Nothing
tests/testthat/test-derive_param_confirmed_bor.R
In admiralonco: Oncology Extension Package for ADaM in 'R' Asset Library
adsl <- tibble::tribble(
~USUBJID, ~TRTSDTC,
"1", "2020-01-01",
"2", "2019-12-12",
"3", "2019-11-11",
"4", "2019-12-30",
"5", "2020-01-01",
"6", "2020-02-02",
"7", "2020-02-02",
"8", "2020-04-01",
"9", "2020-02-01"
) %>%
mutate(
TRTSDT = lubridate::ymd(TRTSDTC),
STUDYID = "XX1234"
)
adrs <- tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"1", "2020-01-01", "PR",
"1", "2020-02-01", "CR",
"1", "2020-02-16", "NE",
"1", "2020-03-01", "CR",
"1", "2020-04-01", "SD",
"2", "2020-01-01", "SD",
"2", "2020-02-01", "PR",
"2", "2020-03-01", "SD",
"2", "2020-03-13", "CR",
"3", "2019-11-12", "CR",
"3", "2019-12-02", "CR",
"3", "2020-01-01", "SD",
"4", "2020-01-01", "PR",
"4", "2020-03-01", "SD",
"4", "2020-04-01", "SD",
"4", "2020-05-01", "PR",
"4", "2020-05-15", "NON-CR/NON-PD",
"5", "2020-01-01", "PR",
"5", "2020-01-10", "SD",
"5", "2020-01-20", "PR",
"5", "2020-05-15", "NON-CR/NON-PD",
"6", "2020-02-06", "PR",
"6", "2020-02-16", "CR",
"6", "2020-03-30", "PR",
"7", "2020-02-06", "PR",
"7", "2020-02-16", "CR",
"7", "2020-04-01", "NE",
"9", "2020-02-16", "PD",
"9", "2020-03-06", "SD"
) %>%
mutate(PARAMCD = "OVR") %>%
bind_rows(tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"9", "2020-02-16", "Y"
) %>%
mutate(PARAMCD = "PD")) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
pd_date <- admiral::date_source(
dataset_name = "adrs",
date = ADT,
filter = PARAMCD == "PD"
)
# derive_param_confirmed_bor ----
## Test 1: default confirmed BOR ----
test_that("derive_param_confirmed_bor Test 1: default confirmed BOR", {
suppress_warning(
actual <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-02-16", "PD", 5
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 2: accept SD, ND handling, missing as NE ----
test_that("derive_param_confirmed_bor Test 2: accept SD, ND handling, missing as NE", {
adrs_ext <- bind_rows(
filter(adrs, USUBJID != "7"),
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"7", "2020-04-02", "ND"
) %>%
mutate(
PARAMCD = "OVR",
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
suppress_warning(
actual <-
derive_param_confirmed_bor(
adrs_ext,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 14,
max_nr_ne = 0,
accept_sd = TRUE,
missing_as_ne = TRUE,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected <- bind_rows(
adrs_ext,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-01-01", "PR", 2,
"2", "2020-02-01", "PR", 2,
"3", "2019-11-12", "CR", 1,
"4", "2020-03-01", "SD", 3,
"5", "2020-01-01", "PR", 2,
"6", "2020-03-30", "SD", 3,
"7", "2020-04-02", "ND", NA,
"8", NA_character_, "NE", 6,
"9", "2020-02-16", "PD", 5
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 3: error if invalid response values ----
test_that("derive_param_confirmed_bor Test 3: error if invalid response values", {
adrs <- tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"1", "2020-01-01", "PR",
"1", "2020-02-01", "CR",
"1", "2020-02-16", "NE",
"1", "2020-03-01", "iCR",
"1", "2020-04-01", "SD",
) %>%
mutate(
PARAMCD = "OVR",
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
expect_error(
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
regexp = "The following invalid values were found:\n`iCR`"
)
})
## Test 4: No source_pd ----
test_that("derive_param_confirmed_bor Test 4: No source_pd", {
suppress_warning(
actual_no_source_pd <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = NULL,
source_datasets = NULL,
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected_no_source_pd <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-03-06", "SD", 3 # expected is now SD
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected_no_source_pd,
compare = actual_no_source_pd,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 5: Deprecation warning for aval_fun ----
test_that("derive_param_confirmed_bor Test 5: Deprecation warning for aval_fun", {
expect_warning(
suppress_warning(
actual_no_source_pd <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = NULL,
source_datasets = NULL,
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
aval_fun = aval_resp,
set_values_to = exprs(
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
),
class = "lifecycle_warning_deprecated"
)
expected_no_source_pd <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-03-06", "SD", 3 # expected is now SD
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected_no_source_pd,
compare = actual_no_source_pd,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
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adsl <- tibble::tribble(
~USUBJID, ~TRTSDTC,
"1", "2020-01-01",
"2", "2019-12-12",
"3", "2019-11-11",
"4", "2019-12-30",
"5", "2020-01-01",
"6", "2020-02-02",
"7", "2020-02-02",
"8", "2020-04-01",
"9", "2020-02-01"
) %>%
mutate(
TRTSDT = lubridate::ymd(TRTSDTC),
STUDYID = "XX1234"
)
adrs <- tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"1", "2020-01-01", "PR",
"1", "2020-02-01", "CR",
"1", "2020-02-16", "NE",
"1", "2020-03-01", "CR",
"1", "2020-04-01", "SD",
"2", "2020-01-01", "SD",
"2", "2020-02-01", "PR",
"2", "2020-03-01", "SD",
"2", "2020-03-13", "CR",
"3", "2019-11-12", "CR",
"3", "2019-12-02", "CR",
"3", "2020-01-01", "SD",
"4", "2020-01-01", "PR",
"4", "2020-03-01", "SD",
"4", "2020-04-01", "SD",
"4", "2020-05-01", "PR",
"4", "2020-05-15", "NON-CR/NON-PD",
"5", "2020-01-01", "PR",
"5", "2020-01-10", "SD",
"5", "2020-01-20", "PR",
"5", "2020-05-15", "NON-CR/NON-PD",
"6", "2020-02-06", "PR",
"6", "2020-02-16", "CR",
"6", "2020-03-30", "PR",
"7", "2020-02-06", "PR",
"7", "2020-02-16", "CR",
"7", "2020-04-01", "NE",
"9", "2020-02-16", "PD",
"9", "2020-03-06", "SD"
) %>%
mutate(PARAMCD = "OVR") %>%
bind_rows(tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"9", "2020-02-16", "Y"
) %>%
mutate(PARAMCD = "PD")) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
pd_date <- admiral::date_source(
dataset_name = "adrs",
date = ADT,
filter = PARAMCD == "PD"
)
# derive_param_confirmed_bor ----
## Test 1: default confirmed BOR ----
test_that("derive_param_confirmed_bor Test 1: default confirmed BOR", {
suppress_warning(
actual <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-02-16", "PD", 5
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 2: accept SD, ND handling, missing as NE ----
test_that("derive_param_confirmed_bor Test 2: accept SD, ND handling, missing as NE", {
adrs_ext <- bind_rows(
filter(adrs, USUBJID != "7"),
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"7", "2020-04-02", "ND"
) %>%
mutate(
PARAMCD = "OVR",
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
suppress_warning(
actual <-
derive_param_confirmed_bor(
adrs_ext,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 14,
max_nr_ne = 0,
accept_sd = TRUE,
missing_as_ne = TRUE,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected <- bind_rows(
adrs_ext,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-01-01", "PR", 2,
"2", "2020-02-01", "PR", 2,
"3", "2019-11-12", "CR", 1,
"4", "2020-03-01", "SD", 3,
"5", "2020-01-01", "PR", 2,
"6", "2020-03-30", "SD", 3,
"7", "2020-04-02", "ND", NA,
"8", NA_character_, "NE", 6,
"9", "2020-02-16", "PD", 5
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 3: error if invalid response values ----
test_that("derive_param_confirmed_bor Test 3: error if invalid response values", {
adrs <- tibble::tribble(
~USUBJID, ~ADTC, ~AVALC,
"1", "2020-01-01", "PR",
"1", "2020-02-01", "CR",
"1", "2020-02-16", "NE",
"1", "2020-03-01", "iCR",
"1", "2020-04-01", "SD",
) %>%
mutate(
PARAMCD = "OVR",
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
expect_error(
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = pd_date,
source_datasets = list(adrs = adrs),
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
regexp = "The following invalid values were found:\n`iCR`"
)
})
## Test 4: No source_pd ----
test_that("derive_param_confirmed_bor Test 4: No source_pd", {
suppress_warning(
actual_no_source_pd <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = NULL,
source_datasets = NULL,
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
set_values_to = exprs(
AVAL = aval_resp(AVALC),
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
)
expected_no_source_pd <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-03-06", "SD", 3 # expected is now SD
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected_no_source_pd,
compare = actual_no_source_pd,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
## Test 5: Deprecation warning for aval_fun ----
test_that("derive_param_confirmed_bor Test 5: Deprecation warning for aval_fun", {
expect_warning(
suppress_warning(
actual_no_source_pd <-
derive_param_confirmed_bor(
adrs,
dataset_adsl = adsl,
filter_source = PARAMCD == "OVR",
source_pd = NULL,
source_datasets = NULL,
reference_date = TRTSDT,
ref_start_window = 28,
ref_confirm = 28,
aval_fun = aval_resp,
set_values_to = exprs(
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
)
),
"Dataset contains CR records followed by PR"
),
class = "lifecycle_warning_deprecated"
)
expected_no_source_pd <- bind_rows(
adrs,
tibble::tribble(
~USUBJID, ~ADTC, ~AVALC, ~AVAL,
"1", "2020-02-01", "CR", 1,
"2", "2020-02-01", "SD", 3,
"3", "2020-01-01", "SD", 3,
"4", "2020-03-01", "SD", 3,
"5", "2020-05-15", "NON-CR/NON-PD", 4,
"6", "2020-03-30", "SD", 3,
"7", "2020-02-06", "NE", 6,
"8", NA_character_, "MISSING", 7,
"9", "2020-03-06", "SD", 3 # expected is now SD
) %>%
mutate(
ADT = lubridate::ymd(ADTC),
STUDYID = "XX1234",
PARAMCD = "CBOR",
PARAM = "Best Confirmed Overall Response by Investigator"
) %>%
derive_vars_merged(
dataset_add = adsl,
by_vars = exprs(STUDYID, USUBJID),
new_vars = exprs(TRTSDT)
)
)
expect_dfs_equal(
base = expected_no_source_pd,
compare = actual_no_source_pd,
keys = c("USUBJID", "PARAMCD", "ADT")
)
})
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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