disease", "2022-02-01",
"TEST01", "PAT02", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-02",
"TEST01", "PAT02", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT02", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01",
"TEST01", "PAT03", 1, "INFORMED CONSENT OBTAINED", "INFORMED CONSENT OBTAINED", "2021-04-03",
"TEST01", "PAT03", 2, "RANDOMIZATION", "RANDOMIZATION", "2021-04-11",
"TEST01", "PAT03", 3, "COMPLETED", "PROTOCOL COMPLETED", "2021-12-01"
)
src_ae <- dthcaus_source(
dataset_name = "ae",
filter = AEOUT == "FATAL",
date = AEDTHDT,
mode = "first",
dthcaus = AEDECOD
)
src_ds <- dthcaus_source(
dataset_name = "ds",
filter = DSDECOD == "DEATH" & grepl("DEATH DUE TO", DSTERM),
date = convert_dtc_to_dt(DSSTDTC),
mode = "first",
dthcaus = str_to_upper(DSTERM)
)
expect_snapshot(
derive_var_dthcaus(
adsl,
source_datasets = list(ae = ae, dd = ds),
src_ae, src_ds
),
error = TRUE
)
})
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