tests/testthat/test-derive_vars_query.R
In Roche-GSK/admiral: ADaM in R Asset Library
# derive_vars_query ----
## Test 1: Derive CQ and SMQ variables with two term levels ----
test_that("derive_vars_query Test 1: Derive CQ and SMQ variables with two term levels", {
# nolint start
queries <- tibble::tribble(
~PREFIX, ~GRPNAME, ~GRPID, ~SCOPE, ~SCOPEN, ~SRCVAR, ~TERMCHAR,
"CQ01", "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, "AEDECOD", "Alanine AMINOTRANSFERASE ABNORMAL",
"CQ01", "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, "AEDECOD", "AMMONIA ABNORMALL",
"SMQ03", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, "AEDECOD", "BASEDOW'S DISEASE",
"SMQ05", "Immune-Mediated Pneumonitis", NA, "NARROW", 1, "AEDECOD", "ALVEOLAR PROTEINOSIS",
"CQ06", "Some query", 11111, NA, NA, "AELLT", "SOME TERM"
) %>% dplyr::mutate(
TERMNUM = as.integer(as.factor(.data$TERMCHAR))
)
adae <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT,
"01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "ALANINE aminotransferase abnormal", NA,
"02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA,
"03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term",
"05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~SMQ03NAM, ~SMQ03CD, ~SMQ03SC, ~SMQ03SCN, ~SMQ05NAM, ~SMQ05SC, ~SMQ05SCN, ~CQ01NAM, ~CQ01CD, ~CQ01SC, ~CQ01SCN, ~CQ06NAM, ~CQ06CD,
"01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "ALANINE aminotransferase abnormal", NA, NA, NA, NA, NA, NA, NA, NA, "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, NA, NA,
"02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA, "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Some query", 11111,
"05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA, NA, NA, NA, NA, "Immune-Mediated Pneumonitis", "NARROW", 1, NA, NA, NA, NA, NA, NA
)
# nolint end
actual_output <- derive_vars_query(adae, queries)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 2: Derive when no unique key excluding `SRCVAR` columns ----
test_that("derive_vars_query Test 2: Derive when no unique key excluding `SRCVAR` columns", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ42", "My Query", "AEDECOD", "PTSI", 1, NA_real_,
"CQ42", "My Query", "AELLT", "LLTSI", 1, NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", "My Query", 1,
"1", 2, "something", "LLTSI", "My Query", 1,
"1", 2, "PTSI", "LLTSI", "My Query", 1,
"1", 2, "something", "other", NA_character_, NA_integer_
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expect_equal(expected_output, actual_output)
})
## Test 3: Derive when an adverse event is in multiple baskets ----
test_that("derive_vars_query Test 3: Derive when an adverse event is in multiple baskets", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA_real_,
"CQ42", "My Query 2", "AELLT", "LLTSI", 2, NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ40NAM, ~CQ40CD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", "My Query 1", 1, NA_character_, NA_integer_,
"1", 2, "something", "LLTSI", NA_character_, NA_integer_, "My Query 2", 2,
"1", 2, "PTSI", "LLTSI", "My Query 1", 1, "My Query 2", 2,
"1", 2, "something", "other", NA_character_, NA_integer_, NA_character_, NA_integer_
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expect_equal(expected_output, actual_output)
})
## Test 4: Derive when no GRPID or SCOPE column ----
test_that("derive_vars_query Test 4: Derive when no GRPID or SCOPE column", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~TERMNUM,
"CQ42", "My Query", "AEDECOD", "PTSI", NA_real_,
"CQ42", "My Query", "AELLT", "LLTSI", NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ42NAM,
"1", 1, "PTSI", "other", "My Query",
"1", 2, "something", "LLTSI", "My Query",
"1", 2, "PTSI", "LLTSI", "My Query",
"1", 2, "something", "other", NA_character_
)
expect_equal(expected_output, actual_output)
})
## Test 5: Derive decides between TERMCHAR and TERMNUM based on type ----
test_that("derive_vars_query Test 5: Derive decides between TERMCHAR and TERMNUM based on type", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ40NAM, ~CQ40CD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", NA, "My Query 1", 1, NA, NA,
"1", 2, "PTSI", "LLTSI", NA, "My Query 1", 1, NA, NA,
"1", 3, NA, NA, 1, NA, NA, "My Query 2", 2
)
expect_equal(expected_output, actual_output)
expect_snapshot(
derive_vars_query(mutate(my_ae, AELLTCD = as.logical(AELLTCD)), query),
error = TRUE
)
})
## Test 6: Error is given if both TERMCHAR/TERMNUM are NA/empty ----
test_that("derive_vars_query Test 6: Error is given if both TERMCHAR/TERMNUM are NA/empty", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", NA_character_, 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
snap <- expect_snapshot(
derive_vars_query(my_ae, query),
error = TRUE
)
})
## Test 7: character SRCVAR and just TERMCHAR is provided ----
test_that("derive_vars_query Test 7: character SRCVAR and just TERMCHAR is provided", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ40NAM, ~CQ40CD,
"1", 1, "PTSI", "other", NA, "My Query 1", 1,
"1", 2, "PTSI", "LLTSI", NA, "My Query 1", 1,
"1", 3, NA, NA, 1, NA, NA
)
expect_equal(expected_output, actual_output)
})
## Test 8: numeric SRCVAR and just TERMNUM is provided ----
test_that("derive_vars_query Test 8: numeric SRCVAR and just TERMNUM is provided", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~GRPID, ~TERMNUM,
"CQ42", "My Query 2", "AELLTCD", 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", NA, NA, NA,
"1", 2, "PTSI", "LLTSI", NA, NA, NA,
"1", 3, NA, NA, 1, "My Query 2", 2
)
expect_equal(expected_output, actual_output)
})
## Test 9: Error if requested variables already exist ----
test_that("derive_vars_query Test 9: Error if requested variables already exist", {
# nolint start
queries <- tibble::tribble(
~PREFIX, ~GRPNAME, ~GRPID, ~SCOPE, ~SCOPEN, ~SRCVAR, ~TERMCHAR,
"SMQ03", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, "AEDECOD", "BASEDOW'S DISEASE",
)
adae <- tibble::tribble(
~USUBJID, ~AEDECOD, ~SMQ03NAM, ~SMQ03CD, ~SMQ03SC, ~SMQ03SCN,
"01", "ALANINE aminotransferase abnormal", NA_character_, NA, NA, NA,
"02", "Basedow's disease", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1,
"03", "Some term", NA_character_, NA, NA, NA,
"05", "Alveolar proteinosis", NA_character_, NA, NA, NA
)
# nolint end
expect_snapshot(
derive_vars_query(adae, queries),
error = TRUE
)
})
# assert_valid_queries ----
## Test 10: assert_valid_queries checks ----
test_that("assert_valid_queries Test 10: assert_valid_queries checks", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("30", "55")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("AA", "BB")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, GRPNAME = c("", "A")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, GRPID = as.character(GRPID)),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, SCOPE = letters[1:2]),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, SCOPEN = 10:11),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("CQ40", "CQ40")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(
query,
PREFIX = c("CQ40", "CQ40"),
GRPNAME = c("My Query 1", "My Query 1")
),
"test"
),
error = TRUE
)
expect_error(
assert_valid_queries(
mutate(
query,
SCOPE = c("BROAD", "NARROW"),
SCOPEN = c(1, 1)
),
"test"
),
class = "assert_one_to_one"
)
expect_snapshot(
assert_valid_queries(
queries = bind_rows(query, query),
queries_name = "test"
),
error = TRUE
)
})
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# derive_vars_query ----
## Test 1: Derive CQ and SMQ variables with two term levels ----
test_that("derive_vars_query Test 1: Derive CQ and SMQ variables with two term levels", {
# nolint start
queries <- tibble::tribble(
~PREFIX, ~GRPNAME, ~GRPID, ~SCOPE, ~SCOPEN, ~SRCVAR, ~TERMCHAR,
"CQ01", "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, "AEDECOD", "Alanine AMINOTRANSFERASE ABNORMAL",
"CQ01", "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, "AEDECOD", "AMMONIA ABNORMALL",
"SMQ03", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, "AEDECOD", "BASEDOW'S DISEASE",
"SMQ05", "Immune-Mediated Pneumonitis", NA, "NARROW", 1, "AEDECOD", "ALVEOLAR PROTEINOSIS",
"CQ06", "Some query", 11111, NA, NA, "AELLT", "SOME TERM"
) %>% dplyr::mutate(
TERMNUM = as.integer(as.factor(.data$TERMCHAR))
)
adae <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT,
"01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "ALANINE aminotransferase abnormal", NA,
"02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA,
"03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term",
"05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDTM, ~AETERM, ~AESEQ, ~AEDECOD, ~AELLT, ~SMQ03NAM, ~SMQ03CD, ~SMQ03SC, ~SMQ03SCN, ~SMQ05NAM, ~SMQ05SC, ~SMQ05SCN, ~CQ01NAM, ~CQ01CD, ~CQ01SC, ~CQ01SCN, ~CQ06NAM, ~CQ06CD,
"01", "2020-06-02 23:59:59", "ALANINE AMINOTRANSFERASE ABNORMAL", 3, "ALANINE aminotransferase abnormal", NA, NA, NA, NA, NA, NA, NA, NA, "Immune-Mediated Hepatitis (Diagnosis and Lab Abnormalities)", 20000008, "NARROW", 1, NA, NA,
"02", "2020-06-05 23:59:59", "BASEDOW'S DISEASE", 5, "Basedow's disease", NA, "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, NA, NA, NA, NA, NA, NA, NA, NA, NA,
"03", "2020-06-07 23:59:59", "SOME TERM", 2, "Some query", "Some term", NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "Some query", 11111,
"05", "2020-06-09 23:59:59", "ALVEOLAR PROTEINOSIS", 7, "Alveolar proteinosis", NA, NA, NA, NA, NA, "Immune-Mediated Pneumonitis", "NARROW", 1, NA, NA, NA, NA, NA, NA
)
# nolint end
actual_output <- derive_vars_query(adae, queries)
expect_dfs_equal(expected_output, actual_output, keys = "USUBJID")
})
## Test 2: Derive when no unique key excluding `SRCVAR` columns ----
test_that("derive_vars_query Test 2: Derive when no unique key excluding `SRCVAR` columns", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ42", "My Query", "AEDECOD", "PTSI", 1, NA_real_,
"CQ42", "My Query", "AELLT", "LLTSI", 1, NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", "My Query", 1,
"1", 2, "something", "LLTSI", "My Query", 1,
"1", 2, "PTSI", "LLTSI", "My Query", 1,
"1", 2, "something", "other", NA_character_, NA_integer_
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expect_equal(expected_output, actual_output)
})
## Test 3: Derive when an adverse event is in multiple baskets ----
test_that("derive_vars_query Test 3: Derive when an adverse event is in multiple baskets", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA_real_,
"CQ42", "My Query 2", "AELLT", "LLTSI", 2, NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ40NAM, ~CQ40CD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", "My Query 1", 1, NA_character_, NA_integer_,
"1", 2, "something", "LLTSI", NA_character_, NA_integer_, "My Query 2", 2,
"1", 2, "PTSI", "LLTSI", "My Query 1", 1, "My Query 2", 2,
"1", 2, "something", "other", NA_character_, NA_integer_, NA_character_, NA_integer_
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expect_equal(expected_output, actual_output)
})
## Test 4: Derive when no GRPID or SCOPE column ----
test_that("derive_vars_query Test 4: Derive when no GRPID or SCOPE column", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~TERMNUM,
"CQ42", "My Query", "AEDECOD", "PTSI", NA_real_,
"CQ42", "My Query", "AELLT", "LLTSI", NA_real_
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT,
"1", 1, "PTSI", "other",
"1", 2, "something", "LLTSI",
"1", 2, "PTSI", "LLTSI",
"1", 2, "something", "other"
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~CQ42NAM,
"1", 1, "PTSI", "other", "My Query",
"1", 2, "something", "LLTSI", "My Query",
"1", 2, "PTSI", "LLTSI", "My Query",
"1", 2, "something", "other", NA_character_
)
expect_equal(expected_output, actual_output)
})
## Test 5: Derive decides between TERMCHAR and TERMNUM based on type ----
test_that("derive_vars_query Test 5: Derive decides between TERMCHAR and TERMNUM based on type", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ40NAM, ~CQ40CD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", NA, "My Query 1", 1, NA, NA,
"1", 2, "PTSI", "LLTSI", NA, "My Query 1", 1, NA, NA,
"1", 3, NA, NA, 1, NA, NA, "My Query 2", 2
)
expect_equal(expected_output, actual_output)
expect_snapshot(
derive_vars_query(mutate(my_ae, AELLTCD = as.logical(AELLTCD)), query),
error = TRUE
)
})
## Test 6: Error is given if both TERMCHAR/TERMNUM are NA/empty ----
test_that("derive_vars_query Test 6: Error is given if both TERMCHAR/TERMNUM are NA/empty", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", NA_character_, 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
snap <- expect_snapshot(
derive_vars_query(my_ae, query),
error = TRUE
)
})
## Test 7: character SRCVAR and just TERMCHAR is provided ----
test_that("derive_vars_query Test 7: character SRCVAR and just TERMCHAR is provided", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ40NAM, ~CQ40CD,
"1", 1, "PTSI", "other", NA, "My Query 1", 1,
"1", 2, "PTSI", "LLTSI", NA, "My Query 1", 1,
"1", 3, NA, NA, 1, NA, NA
)
expect_equal(expected_output, actual_output)
})
## Test 8: numeric SRCVAR and just TERMNUM is provided ----
test_that("derive_vars_query Test 8: numeric SRCVAR and just TERMNUM is provided", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~GRPID, ~TERMNUM,
"CQ42", "My Query 2", "AELLTCD", 2, 1
)
my_ae <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD,
"1", 1, "PTSI", "other", NA,
"1", 2, "PTSI", "LLTSI", NA,
"1", 3, NA, NA, 1
)
actual_output <- derive_vars_query(my_ae, dataset_queries = query)
expected_output <- tibble::tribble(
~USUBJID, ~ASTDY, ~AEDECOD, ~AELLT, ~AELLTCD, ~CQ42NAM, ~CQ42CD,
"1", 1, "PTSI", "other", NA, NA, NA,
"1", 2, "PTSI", "LLTSI", NA, NA, NA,
"1", 3, NA, NA, 1, "My Query 2", 2
)
expect_equal(expected_output, actual_output)
})
## Test 9: Error if requested variables already exist ----
test_that("derive_vars_query Test 9: Error if requested variables already exist", {
# nolint start
queries <- tibble::tribble(
~PREFIX, ~GRPNAME, ~GRPID, ~SCOPE, ~SCOPEN, ~SRCVAR, ~TERMCHAR,
"SMQ03", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1, "AEDECOD", "BASEDOW'S DISEASE",
)
adae <- tibble::tribble(
~USUBJID, ~AEDECOD, ~SMQ03NAM, ~SMQ03CD, ~SMQ03SC, ~SMQ03SCN,
"01", "ALANINE aminotransferase abnormal", NA_character_, NA, NA, NA,
"02", "Basedow's disease", "Immune-Mediated Hypothyroidism", 20000161, "NARROW", 1,
"03", "Some term", NA_character_, NA, NA, NA,
"05", "Alveolar proteinosis", NA_character_, NA, NA, NA
)
# nolint end
expect_snapshot(
derive_vars_query(adae, queries),
error = TRUE
)
})
# assert_valid_queries ----
## Test 10: assert_valid_queries checks ----
test_that("assert_valid_queries Test 10: assert_valid_queries checks", {
query <- tibble::tribble(
~PREFIX, ~GRPNAME, ~SRCVAR, ~TERMCHAR, ~GRPID, ~TERMNUM,
"CQ40", "My Query 1", "AEDECOD", "PTSI", 1, NA,
"CQ42", "My Query 2", "AELLTCD", NA_character_, 2, 1
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("30", "55")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("AA", "BB")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, GRPNAME = c("", "A")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, GRPID = as.character(GRPID)),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, SCOPE = letters[1:2]),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, SCOPEN = 10:11),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(query, PREFIX = c("CQ40", "CQ40")),
"test"
),
error = TRUE
)
expect_snapshot(
assert_valid_queries(
mutate(
query,
PREFIX = c("CQ40", "CQ40"),
GRPNAME = c("My Query 1", "My Query 1")
),
"test"
),
error = TRUE
)
expect_error(
assert_valid_queries(
mutate(
query,
SCOPE = c("BROAD", "NARROW"),
SCOPEN = c(1, 1)
),
"test"
),
class = "assert_one_to_one"
)
expect_snapshot(
assert_valid_queries(
queries = bind_rows(query, query),
queries_name = "test"
),
error = TRUE
)
})
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