Nothing
tests/testthat/test-derive_var_atoxgr.R
In admiral: ADaM in R Asset Library
## Test 1: ATOXGR cannot be graded ----
test_that("derive_var_atoxgr Test 1: ATOXGR cannot be graded", {
exp_out_1 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
"Hypophosphatemia", NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, "Hyperglycemia", NA_character_, NA_character_, NA_character_,
"Hypoglycemia", "Hyperglycemia", NA_character_, NA_character_, NA_character_,
# ATOXGRL is ungradable so cannot say ATOXGR is normal
"Hypoglycemia", "Hyperglycemia", NA_character_, "0", NA_character_,
# ATOXGRH is ungradable so cannot say ATOXGR is normal
"Hypoglycemia", "Hyperglycemia", "0", NA_character_, NA_character_,
)
input_1 <- exp_out_1 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_1,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_1
)
})
## Test 2: ATOXGR = 0 (normal) ----
test_that("derive_var_atoxgr Test 2: ATOXGR = 0 (normal)", {
exp_out_2 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", "0", "0", "0",
NA_character_, "INR Increased", NA_character_, "0", "0",
"Hypophosphatemia", NA_character_, "0", NA_character_, "0",
)
input_2 <- exp_out_2 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_2,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_2
)
})
## Test 3: ATOXGR > 0 (HYPER) ----
test_that("derive_var_atoxgr Test 3: ATOXGR > 0 (HYPER)", {
exp_out_3 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", NA_character_, "1", "1",
"Hypoglycemia", "Hyperglycemia", "0", "4", "4",
NA_character_, "INR Increased", NA_character_, "2", "2",
)
input_3 <- exp_out_3 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_3,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_3
)
})
## Test 4: ATOXGR < 0 (HYPO) ----
test_that("derive_var_atoxgr Test 4: ATOXGR < 0 (HYPO)", {
exp_out_4 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", "3", NA_character_, "-3",
"Hypoglycemia", "Hyperglycemia", "1", "0", "-1",
"Hypophosphatemia", NA_character_, "4", NA_character_, "-4",
)
input_4 <- exp_out_4 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_4,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_4
)
})
# derive_var_atoxgr_dir
## Blood and lymphatic system disorders
### Anemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: <80 g/L
### Grade 2: <100 - 80g/L
### Grade 1: <LLN - 100 g/L
expected_anemia <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, 200, "G/L", NA,
NA_character_, 60, 50, 100, "G/L", NA,
"ANEMIA", 79, 140, NA, "G/L", "3",
"ANEMIA", 80, 140, NA, "G/L", "2",
"Anemia", 99, 140, NA, "G/L", "2",
"Anemia", 100, 140, NA, "G/L", "1",
# wrong UNIT - GRADE should be missing
"anemia", 100, 140, NA, "G/dL", NA,
"Anemia", 139, 140, NA, "G/L", "1",
"ANEMIA", 140, 140, NA, "g/L", "0",
# ANRLO missing AVAL not grade 2 or 3 - cannot grade
"Anemia", 140, NA, NA, "G/L", NA,
"Anemia", 139, NA, NA, "G/L", NA,
"Anemia", 100, NA, NA, "G/L", NA,
# ANRLO missing but AVAL satisfies grade 2
"Anemia", 99, NA, NA, "G/L", "2",
# ANRLO missing but AVAL satisfies grade 3
"Anemia", 79, NA, NA, "G/L", "3",
# Unit missing cannot grade
"Anemia", 140, 140, NA, NA, NA,
# AVAL missing cannot grade
"Anemia", NA, 140, NA, "G/L", NA,
)
input_anemia <- expected_anemia %>%
select(-ATOXGRL)
## Test 5: CTCAEv4 Anemia ----
test_that("derive_var_atoxgr Test 5: CTCAEv4 Anemia", {
actual_anemia_ctcv4 <- derive_var_atoxgr_dir(
input_anemia,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_anemia,
compare = actual_anemia_ctcv4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 6: CTCAEv5 Anemia ----
test_that("derive_var_atoxgr Test 6: CTCAEv5 Anemia", {
actual_anemia_ctcv5 <- derive_var_atoxgr_dir(
input_anemia,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_anemia,
compare = actual_anemia_ctcv5,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Leukocytosis
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >100,000/mm3
expected_leukocytosis <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 99, 0, NA, "10^9/L", NA,
NA, 99, 0, NA, "10^9/L", NA,
"Leukocytosis", 101, 0, 40, "10^9/L", "3",
"leukocytosis", 100, 0, 40, "10^9/L", "0",
"Leukocytosis", 99, 0, NA, "10^9/L", "0",
# wrong UNIT - GRADE should be missing
"Leukocytosis", 99, 0, 40, "10^9/M", NA,
# Unit missing cannot grade
"Leukocytosis", 99, 0, 40, NA, NA,
# AVAL missing cannot grade
"Leukocytosis", NA, 0, 40, "10^9/L", NA,
)
input_leukocytosis <- expected_leukocytosis %>%
select(-ATOXGRH)
## Test 7: CTCAEv4 Leukocytosis ----
test_that("derive_var_atoxgr Test 7: CTCAEv4 Leukocytosis", {
actual_leukocytosis <- derive_var_atoxgr_dir(
input_leukocytosis,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_leukocytosis,
compare = actual_leukocytosis,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 8: CTCAEv5 Leukocytosis ----
test_that("derive_var_atoxgr Test 8: CTCAEv5 Leukocytosis", {
actual_leukocytosis <- derive_var_atoxgr_dir(
input_leukocytosis,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_leukocytosis,
compare = actual_leukocytosis,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Investigations
### Activated partial thromboplastin time prolonged
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >2.5 x ULN
### Grade 2: >1.5 - 2.5 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_aptt <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 100, NA_character_, NA,
NA_character_, 60, 100, NA_character_, NA,
"Activated partial thromboplastin time prolonged", 251, 100, NA_character_, "3",
"Activated Partial thromboplastin time prolonged", 250, 100, NA_character_, "2",
"Activated partial Thromboplastin time prolonged", 151, 100, NA_character_, "2",
"Activated partial thromboplastin time prolonged", 150, 100, NA_character_, "1",
"Activated partial thromboplastin Time prolonged", 101, 100, NA_character_, "1",
"Activated partial thromboplastin time prolonged", 100, 100, NA_character_, "0",
# ANRHI missing - cannot grade
"Activated partial thromboplastin time prolonged", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Activated partial thromboplastin time prolonged", NA, 100, NA_character_, NA,
)
input_aptt <- expected_aptt %>%
select(-ATOXGRH)
## Test 9: CTCAEv4 Activated partial thromboplastin time prolonged ----
test_that("derive_var_atoxgr Test 9: CTCAEv4 Activated partial thromboplastin time prolonged", {
actual_aptt <- derive_var_atoxgr_dir(
input_aptt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_aptt,
compare = actual_aptt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
## Test 10: CTCAEv5 Activated partial thromboplastin time prolonged ----
test_that("derive_var_atoxgr Test 10: CTCAEv5 Activated partial thromboplastin time prolonged", {
actual_aptt <- derive_var_atoxgr_dir(
input_aptt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_aptt,
compare = actual_aptt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Alanine aminotransferase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >3.0 - 5.0 x ULN
### Grade 1: >ULN - 3.0 x ULN
expected_alt_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alanine aminotransferase Increased", 801, 40, NA_character_, "4",
"Alanine aminotransferase Increased", 800, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 201, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 200, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 121, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 120, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 41, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alanine aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alanine aminotransferase Increased", NA, 40, NA_character_, NA,
)
## Test 11: CTCAEv4 Alanine aminotransferase increased ----
test_that("derive_var_atoxgr Test 11: CTCAEv4 Alanine aminotransferase increased", {
input_alt <- expected_alt_ctcv4 %>%
select(-ATOXGRH)
actual_alt <- derive_var_atoxgr_dir(
input_alt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alt_ctcv4,
compare = actual_alt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >3.0 - 5.0 x ULN if BL was normal OR >3.0 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL if BL was abnormal
## Test 12: CTCAEv5 Alanine aminotransferase increased ----
test_that("derive_var_atoxgr Test 12: CTCAEv5 Alanine aminotransferase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_alt_ctcv5_norm <- expected_alt_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_alt_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alanine aminotransferase Increased", 801, 40, NA_character_, "4",
"Alanine aminotransferase Increased", 800, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 201, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 200, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 121, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 120, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 60, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 59, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alanine aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alanine aminotransferase Increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_alt_ctcv5 <- expected_alt_ctcv5_norm %>%
bind_rows(expected_alt_ctcv5_abn)
input_alt <- expected_alt_ctcv5 %>%
select(-ATOXGRH)
actual_alt <- derive_var_atoxgr_dir(
input_alt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alt_ctcv5,
compare = actual_alt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Alkaline phosphatase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_alkph_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alkaline phosphatase increased", 801, 40, NA_character_, "4",
"Alkaline phosphatase increased", 800, 40, NA_character_, "3",
"Alkaline phosphatase increased", 201, 40, NA_character_, "3",
"Alkaline phosphatase increased", 200, 40, NA_character_, "2",
"Alkaline phosphatase increased", 101, 40, NA_character_, "2",
"Alkaline phosphatase increased", 100, 40, NA_character_, "1",
"Alkaline phosphatase increased", 41, 40, NA_character_, "1",
"Alkaline phosphatase increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alkaline phosphatase increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alkaline phosphatase increased", NA, 40, NA_character_, NA,
)
## Test 13: CTCAEv4 Alkaline phosphatase increased ----
test_that("derive_var_atoxgr Test 13: CTCAEv4 Alkaline phosphatase increased", {
input_alkph <- expected_alkph_ctcv4 %>%
select(-ATOXGRH)
actual_alkph <- derive_var_atoxgr_dir(
input_alkph,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkph_ctcv4,
compare = actual_alkph,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Alkaline phosphatase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >2.5 - 5.0 x ULN if BL was normal OR >2.5 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 2.5 x ULN if BL was normal OR >2.0 - 2.5 x BL if BL was abnormal
## Test 14: CTCAEv5 Alkaline phosphatase increased ----
test_that("derive_var_atoxgr Test 14: CTCAEv5 Alkaline phosphatase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_alkph_ctcv5_norm <- expected_alkph_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_alkph_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alkaline phosphatase increased", 801, 40, NA_character_, "4",
"Alkaline phosphatase increased", 800, 40, NA_character_, "3",
"Alkaline phosphatase increased", 201, 40, NA_character_, "3",
"Alkaline phosphatase increased", 200, 40, NA_character_, "2",
"Alkaline phosphatase increased", 101, 40, NA_character_, "2",
"Alkaline phosphatase increased", 100, 40, NA_character_, "1",
"Alkaline phosphatase increased", 80, 40, NA_character_, "1",
"Alkaline phosphatase increased", 79, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alkaline phosphatase increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alkaline phosphatase increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_alkph_ctcv5 <- expected_alkph_ctcv5_norm %>%
bind_rows(expected_alkph_ctcv5_abn)
input_alkph <- expected_alkph_ctcv5 %>%
select(-ATOXGRH)
actual_alkph <- derive_var_atoxgr_dir(
input_alkph,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkph_ctcv5,
compare = actual_alkph,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Aspartate aminotransferase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >3.0 - 5.0 x ULN
### Grade 1: >ULN - 3.0 x ULN
expected_ast_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Aspartate aminotransferase Increased", 801, 40, NA_character_, "4",
"Aspartate aminotransferase Increased", 800, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 201, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 200, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 121, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 120, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 41, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Aspartate aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Aspartate aminotransferase Increased", NA, 40, NA_character_, NA,
)
## Test 15: CTCAEv4 Aspartate aminotransferase increased ----
test_that("derive_var_atoxgr Test 15: CTCAEv4 Aspartate aminotransferase increased", {
input_ast <- expected_ast_ctcv4 %>%
select(-ATOXGRH)
actual_ast <- derive_var_atoxgr_dir(
input_ast,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ast_ctcv4,
compare = actual_ast,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >3.0 - 5.0 x ULN if BL was normal OR >3.0 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL if BL was abnormal
## Test 16: CTCAEv5 Aspartate aminotransferase increased ----
test_that("derive_var_atoxgr Test 16: CTCAEv5 Aspartate aminotransferase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_ast_ctcv5_norm <- expected_ast_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_ast_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Aspartate aminotransferase Increased", 801, 40, NA_character_, "4",
"Aspartate aminotransferase Increased", 800, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 201, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 200, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 121, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 120, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 60, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 59, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Aspartate aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Aspartate aminotransferase Increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_ast_ctcv5 <- expected_ast_ctcv5_norm %>%
bind_rows(expected_ast_ctcv5_abn)
input_ast <- expected_ast_ctcv5 %>%
select(-ATOXGRH)
actual_ast <- derive_var_atoxgr_dir(
input_ast,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ast_ctcv5,
compare = actual_ast,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Blood bilirubin increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >10.0 x ULN
### Grade 3: >3.0 - 10.0 x ULN
### Grade 2: >1.5 - 3.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_bili_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Blood bilirubin increased", 401, 40, NA_character_, "4",
"Blood bilirubin increased", 400, 40, NA_character_, "3",
"Blood bilirubin increased", 121, 40, NA_character_, "3",
"Blood bilirubin increased", 120, 40, NA_character_, "2",
"Blood bilirubin increased", 61, 40, NA_character_, "2",
"Blood bilirubin increased", 60, 40, NA_character_, "1",
"Blood bilirubin increased", 41, 40, NA_character_, "1",
"Blood bilirubin increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Blood bilirubin increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Blood bilirubin increased", NA, 40, NA_character_, NA,
)
## Test 17: CTCAEv4 Blood bilirubin increased ----
test_that("derive_var_atoxgr Test 17: CTCAEv4 Blood bilirubin increased", {
input_bili <- expected_bili_ctcv4 %>%
select(-ATOXGRH)
actual_bili <- derive_var_atoxgr_dir(
input_bili,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bili_ctcv4,
compare = actual_bili,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Blood bilirubin increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >10.0 x ULN if BL was normal OR >10.0 x BL if BL was abnormal
### Grade 3: >3.0 - 10.0 x ULN if BL was normal OR >3.0 - 10.0 x BL
### Grade 2: >1.5 - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL
### Grade 1: >ULN - 1.5 x ULN if BL was normal OR >1.0 - 1.5 x BL
## Test 18: CTCAEv5 Blood bilirubin increased ----
test_that("derive_var_atoxgr Test 18: CTCAEv5 Blood bilirubin increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_bili_ctcv5_norm <- expected_bili_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with abnormal BASE then add records with normal BASE
expected_bili_ctcv5 <- expected_bili_ctcv4 %>%
# set BASE to ANRHI then make ANRHI < BASE
mutate(
BASE = ANRHI,
ANRHI = ANRHI - 1,
FLAG = "ABNORMAL"
) %>%
bind_rows(expected_bili_ctcv5_norm)
input_bili <- expected_bili_ctcv5 %>%
select(-ATOXGRH)
actual_bili <- derive_var_atoxgr_dir(
input_bili,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bili_ctcv5,
compare = actual_bili,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### CD4 Lymphocytes decreased
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: <0.05 x 10e9 /L
### Grade 3: <0.2 x 0.05 - 10e9 /L
### Grade 2: <0.5 - 0.2 x 10e9 /L
### Grade 1: <LLN - 0.5 x 10e9 /L
expected_cd4 <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, "10^9/L", NA,
NA_character_, 60, 50, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.04, 0.8, "10^9/L", "4",
"CD4 lymphocytes decreased", 0.05, 0.8, "10^9/l", "3",
"CD4 lymphocytes decreased", 0.19, 0.8, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.2, 0.8, "10^9/L", "2",
"CD4 lymphocytes decreased", 0.49, 0.8, "10^9/L", "2",
# wrong unit - grade missing
"CD4 lymphocytes decreased", 0.49, 0.8, "10^8/L", NA,
"CD4 lymphocytes decreased", 0.5, 0.8, "10^9/L", "1",
"CD4 lymphocytes decreased", 0.79, 0.8, "10^9/L", "1",
"CD4 lymphocytes decreased", 0.8, 0.8, "10^9/L", "0",
# ANRLO missing - AVAL satisfies grade 2 - 4
"CD4 lymphocytes decreased", 0.04, NA, "10^9/L", "4",
"CD4 lymphocytes decreased", 0.05, NA, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.19, NA, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.2, NA, "10^9/L", "2",
"CD4 lymphocytes decreased", 0.49, NA, "10^9/L", "2",
# ANRLO missing - AVAL does NOT satisfies grade 2 - 4
"CD4 lymphocytes decreased", 0.5, NA, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.79, NA, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.8, NA, "10^9/L", NA,
# Unit missing - cannot grade
"CD4 lymphocytes decreased", 0.8, 0.8, NA, NA,
# AVAL missing cannot grade
"CD4 lymphocytes decreased", NA, 0.8, "10^9/L", NA,
)
input_cd4 <- expected_cd4 %>%
select(-ATOXGRL)
## Test 19: CTCAEv4 CD4 Lymphocytes decreased ----
test_that("derive_var_atoxgr Test 19: CTCAEv4 CD4 Lymphocytes decreased", {
actual_cd4 <- derive_var_atoxgr_dir(
input_cd4,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4,
compare = actual_cd4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "AVALU")
)
})
## Test 20: CTCAEv5 CD4 Lymphocytes decreased ----
test_that("derive_var_atoxgr Test 20: CTCAEv5 CD4 Lymphocytes decreased", {
actual_cd4 <- derive_var_atoxgr_dir(
input_cd4,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4,
compare = actual_cd4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "AVALU")
)
})
### Cholesterol high
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: >12.92 mmol/L
### Grade 3: >10.34 - 12.92 mmol/L
### Grade 2: >7.75 - 10.34 mmol/L
### Grade 1: >ULN - 7.75 mmol/L
expected_choles <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 8, 0, 5, "mmol/L", NA,
NA_character_, 10, 0, 5, "mmol/L", NA,
"Cholesterol high", 12.93, 0, 5, "mmol/L", "4",
"Cholesterol High", 12.92, 0, 5, "mmol/L", "3",
"Cholesterol high", 10.35, 0, 5, "Mmol/L", "3",
# wrong unit - grade missing
"Cholesterol high", 10.35, 0, 5, "umol/L", NA,
"Cholesterol high", 10.34, 0, 5, "mmol/L", "2",
"Cholesterol high", 7.76, 0, 5, "mmol/L", "2",
"Cholesterol high", 7.75, 0, 5, "mmol/L", "1",
"Cholesterol high", 5.1, 0, 5, "mmol/L", "1",
"Cholesterol high", 5, 0, 5, "mmol/L", "0",
# ANRHI missing - AVAL satisfies grade 2 - 4
"Cholesterol high", 12.93, 0, NA, "mmol/L", "4",
"Cholesterol High", 12.92, 0, NA, "mmol/L", "3",
"Cholesterol high", 10.35, 0, NA, "Mmol/L", "3",
"Cholesterol high", 10.34, 0, NA, "mmol/L", "2",
"Cholesterol high", 7.76, 0, NA, "mmol/L", "2",
# ANRHI missing - AVAL does NOT satisfies grade 2 - 4
"Cholesterol high", 7.75, 0, NA, "mmol/L", NA,
"Cholesterol high", 5.1, 0, NA, "mmol/L", NA,
"Cholesterol high", 5, 0, NA, "mmol/L", NA,
# Unit missing - cannot grade
"Cholesterol high", 5, 0, 5, NA, NA,
# AVAL missing cannot grade
"Cholesterol high", NA, 0, 5, "mmol/L", NA,
)
input_choles <- expected_choles %>%
select(-ATOXGRH)
## Test 21: CTCAEv4 Cholesterol high ----
test_that("derive_var_atoxgr Test 21: CTCAEv4 Cholesterol high", {
actual_choles <- derive_var_atoxgr_dir(
input_choles,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_choles,
compare = actual_choles,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 22: CTCAEv5 Cholesterol high ----
test_that("derive_var_atoxgr Test 22: CTCAEv5 Cholesterol high", {
actual_choles <- derive_var_atoxgr_dir(
input_choles,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_choles,
compare = actual_choles,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### CPK increased
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: >10.0 x ULN
### Grade 3: >5.0 - 10.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_cpk <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"CPK increased", 401, 0, 40, NA_character_, "4",
"CPK increased", 400, 0, 40, NA_character_, "3",
"CPK increased", 201, 0, 40, NA_character_, "3",
"CPK increased", 200, 0, 40, NA_character_, "2",
"CPK increased", 101, 0, 40, NA_character_, "2",
"CPK increased", 100, 0, 40, NA_character_, "1",
"CPK increased", 41, 0, 40, NA_character_, "1",
"CPK increased", 40, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"CPK increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"CPK increased", NA, 0, 40, NA_character_, NA,
)
input_cpk <- expected_cpk %>%
select(-ATOXGRH)
## Test 23: CTCAEv4 CPK increased ----
test_that("derive_var_atoxgr Test 23: CTCAEv4 CPK increased", {
actual_cpk <- derive_var_atoxgr_dir(
input_cpk,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cpk,
compare = actual_cpk,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 24: CTCAEv5 CPK increased ----
test_that("derive_var_atoxgr Test 24: CTCAEv5 CPK increased", {
actual_cpk <- derive_var_atoxgr_dir(
input_cpk,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cpk,
compare = actual_cpk,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Creatinine increased (NCICTCv4)
### NCICTCAEv5 same criteria as NCICTCAEv4 except for Grade 1
### Grade 4: >6.0 x ULN
### Grade 3: >3.0 baseline; >3.0 - 6.0 x ULN
### Grade 2: >1.5 - 3.0 x baseline; >1.5 - 3.0 x ULN
### Grade 1: >1 - 1.5 x baseline; >ULN - 1.5 x ULN
# create flag to remove obs not relevant for NCI-CTCAEv5
expected_creatn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~V4, ~V5,
"Not a term", 80, 80, 40, NA_character_, NA, "Y", "Y",
NA_character_, 60, 60, 40, NA_character_, NA, "Y", "Y",
# GRADE derived from AVAL against ANRHI
"Creatinine increased", 241, 241, 40, NA_character_, "4", "Y", "Y",
"Creatinine increased", 240, 230, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 121, 120, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 120, 119, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 61, 60, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 60, 60, 40, NA_character_, "1", "Y", "Y",
"Creatinine increased", 41, 41, 40, NA_character_, "1", "Y", "Y",
"Creatinine increased", 40, 40, 40, NA_character_, "0", "Y", "Y",
# GRADE derived from AVAL against BASE
"Creatinine increased", 42, 6, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 42, 13.9, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 42, 14, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 42.1, 28, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 42, 28, 42, NA_character_, "1", "Y", "N",
"Creatinine increased", 42, 41, 42, NA_character_, "1", "Y", "N",
"Creatinine increased", 42, 42, 42, NA_character_, "0", "Y", "N",
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"Creatinine increased", 42, NA, 42, NA_character_, NA, "Y", "N",
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"Creatinine increased", 42, 42, NA, NA_character_, NA, "Y", "Y",
# AVAL missing cannot grade
"Creatinine increased", NA, 0, 40, NA_character_, NA, "Y", "Y",
)
## Test 25: CTCAEv4 Creatinine increased ----
test_that("derive_var_atoxgr Test 25: CTCAEv4 Creatinine increased", {
input_creatn <- expected_creatn %>%
select(-ATOXGRH)
actual_creatn <- derive_var_atoxgr_dir(
input_creatn,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creatn,
compare = actual_creatn,
keys = c("ATOXDSCH", "AVAL", "BASE", "ANRHI", "AVALU")
)
})
### Creatinine increased (NCICTCv5)
### NCICTCAEv5 same criteria as NCICTCAEv4 except for Grade 1
### Grade 4: >6.0 x ULN
### Grade 3: >3.0 baseline; >3.0 - 6.0 x ULN
### Grade 2: >1.5 - 3.0 x baseline; >1.5 - 3.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
## Test 26: CTCAEv4 Creatinine increased ----
test_that("derive_var_atoxgr Test 26: CTCAEv4 Creatinine increased", {
expected_creatn <- expected_creatn %>%
filter(V5 == "Y")
input_creatn <- expected_creatn %>%
select(-ATOXGRH)
actual_creatn <- derive_var_atoxgr_dir(
input_creatn,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creatn,
compare = actual_creatn,
keys = c("ATOXDSCH", "AVAL", "BASE", "ANRHI", "AVALU")
)
})
### Fibrinogen decreased (NCICTCv4)
### Grade 4: <0.25 x LLN or 75% decrease from baseline or absolute value <50 mg/dL
### Grade 3: <0.5 - 0.25 x LLN or 50 - <75% decrease from baseline
### Grade 2: <0.75 - 0.5 x LLN or 25 - <50% decrease from baseline
### Grade 1: <1.0 - 0.75 x LLN or <25% decrease from baseline
## Test 27: CTCAEv4 Fibrinogen decreased ----
test_that("derive_var_atoxgr Test 27: CTCAEv4 Fibrinogen decreased", {
expected_fib <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~PCHG, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, "g/L", NA,
NA_character_, 10, 10, 40, "g/L", NA,
# Satisfies < 0.5 for grade 4 - other criteria missing
"Fibrinogen decreased", 0.49, NA, NA, "g/L", "4",
# Satisfies < 0.5 for grade 4 - satisfies grade 3 for other criteria
"Fibrinogen decreased", 0.49, 1, -51, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG missing
"Fibrinogen decreased", 0.5, 2.1, NA, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG satisfies grade 3
"Fibrinogen decreased", 0.5, 2.1, -51, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN missing
"Fibrinogen decreased", 1, NA, -75, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN satisfies grade 3
"Fibrinogen decreased", 1, 0.49, -75, "g/L", "4",
# Satisfies < 0.5*LLN for grade 3 - PCHG missing
"Fibrinogen decreased", 1, 2.1, NA, "g/L", "3",
# Satisfies < 0.5*LLN for grade 3 - PCHG satisfies grade 2
"Fibrinogen decreased", 1, 2.1, -49, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN missing
"Fibrinogen decreased", 1, NA, -50, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN satisfies grade 2
"Fibrinogen decreased", 1, 2, -50, "g/L", "3",
# Satisfies < 0.75*LLN for grade 2 - PCHG missing
"Fibrinogen decreased", 1.5, 2.1, NA, "g/L", "2",
# Satisfies < 0.75*LLN for grade 2 - PCHG satisfies grade 1
"Fibrinogen decreased", 1.5, 2.1, -10, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN missing
"Fibrinogen decreased", 1.5, NA, -25, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN satisfies grade 1
"Fibrinogen decreased", 1.5, 1.6, -25, "g/L", "2",
# Satisfies < LLN for grade 1 - PCHG missing
"Fibrinogen decreased", 2, 2.1, NA, "g/L", "1",
# Satisfies < LLN for grade 1 - PCHG satisfies grade 0
"Fibrinogen decreased", 2, 2.1, 10, "g/L", "1",
# Satisfies % decrease for grade 1 - LLN missing
"Fibrinogen decreased", 1.5, NA, -1, "g/L", "1",
# Satisfies % decrease for grade 1 - AVAL = LLN
"Fibrinogen decreased", 1.5, 1.5, -1, "g/L", "1",
# Satisfies grade 0 - AVAL >= LLN AND no % descrease
"Fibrinogen decreased", 1.5, 1.5, 0, "g/L", "0",
# AVAL >= LLN BUT PCT missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, 1.5, NA, "g/L", NA,
# PCT >= 0 BUT LLN missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, NA, 10, "g/L", NA,
# AVAL missing cannot grade
"Fibrinogen decreased", NA, 1.5, 10, "g/L", NA,
# wrong unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, "g/dL", NA,
# missing unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, NA, NA,
)
input_fib <- expected_fib %>%
select(-ATOXGRL)
actual_fib <- derive_var_atoxgr_dir(
input_fib,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fib,
compare = actual_fib,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "PCHG", "AVALU")
)
})
### Fibrinogen decreased (NCICTCv5)
### Grade 4: <0.25 x LLN OR if abnormal, 75% dec. from BL OR absolute value <50 mg/dL
### Grade 3: <0.5 - 0.25 x LLN OR if abnormal, 50 - <75% dec. from BL
### Grade 2: <0.75 - 0.5 x LLN OR if abnormal, 25 - <50% dec. from BL
### Grade 1: <1.0 - 0.75 x LLN OR if abnormal, <25% dec. from BL
## Test 28: CTCAEv5 Fibrinogen decreased ----
test_that("derive_var_atoxgr Test 28: CTCAEv5 Fibrinogen decreased", {
expected_fib <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~PCHG, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, "g/L", NA,
NA_character_, 10, 10, 40, "g/L", NA,
# Satisfies < 0.5 for grade 4 - other criteria missing
"Fibrinogen decreased", 0.49, NA, NA, "g/L", "4",
# Satisfies < 0.5 for grade 4 - satisfies grade 3 for other criteria
"Fibrinogen decreased", 0.49, 1, -51, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG missing
"Fibrinogen decreased", 0.5, 2.1, NA, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG satisfies grade 3
"Fibrinogen decreased", 0.5, 2.1, -51, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN satisfies grade 3
"Fibrinogen decreased", 0.5, 1.1, -75, "g/L", "4",
# Satisfies < 0.5*LLN for grade 3 - PCHG missing
"Fibrinogen decreased", 1, 2.1, NA, "g/L", "3",
# Satisfies < 0.5*LLN for grade 3 - PCHG satisfies grade 2
"Fibrinogen decreased", 1, 2.1, -49, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN satisfies grade 2
"Fibrinogen decreased", 1, 2, -50, "g/L", "3",
# Satisfies < 0.75*LLN for grade 2 - PCHG missing
"Fibrinogen decreased", 1.5, 2.1, NA, "g/L", "2",
# Satisfies < 0.75*LLN for grade 2 - PCHG satisfies grade 1
"Fibrinogen decreased", 1.5, 2.1, -10, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN satisfies grade 1
"Fibrinogen decreased", 1.5, 1.6, -25, "g/L", "2",
# Satisfies < LLN for grade 1 - PCHG missing
"Fibrinogen decreased", 2, 2.1, NA, "g/L", "1",
# Satisfies < LLN for grade 1 - PCHG satisfies grade 0
"Fibrinogen decreased", 2, 2.1, 10, "g/L", "1",
# Satisfies grade 0 - AVAL >= LLN AND no % descrease
"Fibrinogen decreased", 1.5, 1.5, 0, "g/L", "0",
# Satisfies % decrease for grade 1 - AVAL = LLN so not abnormal
"Fibrinogen decreased", 1.5, 1.5, -1, "g/L", "0",
# AVAL >= LLN - PCT missing but its normal so ignore PCT
"Fibrinogen decreased", 1.5, 1.5, NA, "g/L", "0",
# Satisfies <=75% decrease for grade 4 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1, NA, -75, "g/L", NA,
# Satisfies <=50% decrease for grade 3 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1, NA, -50, "g/L", NA,
# Satisfies <=25% decrease for grade 2 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1.5, NA, -25, "g/L", NA,
# Satisfies % decrease for grade 1 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1.5, NA, -1, "g/L", NA,
# PCT >= 0 BUT LLN missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, NA, 10, "g/L", NA,
# AVAL missing cannot grade
"Fibrinogen decreased", NA, 1.5, 10, "g/L", NA,
# wrong unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, "g/dL", NA,
# missing unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, NA, NA,
)
input_fib <- expected_fib %>%
select(-ATOXGRL)
actual_fib <- derive_var_atoxgr_dir(
input_fib,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fib,
compare = actual_fib,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "PCHG", "AVALU")
)
})
### GGT increased (NCICTCv4)
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_ggt_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"GGT increased", 801, 0, 40, NA_character_, "4",
"GGT increased", 800, 0, 40, NA_character_, "3",
"GGT increased", 201, 0, 40, NA_character_, "3",
"GGT increased", 200, 0, 40, NA_character_, "2",
"GGT increased", 101, 0, 40, NA_character_, "2",
"GGT increased", 100, 0, 40, NA_character_, "1",
"GGT increased", 41, 0, 40, NA_character_, "1",
"GGT increased", 40, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"GGT increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"GGT increased", NA, 0, NA, NA_character_, NA,
)
## Test 29: CTCAEv4 GGT increased ----
test_that("derive_var_atoxgr Test 29: CTCAEv4 GGT increased", {
input_ggt <- expected_ggt_ctcv4 %>%
select(-ATOXGRH)
actual_ggt <- derive_var_atoxgr_dir(
input_ggt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ggt_ctcv4,
compare = actual_ggt,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### GGT increased (NCICTCv5)
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >2.5 - 5.0 x ULN if BL was normal OR >2.5 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 2.5 x ULN if BL was normal OR >2.0 - 2.5 x BL if BL was abnormal
## Test 30: CTCAEv5 GGT increased ----
test_that("derive_var_atoxgr Test 30: CTCAEv5 GGT increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_ggt_ctcv5_norm <- expected_ggt_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_ggt_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"GGT increased", 801, 0, 40, NA_character_, "4",
"GGT increased", 800, 0, 40, NA_character_, "3",
"GGT increased", 201, 0, 40, NA_character_, "3",
"GGT increased", 200, 0, 40, NA_character_, "2",
"GGT increased", 101, 0, 40, NA_character_, "2",
"GGT increased", 100, 0, 40, NA_character_, "1",
"GGT increased", 81, 0, 40, NA_character_, "1",
"GGT increased", 80, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"GGT increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"GGT increased", NA, 0, NA, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_ggt_ctcv5 <- expected_ggt_ctcv5_norm %>%
bind_rows(expected_ggt_ctcv5_abn)
input_ggt <- expected_ggt_ctcv5 %>%
select(-ATOXGRH)
actual_ggt <- derive_var_atoxgr_dir(
input_ggt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ggt_ctcv5,
compare = actual_ggt,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "FLAG", "AVALU")
)
})
### Haptoglobin decreased (NCICTCv4)
# Same as NCICTCv5
### Grade 1: <LLN
expected_hapt <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, NA_character_, NA,
NA_character_, 10, 10, 40, NA_character_, NA,
"Haptoglobin decreased", 9, 10, 40, NA_character_, "1",
"Haptoglobin decreased", 10, 10, 40, NA_character_, "0",
"Haptoglobin decreased", 11, 10, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Haptoglobin decreased", NA, 10, 40, NA_character_, NA,
# AVAL missing cannot grade
"Haptoglobin decreased", 10, NA, NA, NA_character_, NA,
)
input_hapt <- expected_hapt %>%
select(-ATOXGRL)
## Test 31: CTCAEv4 Haptoglobin decreased ----
test_that("derive_var_atoxgr Test 31: CTCAEv4 Haptoglobin decreased", {
actual_hapt <- derive_var_atoxgr_dir(
input_hapt,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hapt,
compare = actual_hapt,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 32: CTCAEv5 Haptoglobin decreased ----
test_that("derive_var_atoxgr Test 32: CTCAEv5 Haptoglobin decreased", {
actual_hapt <- derive_var_atoxgr_dir(
input_hapt,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hapt,
compare = actual_hapt,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hemoglobin increased
# NCICTCAEv5 same as NCICTCAEv4 when BASE is normal
### Grade 3: Increase in >4 gm/dL above ULN or above baseline if baseline is above ULN
### Grade 2: Increase in >2 - 4 gm/dL above ULN or above baseline if baseline is above ULN
### Grade 1: Increase in >0 - 2 gm/dL above ULN or above baseline if baseline is above ULN
expected_hgbi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM, ~V5,
"Not a term", 80, 120, 200, "g/L", NA, 1, "Y",
NA_character_, 60, 50, 100, "g/L", NA, 2, "Y",
# BASE greater than ANRHI
"Hemoglobin increased", 106, 65, 60, "g/L", "3", 3, "N",
"Hemoglobin increased", 105, 65, 60, "g/L", "2", 4, "N",
"Hemoglobin increased", 86, 65, 60, "g/L", "2", 5, "N",
"Hemoglobin increased", 85, 65, 60, "g/L", "1", 6, "N",
"Hemoglobin increased", 66, 65, 60, "g/L", "1", 7, "N",
"Hemoglobin increased", 65, 65, 60, "g/L", "0", 8, "N",
"Hemoglobin increased", NA, 65, 60, "g/L", NA, 9, "N",
# BASE less than or equal to ANRHI
"Hemoglobin increased", 106, 60, 65, "g/L", "3", 10, "Y",
"Hemoglobin increased", 105, 60, 65, "g/L", "2", 11, "Y",
"Hemoglobin increased", 86, 60, 65, "g/L", "2", 12, "Y",
"Hemoglobin increased", 85, 60, 65, "g/L", "1", 13, "Y",
"Hemoglobin increased", 66, 60, 65, "g/L", "1", 14, "Y",
"Hemoglobin increased", 65, 60, 65, "g/L", "0", 15, "Y",
"Hemoglobin increased", NA, 60, 65, "g/L", NA, 16, "Y",
# BASE missing
"Hemoglobin increased", 106, NA, 65, "g/L", "3", 17, "N",
"Hemoglobin increased", 105, NA, 65, "g/L", "2", 18, "N",
"Hemoglobin increased", 86, NA, 65, "g/L", "2", 19, "N",
"Hemoglobin increased", 85, NA, 65, "g/L", "1", 20, "N",
"Hemoglobin increased", 66, NA, 65, "g/L", "1", 21, "N",
"Hemoglobin increased", 65, NA, 65, "g/L", "0", 22, "N",
"Hemoglobin increased", NA, NA, 65, "g/L", NA, 23, "N",
# Unit missing cannot grade
"Hemoglobin increased", 200, 61, 65, NA, NA, 24, "Y",
# ANRHI missing - cannot grade
"Hemoglobin increased", 200, 60, NA, "g/L", NA, 25, "Y",
# AVAL missing cannot grade
"Hemoglobin increased", NA, 60, 65, "g/L", NA, 26, "Y",
)
## Test 33: CTCAEv4 Hemoglobin increased ----
test_that("derive_var_atoxgr Test 33: CTCAEv4 Hemoglobin increased", {
input_hgbi <- expected_hgbi %>%
select(-ATOXGRH)
actual_hgbi <- derive_var_atoxgr_dir(
input_hgbi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbi,
compare = actual_hgbi,
keys = c("TESTNUM")
)
})
## Test 34: CTCAEv5 Hemoglobin increased ----
test_that("derive_var_atoxgr Test 34: CTCAEv5 Hemoglobin increased", {
expected_hgbi <- expected_hgbi %>%
filter(V5 == "Y")
input_hgbi <- expected_hgbi %>%
select(-ATOXGRH)
actual_hgbi <- derive_var_atoxgr_dir(
input_hgbi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbi,
compare = actual_hgbi,
keys = c("TESTNUM")
)
})
### INR increased (NCICTCV4)
### NCICTCV5 different for grade 1
### Grade 3: >2.5 x ULN; >2.5 times above baseline if on anticoagulation
### Grade 2: >1.5 - 2.5 x ULN; >1.5 - 2.5 times above baseline if on anticoagulation
### Grade 1: >1 - 1.5 x ULN; >1 - 1.5 times above baseline if on anticoagulation
## Test 35: CTCAEv4 INR increased ----
test_that("derive_var_atoxgr Test 35: CTCAEv4 INR increased", {
expected_inri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 120, 200, NA_character_, NA, 1,
NA_character_, 60, 50, 100, NA_character_, NA, 2,
# GRADE derived from AVAL against ANRHI
"INR IncreaSed", 251, 200, 100, NA_character_, "3", 3,
"INR Increased", 250, 199, 100, NA_character_, "2", 4,
"INR Increased", 151, 150, 100, NA_character_, "2", 5,
"INR Increased", 150, 150, 100, NA_character_, "1", 6,
"INR Increased", 101, 150, 100, NA_character_, "1", 7,
"INR Increased", 100, 100, 100, NA_character_, "0", 8,
# GRADE derived from AVAL against BASE
"INR IncreaSed", 251, 100, 200, NA_character_, "3", 9,
"INR Increased", 250, 100, 199, NA_character_, "2", 10,
"INR Increased", 151, 100, 150, NA_character_, "2", 11,
"INR Increased", 150, 100, 150, NA_character_, "1", 12,
"INR Increased", 101, 100, 150, NA_character_, "1", 13,
"INR Increased", 100, 100, 100, NA_character_, "0", 14,
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"INR Increased", 100, NA, 100, NA_character_, NA, 15,
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"INR Increased", 100, 100, NA, NA_character_, NA, 16,
# AVAL missing cannot grade
"INR Increased", NA, 100, 100, NA_character_, NA, 17,
)
input_inri <- expected_inri %>%
select(-ATOXGRH)
actual_inri <- derive_var_atoxgr_dir(
input_inri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri,
compare = actual_inri,
keys = c("TESTNUM")
)
})
### INR increased (NCICTCV4)
### NCICTCV5 different for grade 1
### Grade 3: >2.5 x ULN; >2.5 times above baseline if on anticoagulation
### Grade 2: >1.5 - 2.5 x ULN; >1.5 - 2.5 times above baseline if on anticoagulation
### Grade 1: >1.2 - 1.5 x ULN; >1 - 1.5 times above baseline if on anticoagulation
## Test 36: CTCAEv5 INR increased ----
test_that("derive_var_atoxgr Test 36: CTCAEv5 INR increased", {
expected_inri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 120, 200, NA_character_, NA, 1,
NA_character_, 60, 50, 100, NA_character_, NA, 2,
# GRADE derived from AVAL against ANRHI
"INR IncreaSed", 251, 200, 100, NA_character_, "3", 3,
"INR Increased", 250, 199, 100, NA_character_, "2", 4,
"INR Increased", 151, 150, 100, NA_character_, "2", 5,
"INR Increased", 150, 150, 100, NA_character_, "1", 6,
"INR Increased", 121, 150, 100, NA_character_, "1", 7,
"INR Increased", 120, 120, 100, NA_character_, "0", 8,
# GRADE derived from AVAL against BASE
"INR IncreaSed", 251, 100, 200, NA_character_, "3", 9,
"INR Increased", 250, 100, 199, NA_character_, "2", 10,
"INR Increased", 151, 100, 150, NA_character_, "2", 11,
"INR Increased", 150, 100, 150, NA_character_, "1", 12,
"INR Increased", 101, 100, 150, NA_character_, "1", 13,
"INR Increased", 100, 100, 100, NA_character_, "0", 14,
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"INR Increased", 100, NA, 100, NA_character_, NA, 15,
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"INR Increased", 100, 100, NA, NA_character_, NA, 16,
# AVAL missing cannot grade
"INR Increased", NA, 100, 100, NA_character_, NA, 17,
)
input_inri <- expected_inri %>%
select(-ATOXGRH)
actual_inri <- derive_var_atoxgr_dir(
input_inri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri,
compare = actual_inri,
keys = c("TESTNUM")
)
})
### Lipase increased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >5.0 x ULN
### Grade 3: >2.0 - 5.0 x ULN
### Grade 2: >1.5 - 2.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_lip <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, NA_character_, NA,
NA_character_, 60, 50, 100, NA_character_, NA,
"Lipase IncreaSed", 501, 0, 100, NA_character_, "4",
"Lipase Increased", 500, 0, 100, NA_character_, "3",
"Lipase Increased", 201, 0, 100, NA_character_, "3",
"Lipase Increased", 200, 0, 100, NA_character_, "2",
"Lipase Increased", 151, 0, 100, NA_character_, "2",
"Lipase Increased", 150, 0, 100, NA_character_, "1",
"Lipase Increased", 101, 0, 100, NA_character_, "1",
"Lipase Increased", 100, 0, 100, NA_character_, "0",
# ANRHI missing cannot grade
"Lipase Increased", 200, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"Lipase Increased", NA, 0, 100, NA_character_, NA,
)
input_lip <- expected_lip %>%
select(-ATOXGRH)
## Test 37: CTCAEv4 Lipase increased ----
test_that("derive_var_atoxgr Test 37: CTCAEv4 Lipase increased", {
actual_lip <- derive_var_atoxgr_dir(
input_lip,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lip,
compare = actual_lip,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 38: CTCAEv5 Lipase increased ----
test_that("derive_var_atoxgr Test 38: CTCAEv5 Lipase increased", {
actual_lip <- derive_var_atoxgr_dir(
input_lip,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lip,
compare = actual_lip,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Lymphocyte count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.2 x 10e9 /L
### Grade 3: <0.5 - 0.2 x 10e9 /L
### Grade 2: <0.8 - 0.5 x 10e9 /L
### Grade 1: <LLN - 0.8 x 10e9/L
expected_lymd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 80, 120, 200, "10^9/L", NA, 1,
NA_character_, 60, 50, 100, "10^9/L", NA, 2,
# ANRLO not missing
"Lymphocyte count decreased", 0.19, 140, NA, "10^9/L", "4", 3,
"Lymphocyte count decreased", 0.2, 140, NA, "10^9/L", "3", 4,
"Lymphocyte count decreased", 0.49, 140, NA, "10^9/L", "3", 5,
"Lymphocyte count decreased", 0.5, 140, NA, "10^9/L", "2", 6,
"Lymphocyte count decreased", 0.79, 140, NA, "10^9/L", "2", 7,
"Lymphocyte count decreased", 0.8, 140, NA, "10^9/L", "1", 8,
"Lymphocyte count decreased", 1.09, 1.1, NA, "10^9/L", "1", 9,
"Lymphocyte count decreased", 1.1, 1.1, NA, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4
"Lymphocyte count decreased", 0.19, NA, NA, "10^9/L", "4", 11,
"Lymphocyte count decreased", 0.2, NA, NA, "10^9/L", "3", 12,
"Lymphocyte count decreased", 0.49, NA, NA, "10^9/L", "3", 13,
"Lymphocyte count decreased", 0.5, NA, NA, "10^9/L", "2", 14,
"Lymphocyte count decreased", 0.79, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Lymphocyte count decreased", 0.8, NA, NA, "10^9/L", NA, 16,
"Lymphocyte count decreased", 1.09, NA, NA, "10^9/L", NA, 17,
"Lymphocyte count decreased", 1.1, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"Lymphocyte count decreased", 1.1, 1.1, NA, NA, NA, 19,
# AVAL missing cannot grade
"Lymphocyte count decreased", 1.1, 1.1, NA, "10^9/L", "0", 20,
)
input_lymd <- expected_lymd %>%
select(-ATOXGRL)
## Test 39: CTCAEv4 Lymphocyte count decreased ----
test_that("derive_var_atoxgr Test 39: CTCAEv4 Lymphocyte count decreased", {
actual_lymd <- derive_var_atoxgr_dir(
input_lymd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymd,
compare = actual_lymd,
keys = c("TESTNUM")
)
})
## Test 40: CTCAEv5 Lymphocyte count decreased ----
test_that("derive_var_atoxgr Test 40: CTCAEv5 Lymphocyte count decreased", {
actual_lymd <- derive_var_atoxgr_dir(
input_lymd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymd,
compare = actual_lymd,
keys = c("TESTNUM")
)
})
### Lymphocyte count increased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >20,000/mm3
### Grade 2: >4000/mm3 - 20,000/mm3
expected_lymi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, "10^9/L", NA,
NA_character_, 60, 50, 100, "10^9/L", NA,
"Lymphocyte count increased", 21, NA, NA, "10^9/L", "3",
"Lymphocyte count increased", 20, NA, NA, "10^9/L", "2",
"Lymphocyte count increased", 4.1, NA, NA, "10^9/L", "2",
"Lymphocyte count increased", 4, NA, NA, "10^9/L", "0",
# Unit missing cannot grade
"Lymphocyte count increased", 4, NA, NA, NA, NA,
# AVAL missing cannot grade
"Lymphocyte count increased", NA, NA, NA, "10^9/L", NA,
)
input_lymi <- expected_lymi %>%
select(-ATOXGRH)
## Test 41: CTCAEv4 Lymphocyte count increased ----
test_that("derive_var_atoxgr Test 41: CTCAEv4 Lymphocyte count increased", {
actual_lymi <- derive_var_atoxgr_dir(
input_lymi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymi,
compare = actual_lymi,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 42: CTCAEv5 Lymphocyte count increased ----
test_that("derive_var_atoxgr Test 42: CTCAEv5 Lymphocyte count increased", {
actual_lymi <- derive_var_atoxgr_dir(
input_lymi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymi,
compare = actual_lymi,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Neutrophil count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <25.0 x 10e9 /L
### Grade 3: <1.0 - 0.5 x 10e9 /L
### Grade 2: <1.5 - 1.0 x 10e9 /L
### Grade 1: <LLN - 1.5 x 10e9 /L
expected_neut <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, 200, "10^9/L", NA,
NA_character_, 60, 50, 100, "10^9/L", NA,
# ANRLO not missing
"Neutrophil count decreased", 0.49, 2, NA, "10^9/L", "4",
"Neutrophil count decreased", 0.5, 2, NA, "10^9/L", "3",
"Neutrophil count decreased", 0.99, 2, NA, "10^9/L", "3",
"Neutrophil count decreased", 1, 2, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.49, 2, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.5, 2, NA, "10^9/L", "1",
"Neutrophil count decreased", 1.9, 2, NA, "10^9/L", "1",
"Neutrophil count decreased", 2, 2, NA, "10^9/L", "0",
# ANRLO missing - can grade 2-4
"Neutrophil count decreased", 0.49, NA, NA, "10^9/L", "4",
"Neutrophil count decreased", 0.5, NA, NA, "10^9/L", "3",
"Neutrophil count decreased", 0.99, NA, NA, "10^9/L", "3",
"Neutrophil count decreased", 1, NA, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.49, NA, NA, "10^9/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Neutrophil count decreased", 1.5, NA, NA, "10^9/L", NA,
"Neutrophil count decreased", 1.9, NA, NA, "10^9/L", NA,
"Neutrophil count decreased", 2, NA, NA, "10^9/L", NA,
# Unit missing cannot grade
"Neutrophil count decreased", 2, 2, NA, NA, NA,
# AVAL missing cannot grade
"Neutrophil count decreased", NA, 2, NA, "10^9/L", NA,
)
input_neut <- expected_neut %>%
select(-ATOXGRL)
## Test 43: CTCAEv4 Neutrophil count decreased ----
test_that("derive_var_atoxgr Test 43: CTCAEv4 Neutrophil count decreased", {
actual_neut <- derive_var_atoxgr_dir(
input_neut,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_neut,
compare = actual_neut,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 44: CTCAEv5 Neutrophil count decreased ----
test_that("derive_var_atoxgr Test 44: CTCAEv5 Neutrophil count decreased", {
actual_neut <- derive_var_atoxgr_dir(
input_neut,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_neut,
compare = actual_neut,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Platelet count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <25.0 x 10e9 /L
### Grade 3: <50.0 - 25.0 x 10e9 /L
### Grade 2: <75.0 - 50.0 x 10e9 /L
### Grade 1: <LLN - 75.0 x 10e9 /L
expected_plate <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 80, 120, 200, "10^9/L", NA, 1,
NA_character_, 60, 50, 100, "10^9/L", NA, 2,
# ANRLO not missing
"Platelet count decreased", 24, 100, 150, "10^9/L", "4", 3,
"Platelet count decreased", 25, 100, 150, "10^9/L", "3", 4,
"Platelet count decreased", 49, 100, 150, "10^9/L", "3", 5,
"Platelet count decreased", 50, 100, 150, "10^9/L", "2", 6,
"Platelet count decreased", 74, 100, 150, "10^9/L", "2", 7,
"Platelet count decreased", 75, 100, 150, "10^9/L", "1", 8,
"Platelet count decreased", 99, 100, NA, "10^9/L", "1", 9,
"Platelet count decreased", 100, 100, NA, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4 1,
"Platelet count decreased", 24, NA, NA, "10^9/L", "4", 11,
"Platelet count decreased", 25, NA, NA, "10^9/L", "3", 12,
"Platelet count decreased", 49, NA, NA, "10^9/L", "3", 13,
"Platelet count decreased", 50, NA, NA, "10^9/L", "2", 14,
"Platelet count decreased", 74, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Platelet count decreased", 75, NA, NA, "10^9/L", NA, 16,
"Platelet count decreased", 99, NA, NA, "10^9/L", NA, 17,
"Platelet count decreased", 100, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"Platelet count decreased", 100, 100, NA, NA, NA, 19,
# AVAL missing cannot grade
"Platelet count decreased", NA, 100, NA, "10^9/L", NA, 20,
)
input_plate <- expected_plate %>%
select(-ATOXGRL)
## Test 45: CTCAEv4 Platelet count decreased ----
test_that("derive_var_atoxgr Test 45: CTCAEv4 Platelet count decreased", {
actual_plate <- derive_var_atoxgr_dir(
input_plate,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plate,
compare = actual_plate,
keys = c("TESTNUM")
)
})
## Test 46: CTCAEv5 Platelet count decreased ----
test_that("derive_var_atoxgr Test 46: CTCAEv5 Platelet count decreased", {
actual_plate <- derive_var_atoxgr_dir(
input_plate,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plate,
compare = actual_plate,
keys = c("TESTNUM")
)
})
### Serum amylase increased
### NCICTCAEv4 and NCICTCAEv5 criteria essentially the same
### Grade 4: >5.0 x ULN
### Grade 3: >2.0 - 5.0 x ULN
### Grade 2: >1.5 - 2.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_seri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, NA_character_, NA,
NA_character_, 60, 50, 100, NA_character_, NA,
"Serum amylase increased", 501, 0, 100, NA_character_, "4",
"Serum amylase increased", 500, 0, 100, NA_character_, "3",
"Serum amylase increased", 201, 0, 100, NA_character_, "3",
"Serum amylase increased", 200, 0, 100, NA_character_, "2",
"Serum amylase increased", 151, 0, 100, NA_character_, "2",
"Serum amylase increased", 150, 0, 100, NA_character_, "1",
"Serum amylase increased", 101, 0, 100, NA_character_, "1",
"Serum amylase increased", 100, 0, 100, NA_character_, "0",
# ANRHI missing cannot grade
"Serum amylase increased", 200, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"Serum amylase increased", NA, 0, 100, NA_character_, NA,
)
input_seri <- expected_seri %>%
select(-ATOXGRH)
## Test 47: CTCAEv4 Serum amylase increased ----
test_that("derive_var_atoxgr Test 47: CTCAEv4 Serum amylase increased", {
actual_seri <- derive_var_atoxgr_dir(
input_seri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_seri,
compare = actual_seri,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 48: CTCAEv5 Serum amylase increased ----
test_that("derive_var_atoxgr Test 48: CTCAEv5 Serum amylase increased", {
actual_seri <- derive_var_atoxgr_dir(
input_seri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_seri,
compare = actual_seri,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### White blood cell decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.0 x 10e9 /L
### Grade 3: <2.0 - 1.0 x 10e9 /L
### Grade 2: <3.0 - 2.0 x 10e9 /L
### Grade 1: <LLN - 3.0 x 10e9 /L
expected_wbcd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 1, 5, 15, "10^9/L", NA, 1,
NA_character_, 2, 5, 15, "10^9/L", NA, 2,
# ANRLO not missing
"White blood cell decreased", 0.9, 5, 15, "10^9/L", "4", 3,
"White blood cell decreased", 1, 5, 15, "10^9/L", "3", 4,
"White blood cell decreased", 1.9, 5, 15, "10^9/L", "3", 5,
"White blood cell decreased", 2, 5, 15, "10^9/L", "2", 6,
"White blood cell decreased", 2.9, 5, 15, "10^9/L", "2", 7,
"White blood cell decreased", 3, 5, 15, "10^9/L", "1", 8,
"White blood cell decreased", 4.9, 5, 15, "10^9/L", "1", 9,
"White blood cell decreased", 5, 5, 15, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4
"White blood cell decreased", 0.9, NA, NA, "10^9/L", "4", 11,
"White blood cell decreased", 1, NA, NA, "10^9/L", "3", 12,
"White blood cell decreased", 1.9, NA, NA, "10^9/L", "3", 13,
"White blood cell decreased", 2, NA, NA, "10^9/L", "2", 14,
"White blood cell decreased", 2.9, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 16,
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 17,
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"White blood cell decreased", 3, 100, NA, NA, NA, 19,
# AVAL missing cannot grade
"White blood cell decreased", NA, 100, NA, "10^9/L", NA, 20,
)
input_wbcd <- expected_wbcd %>%
select(-ATOXGRL)
## Test 49: CTCAEv4 White blood cell decreased ----
test_that("derive_var_atoxgr Test 49: CTCAEv4 White blood cell decreased", {
actual_wbcd <- derive_var_atoxgr_dir(
input_wbcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd,
compare = actual_wbcd,
keys = c("TESTNUM")
)
})
## Test 50: CTCAEv5 White blood cell decreased ----
test_that("derive_var_atoxgr Test 50: CTCAEv5 White blood cell decreased", {
actual_wbcd <- derive_var_atoxgr_dir(
input_wbcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd,
compare = actual_wbcd,
keys = c("TESTNUM")
)
})
## Metabolism and nutrition disorders
### Hypercalcemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >3.4 mmol/L
### Grade 3: >3.1 - 3.4 mmol/L
### Grade 2: >2.9 - 3.1 mmol/L
### Grade 1: >ULN - 2.9 mmol/L
expected_calci <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, 0, 2.5, "mmol/L", NA, 1,
NA_character_, 3.5, 0, 2.5, "mmol/L", NA, 2,
# ANRHI not missing
"Hypercalcemia", 3.5, 0, 2.5, "mmol/L", "4", 3,
"Hypercalcemia", 3.4, 0, 2.5, "mmol/L", "3", 4,
"Hypercalcemia", 3.2, 0, 2.5, "mmol/L", "3", 5,
"Hypercalcemia", 3.1, 0, 2.5, "mmol/L", "2", 6,
"Hypercalcemia", 3, 0, 2.5, "mmol/L", "2", 7,
"Hypercalcemia", 2.9, 0, 2.5, "mmol/L", "1", 8,
"Hypercalcemia", 2.6, 0, 2.5, "mmol/L", "1", 9,
"Hypercalcemia", 2.5, 0, 2.5, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hypercalcemia", 3.5, 0, NA, "mmol/L", "4", 11,
"Hypercalcemia", 3.4, 0, NA, "mmol/L", "3", 12,
"Hypercalcemia", 3.2, 0, NA, "mmol/L", "3", 13,
"Hypercalcemia", 3.1, 0, NA, "mmol/L", "2", 14,
"Hypercalcemia", 3, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypercalcemia", 2.9, 0, NA, "mmol/L", NA, 16,
"Hypercalcemia", 2.6, 0, NA, "mmol/L", NA, 17,
"Hypercalcemia", 2.5, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hypercalcemia", 2.5, 0, 2.5, NA, NA, 19,
# AVAL missing cannot grade
"Hypercalcemia", NA, 0, 2.5, "mmol/L", NA, 20,
)
input_calci <- expected_calci %>%
select(-ATOXGRH)
## Test 51: CTCAEv4 Hypercalcemia ----
test_that("derive_var_atoxgr Test 51: CTCAEv4 Hypercalcemia", {
actual_calci <- derive_var_atoxgr_dir(
input_calci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci,
compare = actual_calci,
keys = c("TESTNUM")
)
})
## Test 52: CTCAEv5 Hypercalcemia ----
test_that("derive_var_atoxgr Test 52: CTCAEv5 Hypercalcemia", {
actual_calci <- derive_var_atoxgr_dir(
input_calci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci,
compare = actual_calci,
keys = c("TESTNUM")
)
})
### Hypercalcemia (Ionized)
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >1.8 mmol/L
### Grade 3: >1.6 - 1.8 mmol/L
### Grade 2: >1.5 - 1.6 mmol/L
### Grade 1: >ULN - 1.5 mmol/L
expected_calioni <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.9, 0, 1.3, "mmol/L", NA, 1,
NA_character_, 1.9, 0, 1.3, "mmol/L", NA, 2,
# ANRHI not missing
"Hypercalcemia (Ionized)", 1.9, 0, 1.3, "mmol/L", "4", 3,
"Hypercalcemia (Ionized)", 1.8, 0, 1.3, "mmol/L", "3", 4,
"Hypercalcemia (Ionized)", 1.7, 0, 1.3, "mmol/L", "3", 5,
"Hypercalcemia (Ionized)", 1.6, 0, 1.3, "mmol/L", "2", 6,
"Hypercalcemia (Ionized)", 1.51, 0, 1.3, "mmol/L", "2", 7,
"Hypercalcemia (Ionized)", 1.5, 0, 1.3, "mmol/L", "1", 8,
"Hypercalcemia (Ionized)", 1.4, 0, 1.3, "mmol/L", "1", 9,
"Hypercalcemia (Ionized)", 1.3, 0, 1.3, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hypercalcemia (Ionized)", 1.9, 0, NA, "mmol/L", "4", 11,
"Hypercalcemia (Ionized)", 1.8, 0, NA, "mmol/L", "3", 12,
"Hypercalcemia (Ionized)", 1.7, 0, NA, "mmol/L", "3", 13,
"Hypercalcemia (Ionized)", 1.6, 0, NA, "mmol/L", "2", 14,
"Hypercalcemia (Ionized)", 1.51, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypercalcemia (Ionized)", 1.5, 0, NA, "mmol/L", NA, 16,
"Hypercalcemia (Ionized)", 1.4, 0, NA, "mmol/L", NA, 17,
"Hypercalcemia (Ionized)", 1.3, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade 1,
"Hypercalcemia (Ionized)", 1.3, 0, 1.3, NA, NA, 19,
# AVAL missing cannot grade
"Hypercalcemia (Ionized)", NA, 0, 1.3, "mmol/L", NA, 20,
)
input_calioni <- expected_calioni %>%
select(-ATOXGRH)
## Test 53: CTCAEv4 Hypercalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 53: CTCAEv4 Hypercalcemia (Ionized)", {
actual_calioni <- derive_var_atoxgr_dir(
input_calioni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni,
compare = actual_calioni,
keys = c("TESTNUM")
)
})
## Test 54: CTCAEv5 Hypercalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 54: CTCAEv5 Hypercalcemia (Ionized)", {
actual_calioni <- derive_var_atoxgr_dir(
input_calioni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni,
compare = actual_calioni,
keys = c("TESTNUM")
)
})
### Hyperglycemia (Fasting) (NCICTCAEv4)
### not included in NCICTCAEv5
### Grade 4: >27.8 mmol/L
### Grade 3: >13.9 - 27.8 mmol/L
### Grade 2: >8.9 - 13.9 mmol/L
### Grade 1: >ULN - 8.9 mmol/L
## Test 55: CTCAEv4 Hyperglycemia (Fasting) ----
test_that("derive_var_atoxgr Test 55: CTCAEv4 Hyperglycemia (Fasting)", {
expected_glycfi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 27.9, 0, 5.3, "mmol/L", NA, 1,
NA_character_, 27.9, 0, 5.3, "mmol/L", NA, 2,
# ANRHI not missing
"Hyperglycemia (Fasting)", 27.9, 0, 5.3, "mmol/L", "4", 3,
"Hyperglycemia (Fasting)", 27.8, 0, 5.3, "mmol/L", "3", 4,
"Hyperglycemia (Fasting)", 14, 0, 5.3, "mmol/L", "3", 5,
"Hyperglycemia (Fasting)", 13.9, 0, 5.3, "mmol/L", "2", 6,
"Hyperglycemia (Fasting)", 9, 0, 5.3, "mmol/L", "2", 7,
"Hyperglycemia (Fasting)", 8.9, 0, 5.3, "mmol/L", "1", 8,
"Hyperglycemia (Fasting)", 5.4, 0, 5.3, "mmol/L", "1", 9,
"Hyperglycemia (Fasting)", 5.3, 0, 5.3, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hyperglycemia (Fasting)", 27.9, 0, NA, "mmol/L", "4", 11,
"Hyperglycemia (Fasting)", 27.8, 0, NA, "mmol/L", "3", 12,
"Hyperglycemia (Fasting)", 14, 0, NA, "mmol/L", "3", 13,
"Hyperglycemia (Fasting)", 13.9, 0, NA, "mmol/L", "2", 14,
"Hyperglycemia (Fasting)", 9, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hyperglycemia (Fasting)", 8.9, 0, NA, "mmol/L", NA, 16,
"Hyperglycemia (Fasting)", 5.4, 0, NA, "mmol/L", NA, 17,
"Hyperglycemia (Fasting)", 5.3, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hyperglycemia (Fasting)", 5.3, 0, 5.3, NA, NA, 19,
# AVAL missing cannot grade
"Hyperglycemia (Fasting)", NA, 0, 5.3, "mmol/L", NA, 20,
)
input_glycfi <- expected_glycfi %>%
select(-ATOXGRH)
actual_glycfi <- derive_var_atoxgr_dir(
input_glycfi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycfi,
compare = actual_glycfi,
keys = c("TESTNUM")
)
})
### Hyperglycemia (NCICTCAEv4)
### not included in NCICTCAEv5
### Grade 4: >27.8 mmol/L
### Grade 3: >13.9 - 27.8 mmol/L
## Test 56: CTCAEv4 Hyperglycemia ----
test_that("derive_var_atoxgr Test 56: CTCAEv4 Hyperglycemia", {
expected_glyci <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 27.9, 0, 5.3, "mmol/L", NA, 1,
NA_character_, 27.9, 0, 5.3, "mmol/L", NA, 2,
"Hyperglycemia", 27.9, 0, 5.3, "mmol/L", "4", 3,
"Hyperglycemia", 27.8, 0, 5.3, "mmol/L", "3", 4,
"Hyperglycemia", 14, 0, 5.3, "mmol/L", "3", 5,
"Hyperglycemia", 13.9, 0, 5.3, "mmol/L", "0", 6,
"Hyperglycemia", 5.3, 0, NA, "mmol/L", "0", 7,
# Unit missing cannot grade
"Hyperglycemia", 5.3, 0, 5.3, NA, NA, 8,
# AVAL missing cannot grade
"Hyperglycemia", NA, 0, 5.3, "mmol/L", NA, 9,
)
input_glyci <- expected_glyci %>%
select(-ATOXGRH)
actual_glyci <- derive_var_atoxgr_dir(
input_glyci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glyci,
compare = actual_glyci,
keys = c("TESTNUM")
)
})
### Hyperkalemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >7.0 mmol/L
### Grade 3: >6.0 - 7.0 mmol/L
### Grade 2: >5.5 - 6.0 mmol/L
### Grade 1: >ULN - 5.5 mmol/L
expected_kalei <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7.1, 0, 5.1, "mmol/L", NA, 1,
NA_character_, 7.1, 0, 5.1, "mmol/L", NA, 2,
# ANRHI not missing
"Hyperkalemia", 7.1, 0, 5.1, "mmol/L", "4", 3,
"Hyperkalemia", 7, 0, 5.1, "mmol/L", "3", 4,
"Hyperkalemia", 6.1, 0, 5.1, "mmol/L", "3", 5,
"Hyperkalemia", 6, 0, 5.1, "mmol/L", "2", 6,
"Hyperkalemia", 5.6, 0, 5.1, "mmol/L", "2", 7,
"Hyperkalemia", 5.5, 0, 5.1, "mmol/L", "1", 8,
"Hyperkalemia", 5.2, 0, 5.1, "mmol/L", "1", 9,
"Hyperkalemia", 5.1, 0, 5.1, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hyperkalemia", 7.1, 0, NA, "mmol/L", "4", 11,
"Hyperkalemia", 7, 0, NA, "mmol/L", "3", 12,
"Hyperkalemia", 6.1, 0, NA, "mmol/L", "3", 13,
"Hyperkalemia", 6, 0, NA, "mmol/L", "2", 14,
"Hyperkalemia", 5.6, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hyperkalemia", 5.5, 0, NA, "mmol/L", NA, 16,
"Hyperkalemia", 5.2, 0, NA, "mmol/L", NA, 17,
"Hyperkalemia", 5.1, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hyperkalemia", 5.1, 0, 5.1, NA, NA, 19,
# AVAL missing cannot grade
"Hyperkalemia", NA, 0, 5.1, "mmol/L", NA, 20,
)
input_kalei <- expected_kalei %>%
select(-ATOXGRH)
## Test 57: CTCAEv4 Hyperkalemia ----
test_that("derive_var_atoxgr Test 57: CTCAEv4 Hyperkalemia", {
actual_kalei <- derive_var_atoxgr_dir(
input_kalei,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kalei,
compare = actual_kalei,
keys = c("TESTNUM")
)
})
## Test 58: CTCAEv5 Hyperkalemia ----
test_that("derive_var_atoxgr Test 58: CTCAEv5 Hyperkalemia", {
actual_kalei <- derive_var_atoxgr_dir(
input_kalei,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kalei,
compare = actual_kalei,
keys = c("TESTNUM")
)
})
### Hypermagnesemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >3.30 mmol/L
### Grade 3: >1.23 - 3.30 mmol/L
### Grade 1: >ULN - 1.23 mmol/L
expected_magni <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.4, 0, 0.8, "mmol/L", NA, 1,
NA_character_, 3.4, 0, 0.8, "mmol/L", NA, 2,
# ANRHI not missing
"Hypermagnesemia", 3.4, 0, 0.8, "mmol/L", "4", 3,
"Hypermagnesemia", 3.3, 0, 0.8, "mmol/L", "3", 4,
"Hypermagnesemia", 1.24, 0, 0.8, "mmol/L", "3", 5,
"Hypermagnesemia", 1.23, 0, 0.8, "mmol/L", "1", 6,
"Hypermagnesemia", 0.81, 0, 0.8, "mmol/L", "1", 7,
"Hypermagnesemia", 0.8, 0, 0.8, "mmol/L", "0", 8,
# ANRHI missing - can grade 3-4
"Hypermagnesemia", 3.4, 0, NA, "mmol/L", "4", 9,
"Hypermagnesemia", 3.3, 0, NA, "mmol/L", "3", 10,
"Hypermagnesemia", 1.24, 0, NA, "mmol/L", "3", 11,
# ANRHI missing - can NOT grade 0 or 1
"Hypermagnesemia", 1.23, 0, NA, "mmol/L", NA, 12,
"Hypermagnesemia", 0.81, 0, NA, "mmol/L", NA, 13,
"Hypermagnesemia", 0.8, 0, NA, "mmol/L", NA, 14,
# Unit missing cannot grade
"Hypermagnesemia", 0.8, 0, 0.8, NA, NA, 15,
# AVAL missing cannot grade
"Hypermagnesemia", NA, 0, 0.8, "mmol/L", NA, 16,
)
input_magni <- expected_magni %>%
select(-ATOXGRH)
## Test 59: CTCAEv4 Hypermagnesemia ----
test_that("derive_var_atoxgr Test 59: CTCAEv4 Hypermagnesemia", {
actual_magni <- derive_var_atoxgr_dir(
input_magni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magni,
compare = actual_magni,
keys = c("TESTNUM")
)
})
## Test 60: CTCAEv5 Hypermagnesemia ----
test_that("derive_var_atoxgr Test 60: CTCAEv5 Hypermagnesemia", {
actual_magni <- derive_var_atoxgr_dir(
input_magni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magni,
compare = actual_magni,
keys = c("TESTNUM")
)
})
### Hypernatremia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >160 mmol/L
### Grade 3: >155 - 160 mmol/L
### Grade 2: >150 - 155 mmol/L
### Grade 1: >ULN - 150 mmol/L
expected_natri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 161, 0, 140, "mmol/L", NA, 1,
NA_character_, 161, 0, 140, "mmol/L", NA, 2,
# ANRHI not missing
"Hypernatremia", 161, 0, 140, "mmol/L", "4", 3,
"Hypernatremia", 160, 0, 140, "mmol/L", "3", 4,
"Hypernatremia", 156, 0, 140, "mmol/L", "3", 5,
"Hypernatremia", 155, 0, 140, "mmol/L", "2", 6,
"Hypernatremia", 151, 0, 140, "mmol/L", "2", 7,
"Hypernatremia", 150, 0, 140, "mmol/L", "1", 8,
"Hypernatremia", 141, 0, 140, "mmol/L", "1", 9,
"Hypernatremia", 140, 0, 140, "mmol/L", "0", 10,
# ANRHI missing - can grade 3-4
"Hypernatremia", 161, 0, NA, "mmol/L", "4", 11,
"Hypernatremia", 160, 0, NA, "mmol/L", "3", 12,
"Hypernatremia", 156, 0, NA, "mmol/L", "3", 13,
"Hypernatremia", 155, 0, NA, "mmol/L", "2", 14,
"Hypernatremia", 151, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypernatremia", 150, 0, NA, "mmol/L", NA, 16,
"Hypernatremia", 141, 0, NA, "mmol/L", NA, 17,
"Hypernatremia", 140, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hypernatremia", 140, 0, 140, NA, NA, 19,
# AVAL missing cannot grade
"Hypernatremia", NA, 0, 140, "mmol/L", NA, 20,
)
input_natri <- expected_natri %>%
select(-ATOXGRH)
## Test 61: CTCAEv4 Hypernatremia ----
test_that("derive_var_atoxgr Test 61: CTCAEv4 Hypernatremia", {
actual_natri <- derive_var_atoxgr_dir(
input_natri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natri,
compare = actual_natri,
keys = c("TESTNUM")
)
})
## Test 62: CTCAEv5 Hypernatremia ----
test_that("derive_var_atoxgr Test 62: CTCAEv5 Hypernatremia", {
actual_natri <- derive_var_atoxgr_dir(
input_natri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natri,
compare = actual_natri,
keys = c("TESTNUM")
)
})
### Hypertriglyceridemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >11.4 mmol/L
### Grade 3: >5.7 mmol/L - 11.4 mmol/L
### Grade 2: >3.42 mmol/L - 5.7 mmol/L
### Grade 1: 1.71 mmol/L - 3.42 mmol/L
expected_trigi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 11.5, 0, 2.1, "mmol/L", NA,
NA_character_, 11.5, 0, 2.1, "mmol/L", NA,
"Hypertriglyceridemia", 11.5, 0, 2.1, "mmol/L", "4",
"Hypertriglyceridemia", 11.4, 0, 2.1, "mmol/L", "3",
"Hypertriglyceridemia", 5.8, 0, 2.1, "mmol/L", "3",
"Hypertriglyceridemia", 5.7, 0, 2.1, "mmol/L", "2",
"Hypertriglyceridemia", 3.43, 0, 2.1, "mmol/L", "2",
"Hypertriglyceridemia", 3.42, 0, 2.1, "mmol/L", "1",
"Hypertriglyceridemia", 1.72, 0, 2.1, "mmol/L", "1",
"Hypertriglyceridemia", 1.71, 0, 2.1, "mmol/L", "0",
# Unit missing cannot grade
"Hypertriglyceridemia", 1.71, 0, 2.1, NA, NA,
# AVAL missing cannot grade
"Hypertriglyceridemia", NA, 0, 2.1, "mmol/L", NA,
)
input_trigi <- expected_trigi %>%
select(-ATOXGRH)
## Test 63: CTCAEv4 Hypertriglyceridemia ----
test_that("derive_var_atoxgr Test 63: CTCAEv4 Hypertriglyceridemia", {
actual_trigi <- derive_var_atoxgr_dir(
input_trigi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigi,
compare = actual_trigi,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
## Test 64: CTCAEv5 Hypertriglyceridemia ----
test_that("derive_var_atoxgr Test 64: CTCAEv5 Hypertriglyceridemia", {
actual_trigi <- derive_var_atoxgr_dir(
input_trigi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigi,
compare = actual_trigi,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
### Hyperuricemia (NCICTCAEv4)
### NCICTCAEv5 only has grade 3
### Grade 4: >0.59 mmol/L;
### Grade 3: >ULN - 10 mg/dL (0.59 mmol/L)
expected_urici <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 591, 0, 200, "umol/L", NA,
NA_character_, 591, 0, 200, "umol/L", NA,
# ANRHI not missing
"Hyperuricemia", 591, 0, 200, "umol/L", "4",
"Hyperuricemia", 590, 0, 200, "umol/L", "3",
"Hyperuricemia", 201, 0, 200, "umol/L", "3",
"Hyperuricemia", 200, 0, 200, "umol/L", "0",
# ANRHI missing - can grade 4
"Hyperuricemia", 591, 0, NA, "umol/L", "4",
# ANRHI missing - can NOT grade 0 or 3
"Hyperuricemia", 590, 0, NA, "umol/L", NA,
"Hyperuricemia", 201, 0, NA, "umol/L", NA,
"Hyperuricemia", 200, 0, NA, "umol/L", NA,
# Unit missing cannot grade
"Hyperuricemia", 200, 0, 200, NA, "0",
# AVAL missing cannot grade
"Hyperuricemia", NA, 0, 200, "umol/L", NA,
)
input_urici <- expected_urici %>%
select(-ATOXGRH)
### Hyperuricemia (NCICTCAEv5)
### NCICTCAEv5 only has grade 3
### Grade 3: >ULN
## Test 65: CTCAEv5 Hyperuricemia ----
test_that("derive_var_atoxgr Test 65: CTCAEv5 Hyperuricemia", {
expected_urici <- expected_urici %>%
filter(is.na(ATOXGRH) | ATOXGRH != "4")
input_urici <- expected_urici %>%
select(-ATOXGRH)
actual_urici <- derive_var_atoxgr_dir(
input_urici,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici,
compare = actual_urici,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
# If unit missing then grade CANNOT be calculated as needed for grade 4
## Test 66: CTCAEv4 Hyperuricemia ----
test_that("derive_var_atoxgr Test 66: CTCAEv4 Hyperuricemia", {
expected_urici <- expected_urici %>%
mutate(ATOXGRH = if_else(is.na(AVALU), NA_character_, ATOXGRH))
input_urici <- expected_urici %>%
select(-ATOXGRH)
actual_urici <- derive_var_atoxgr_dir(
input_urici,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici,
compare = actual_urici,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Hypoalbuminemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: <20 g/L
### Grade 2: <30 - 20 g/L
### Grade 1: <LLN - 30 g/L
expected_albd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 19, 40, 100, "G/L", NA,
NA_character_, 19, 40, 100, "G/L", NA,
# ANRLO not missing
"Hypoalbuminemia", 19, 40, 100, "G/L", "3",
"Hypoalbuminemia", 20, 40, 100, "G/L", "2",
"Hypoalbuminemia", 29, 40, 100, "G/L", "2",
"Hypoalbuminemia", 30, 40, 100, "G/L", "1",
"Hypoalbuminemia", 39, 40, 100, "G/L", "1",
"Hypoalbuminemia", 40, 40, 100, "G/L", "0",
"Hypoalbuminemia", 40, 40, NA, "G/L", "0",
# ANRLO missing - can grade 2-3
"Hypoalbuminemia", 19, NA, 100, "G/L", "3",
"Hypoalbuminemia", 20, NA, 100, "G/L", "2",
"Hypoalbuminemia", 29, NA, 100, "G/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypoalbuminemia", 30, NA, 100, "G/L", NA,
"Hypoalbuminemia", 39, NA, 100, "G/L", NA,
"Hypoalbuminemia", 40, NA, 100, "G/L", NA,
# Unit missing cannot grade
"Hypoalbuminemia", 40, 40, 100, NA, NA,
# AVAL missing cannot grade
"Hypoalbuminemia", NA, 40, 100, "G/L", NA,
)
input_albd <- expected_albd %>%
select(-ATOXGRL)
## Test 67: CTCAEv4 Hypoalbuminemia ----
test_that("derive_var_atoxgr Test 67: CTCAEv4 Hypoalbuminemia", {
actual_albd <- derive_var_atoxgr_dir(
input_albd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albd,
compare = actual_albd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 68: CTCAEv5 Hypoalbuminemia ----
test_that("derive_var_atoxgr Test 68: CTCAEv5 Hypoalbuminemia", {
actual_albd <- derive_var_atoxgr_dir(
input_albd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albd,
compare = actual_albd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypocalcemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.5 mmol/L
### Grade 3: <1.75 - 1.5 mmol/L
### Grade 2: <2.0 - 1.75 mmol/L
### Grade 1: <LLN - 2.0 mmol/L
expected_calcd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 1.4, 4, 100, "mmol/L", NA,
NA_character_, 1.4, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypocalcemia", 1.4, 4, 100, "mmol/L", "4",
"Hypocalcemia", 1.5, 4, 100, "mmol/L", "3",
"Hypocalcemia", 1.74, 4, 100, "mmol/L", "3",
"Hypocalcemia", 1.75, 4, 100, "mmol/L", "2",
"Hypocalcemia", 1.9, 4, 100, "mmol/L", "2",
"Hypocalcemia", 2, 4, 100, "mmol/L", "1",
"Hypocalcemia", 3, 4, 100, "mmol/L", "1",
"Hypocalcemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypocalcemia", 1.4, 4, NA, "mmol/L", "4",
"Hypocalcemia", 1.5, 4, NA, "mmol/L", "3",
"Hypocalcemia", 1.74, 4, NA, "mmol/L", "3",
"Hypocalcemia", 1.75, 4, NA, "mmol/L", "2",
"Hypocalcemia", 1.9, 4, NA, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypocalcemia", 2, 4, NA, "mmol/L", "1",
"Hypocalcemia", 3, 4, NA, "mmol/L", "1",
"Hypocalcemia", 4, 4, NA, "mmol/L", "0",
# Unit missing cannot grade
"Hypocalcemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypocalcemia", NA, 4, 100, "mmol/L", NA,
)
input_calcd <- expected_calcd %>%
select(-ATOXGRL)
## Test 69: CTCAEv4 Hypocalcemia ----
test_that("derive_var_atoxgr Test 69: CTCAEv4 Hypocalcemia", {
actual_calcd <- derive_var_atoxgr_dir(
input_calcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd,
compare = actual_calcd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 70: CTCAEv5 Hypocalcemia ----
test_that("derive_var_atoxgr Test 70: CTCAEv5 Hypocalcemia", {
actual_calcd <- derive_var_atoxgr_dir(
input_calcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd,
compare = actual_calcd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypocalcemia (Ionized)
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.8 mmol/L
### Grade 3: <0.9 - 0.8 mmol/L
### Grade 2: <1.0 - 0.9 mmol/L
### Grade 1: <LLN - 1.0 mmol/L
expected_caliond <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.79, 1.3, 100, "mmol/L", NA,
NA_character_, 0.79, 1.3, 100, "mmol/L", NA,
# ANRLO not missing
"Hypocalcemia (Ionized)", 0.79, 1.3, 100, "mmol/L", "4",
"Hypocalcemia (Ionized)", 0.8, 1.3, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.89, 1.3, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.9, 1.3, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 0.99, 1.3, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 1, 1.3, 100, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.29, 1.3, 100, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.3, 1.3, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypocalcemia (Ionized)", 0.79, NA, 100, "mmol/L", "4",
"Hypocalcemia (Ionized)", 0.8, NA, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.89, NA, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.9, NA, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 0.99, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypocalcemia (Ionized)", 1, 1.3, NA, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.29, 1.3, NA, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.3, 1.3, NA, "mmol/L", "0",
# Unit missing cannot grade
"Hypocalcemia (Ionized)", 1.3, 1.3, 100, NA, NA,
# AVAL missing cannot grade
"Hypocalcemia (Ionized)", NA, 1.3, 100, "mmol/L", NA,
)
input_caliond <- expected_caliond %>%
select(-ATOXGRL)
## Test 71: CTCAEv4 Hypocalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 71: CTCAEv4 Hypocalcemia (Ionized)", {
actual_caliond <- derive_var_atoxgr_dir(
input_caliond,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond,
compare = actual_caliond,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 72: CTCAEv5 Hypocalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 72: CTCAEv5 Hypocalcemia (Ionized)", {
actual_caliond <- derive_var_atoxgr_dir(
input_caliond,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond,
compare = actual_caliond,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypoglycemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.7 mmol/L
### Grade 3: <2.2 - 1.7 mmol/L
### Grade 2: <3.0 - 2.2 mmol/L
### Grade 1: <LLN - 3.0 mmol/L
expected_glycd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 1.69, 4, 100, "mmol/L", NA,
NA_character_, 1.69, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypoglycemia", 1.69, 4, 100, "mmol/L", "4",
"Hypoglycemia", 1.7, 4, 100, "mmol/L", "3",
"Hypoglycemia", 2.19, 4, 100, "mmol/L", "3",
"Hypoglycemia", 2.2, 4, 100, "mmol/L", "2",
"Hypoglycemia", 2.9, 4, 100, "mmol/L", "2",
"Hypoglycemia", 3, 4, 100, "mmol/L", "1",
"Hypoglycemia", 3.9, 4, 100, "mmol/L", "1",
"Hypoglycemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypoglycemia", 1.69, NA, 100, "mmol/L", "4",
"Hypoglycemia", 1.7, NA, 100, "mmol/L", "3",
"Hypoglycemia", 2.19, NA, 100, "mmol/L", "3",
"Hypoglycemia", 2.2, NA, 100, "mmol/L", "2",
"Hypoglycemia", 2.9, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypoglycemia", 3, NA, 100, "mmol/L", NA,
"Hypoglycemia", 3.9, NA, 100, "mmol/L", NA,
"Hypoglycemia", 4, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypoglycemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypoglycemia", NA, 4, 100, "mmol/L", NA,
)
input_glycd <- expected_glycd %>%
select(-ATOXGRL)
## Test 73: CTCAEv4 Hypoglycemia ----
test_that("derive_var_atoxgr Test 73: CTCAEv4 Hypoglycemia", {
actual_glycd <- derive_var_atoxgr_dir(
input_glycd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycd,
compare = actual_glycd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 74: CTCAEv5 Hypoglycemia ----
test_that("derive_var_atoxgr Test 74: CTCAEv5 Hypoglycemia", {
actual_glycd <- derive_var_atoxgr_dir(
input_glycd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycd,
compare = actual_glycd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypokalemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <2.5 mmol/L
### Grade 3: <3.0 - 2.5 mmol/L
### Grade 2: <LLN - 3.0 mmol/L
expected_kaled <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 2.49, 4, 100, "mmol/L", NA,
NA_character_, 2.49, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypokalemia", 2.49, 4, 100, "mmol/L", "4",
"Hypokalemia", 2.5, 4, 100, "mmol/L", "3",
"Hypokalemia", 2.9, 4, 100, "mmol/L", "3",
"Hypokalemia", 3, 4, 100, "mmol/L", "2",
"Hypokalemia", 3.9, 4, 100, "mmol/L", "2",
"Hypokalemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hypokalemia", 2.49, NA, 100, "mmol/L", "4",
"Hypokalemia", 2.5, NA, 100, "mmol/L", "3",
"Hypokalemia", 2.9, NA, 100, "mmol/L", "3",
# ANRLO missing - can NOT grade 0 or 2
"Hypokalemia", 3, NA, 100, "mmol/L", NA,
"Hypokalemia", 3.9, NA, 100, "mmol/L", NA,
"Hypokalemia", 4, NA, NA, "mmol/L", NA,
# Unit missing cannot grade
"Hypokalemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypokalemia", NA, 4, 100, "mmol/L", NA,
)
input_kaled <- expected_kaled %>%
select(-ATOXGRL)
## Test 75: CTCAEv4 Hypokalemia ----
test_that("derive_var_atoxgr Test 75: CTCAEv4 Hypokalemia", {
actual_kaled <- derive_var_atoxgr_dir(
input_kaled,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kaled,
compare = actual_kaled,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 76: CTCAEv5 Hypokalemia ----
test_that("derive_var_atoxgr Test 76: CTCAEv5 Hypokalemia", {
actual_kaled <- derive_var_atoxgr_dir(
input_kaled,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kaled,
compare = actual_kaled,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypomagnesemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.3 mmol/L
### Grade 3: <0.4 - 0.3 mmol/L
### Grade 2: <0.5 - 0.4 mmol/L
### Grade 1: <LLN - 0.5 mmol/L
expected_magnd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.29, 1, 100, "mmol/L", NA,
NA_character_, 0.29, 1, 100, "mmol/L", NA,
# ANRLO not missing
"Hypomagnesemia", 0.29, 1, 100, "mmol/L", "4",
"Hypomagnesemia", 0.3, 1, 100, "mmol/L", "3",
"Hypomagnesemia", 0.39, 1, 100, "mmol/L", "3",
"Hypomagnesemia", 0.4, 1, 100, "mmol/L", "2",
"Hypomagnesemia", 0.49, 1, 100, "mmol/L", "2",
"Hypomagnesemia", 0.5, 1, 100, "mmol/L", "1",
"Hypomagnesemia", 0.9, 1, 100, "mmol/L", "1",
"Hypomagnesemia", 1, 1, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypomagnesemia", 0.29, NA, 100, "mmol/L", "4",
"Hypomagnesemia", 0.3, NA, 100, "mmol/L", "3",
"Hypomagnesemia", 0.39, NA, 100, "mmol/L", "3",
"Hypomagnesemia", 0.4, NA, 100, "mmol/L", "2",
"Hypomagnesemia", 0.49, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypomagnesemia", 0.5, NA, 100, "mmol/L", NA,
"Hypomagnesemia", 0.9, NA, 100, "mmol/L", NA,
"Hypomagnesemia", 1, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypomagnesemia", 1, 1, 100, NA, NA,
# AVAL missing cannot grade
"Hypomagnesemia", NA, 1, 100, "mmol/L", NA,
)
input_magnd <- expected_magnd %>%
select(-ATOXGRL)
## Test 77: CTCAEv4 Hypomagnesemia ----
test_that("derive_var_atoxgr Test 77: CTCAEv4 Hypomagnesemia", {
actual_magnd <- derive_var_atoxgr_dir(
input_magnd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magnd,
compare = actual_magnd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 78: CTCAEv5 Hypomagnesemia ----
test_that("derive_var_atoxgr Test 78: CTCAEv5 Hypomagnesemia", {
actual_magnd <- derive_var_atoxgr_dir(
input_magnd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magnd,
compare = actual_magnd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hyponatremia (NCICTCAEv4)
### NCICTCAEv4 and NCICTCAEv5 essentially the same (slightly different text)
### Grade 4: <120 mmol/L
### Grade 3: <130 - 120 mmol/L
### Grade 1: <LLN - 130 mmol/L
expected_natrd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 119, 140, 100, "mmol/L", NA,
NA_character_, 119, 140, 100, "mmol/L", NA,
# ANRLO not missing
"Hyponatremia", 119, 140, 100, "mmol/L", "4",
"Hyponatremia", 120, 140, 100, "mmol/L", "3",
"Hyponatremia", 129, 140, 100, "mmol/L", "3",
"Hyponatremia", 130, 140, 100, "mmol/L", "1",
"Hyponatremia", 139, 140, 100, "mmol/L", "1",
"Hyponatremia", 140, 140, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hyponatremia", 119, NA, 100, "mmol/L", "4",
"Hyponatremia", 120, NA, 100, "mmol/L", "3",
"Hyponatremia", 129, NA, 100, "mmol/L", "3",
# ANRLO missing - can NOT grade 0 or 1
"Hyponatremia", 130, NA, 100, "mmol/L", NA,
"Hyponatremia", 139, NA, 100, "mmol/L", NA,
"Hyponatremia", 140, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hyponatremia", 140, 140, 100, NA, NA,
# AVAL missing cannot grade
"Hyponatremia", NA, 140, 100, "mmol/L", NA,
)
input_natrd <- expected_natrd %>%
select(-ATOXGRL)
## Test 79: CTCAEv4 Hyponatremia ----
test_that("derive_var_atoxgr Test 79: CTCAEv4 Hyponatremia", {
actual_natrd <- derive_var_atoxgr_dir(
input_natrd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natrd,
compare = actual_natrd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 80: CTCAEv5 Hyponatremia ----
test_that("derive_var_atoxgr Test 80: CTCAEv5 Hyponatremia", {
actual_natrd <- derive_var_atoxgr_dir(
input_natrd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natrd,
compare = actual_natrd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypophosphatemia
### Only in NCICTCAEv4 (not NCICTCAEv5)
### Grade 4: <0.3 mmol/L
### Grade 3: <0.6 - 0.3 mmol/L
### Grade 2: <0.8 - 0.6 mmol/L
### Grade 1: <LLN - 0.8 mmol/L
## Test 81: CTCAEv4 Hypophosphatemia ----
test_that("derive_var_atoxgr Test 81: CTCAEv4 Hypophosphatemia", {
expected_phosd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.29, 1, 100, "mmol/L", NA,
NA_character_, 0.29, 1, 100, "mmol/L", NA,
# ANRLO not missing
"Hypophosphatemia", 0.29, 1, 100, "mmol/L", "4",
"Hypophosphatemia", 0.3, 1, 100, "mmol/L", "3",
"Hypophosphatemia", 0.59, 1, 100, "mmol/L", "3",
"Hypophosphatemia", 0.6, 1, 100, "mmol/L", "2",
"Hypophosphatemia", 0.79, 1, 100, "mmol/L", "2",
"Hypophosphatemia", 0.8, 1, 100, "mmol/L", "1",
"Hypophosphatemia", 0.9, 1, 100, "mmol/L", "1",
"Hypophosphatemia", 1, 1, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hypophosphatemia", 0.29, NA, 100, "mmol/L", "4",
"Hypophosphatemia", 0.3, NA, 100, "mmol/L", "3",
"Hypophosphatemia", 0.59, NA, 100, "mmol/L", "3",
"Hypophosphatemia", 0.6, NA, 100, "mmol/L", "2",
"Hypophosphatemia", 0.79, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypophosphatemia", 0.8, NA, 100, "mmol/L", NA,
"Hypophosphatemia", 0.9, NA, 100, "mmol/L", NA,
"Hypophosphatemia", 1, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypophosphatemia", 1, 1, 100, NA, NA,
# AVAL missing cannot grade
"Hypophosphatemia", NA, 1, 100, "mmol/L", NA,
)
input_phosd <- expected_phosd %>%
select(-ATOXGRL)
actual_phosd <- derive_var_atoxgr_dir(
input_phosd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_phosd,
compare = actual_phosd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
# DAIDS grading----
### Acidosis
### Grade 4: pH < 7.3 with lifethreatening consequences
### Grade 3: pH < 7.3 without lifethreatening consequences
### Grade 2: pH ≥ 7.3 to < LLN
## Test 82: DAIDS Acidosis ----
test_that("derive_var_atoxgr Test 82: DAIDS Acidosis", {
expected_acido_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~ATOXGRL, ~TESTNUM,
"Not a term", 7.3, 7.35, 7.4, NA, 1,
NA_character_, 7.3, 7.35, 7.4, NA, 2,
# ANRLO not missing
"Acidosis", 7.29, 7.35, 7.4, "4", 3,
"Acidosis", 7.3, 7.35, 7.4, "2", 4,
"Acidosis", 7.34, 7.35, 7.4, "2", 5,
"Acidosis", 7.35, 7.35, 7.4, "0", 6,
"Acidosis", 7.36, 7.35, 7.4, "0", 7,
# ANRLO missing - can grade 4
"Acidosis", 7.29, NA, 7.4, "4", 8,
# ANRLO missing - can NOT grade 0 or 2
"Acidosis", 7.3, NA, 7.4, NA, 9,
"Acidosis", 7.34, NA, 7.4, NA, 10,
"Acidosis", 7.35, NA, 7.4, NA, 11,
"Acidosis", 7.36, NA, 7.4, NA, 12,
# AVAL missing cannot grade
"Acidosis", NA, 1.1, 1.4, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_acido_daids <- expected_acido_daids %>%
select(-ATOXGRL)
actual_acido_daids <- derive_var_atoxgr_dir(
input_acido_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_acido_daids,
compare = actual_acido_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Albumin, Low
### Grade 3: < 20
### Grade 2: >= 20 to < 30
### Grade 1: 30 to < LLN
## Test 83: DAIDS Albumin, Low ----
test_that("derive_var_atoxgr Test 83: DAIDS Albumin, Low", {
expected_albl_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 35, 40, "g/L", NA, 1,
NA_character_, 35, 40, "g/L", NA, 2,
# ANRLO not missing
"Albumin, Low", 19, 40, "g/L", "3", 3,
"Albumin, Low", 20, 40, "g/L", "2", 4,
"Albumin, Low", 29, 40, "g/L", "2", 5,
"Albumin, Low", 30, 40, "g/L", "1", 6,
"Albumin, Low", 39, 40, "g/L", "1", 7,
"Albumin, Low", 40, 40, "g/L", "0", 8,
# ANRLO missing - can grade 2 and 3
"Albumin, Low", 19, NA, "g/L", "3", 9,
"Albumin, Low", 20, NA, "g/L", "2", 10,
"Albumin, Low", 29, NA, "g/L", "2", 11,
# ANRLO missing - can NOT grade 0 or 1
"Albumin, Low", 30, NA, "g/L", NA, 12,
"Albumin, Low", 39, NA, "g/L", NA, 13,
"Albumin, Low", 40, NA, "g/L", NA, 14,
# AVALU missing cannot grade
"Albumin, Low", 40, 40, NA, NA, 15,
# AVAL missing cannot grade
"Albumin, Low", NA, 40, "g/L", NA, 16,
)
input_albl_daids <- expected_albl_daids %>%
select(-ATOXGRL)
actual_albl_daids <- derive_var_atoxgr_dir(
input_albl_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albl_daids,
compare = actual_albl_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Alkaline Phosphatase, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 84: DAIDS Alkaline Phosphatase, High ----
test_that("derive_var_atoxgr Test 84: DAIDS Alkaline Phosphatase, High", {
expected_alkphi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 40, NA, 1,
NA_character_, 30, 40, NA, 2,
# ANRHI not missing
"Alkaline Phosphatase, High", 401, 40, "4", 3,
"Alkaline Phosphatase, High", 400, 40, "4", 4,
"Alkaline Phosphatase, High", 399, 40, "3", 5,
"Alkaline Phosphatase, High", 200, 40, "3", 6,
"Alkaline Phosphatase, High", 199, 40, "2", 7,
"Alkaline Phosphatase, High", 100, 40, "2", 8,
"Alkaline Phosphatase, High", 99, 40, "1", 9,
"Alkaline Phosphatase, High", 51, 40, "1", 10,
"Alkaline Phosphatase, High", 50, 40, "1", 11,
"Alkaline Phosphatase, High", 49, 40, "0", 12,
# ANRHI missing cannot grade
"Alkaline Phosphatase, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"Alkaline Phosphatase, High", NA, 40, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_alkphi_daids <- expected_alkphi_daids %>%
select(-ATOXGRH)
actual_alkphi_daids <- derive_var_atoxgr_dir(
input_alkphi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkphi_daids,
compare = actual_alkphi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Alkalosis
### Grade 4: pH > 7.5 with lifethreatening consequences
### Grade 3: pH > 7.5 without lifethreatening consequences
### Grade 2: pH > ULN to ≤ 7.5
## Test 85: DAIDS Alkalosis ----
test_that("derive_var_atoxgr Test 85: DAIDS Alkalosis", {
expected_alkalo_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 7.3, 7.35, 7.4, NA, 1,
NA_character_, 7.3, 7.35, 7.4, NA, 2,
# ANRHI not missing
"Alkalosis", 7.51, 7.35, 7.4, "4", 3,
"Alkalosis", 7.5, 7.35, 7.4, "2", 4,
"Alkalosis", 7.41, 7.35, 7.4, "2", 5,
"Alkalosis", 7.4, 7.35, 7.4, "0", 6,
"Alkalosis", 7.39, 7.35, 7.4, "0", 7,
# ANRHI missing - can grade 4
"Alkalosis", 7.51, 7.35, NA, "4", 8,
# ANRHI missing - can NOT grade 0 or 2
"Alkalosis", 7.5, 7.35, NA, NA, 9,
"Alkalosis", 7.41, 7.35, NA, NA, 10,
"Alkalosis", 7.4, 7.35, NA, NA, 11,
"Alkalosis", 7.39, 7.35, NA, NA, 12,
# AVAL missing cannot grade
"Alkalosis", NA, 1.1, NA, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_alkalo_daids <- expected_alkalo_daids %>%
select(-ATOXGRH)
actual_alkalo_daids <- derive_var_atoxgr_dir(
input_alkalo_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkalo_daids,
compare = actual_alkalo_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### ALT, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 86: DAIDS ALT, High ----
test_that("derive_var_atoxgr Test 86: DAIDS ALT, High", {
expected_alti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"ALT, High", 601, 60, "4", 3,
"ALT, High", 600, 60, "4", 4,
"ALT, High", 599, 60, "3", 5,
"ALT, High", 300, 60, "3", 6,
"ALT, High", 299, 60, "2", 7,
"ALT, High", 150, 60, "2", 8,
"ALT, High", 149, 60, "1", 9,
"ALT, High", 76, 60, "1", 10,
"ALT, High", 75, 60, "1", 11,
"ALT, High", 74, 60, "0", 12,
# ANRHI missing cannot grade
"ALT, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"ALT, High", NA, 60, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_alti_daids <- expected_alti_daids %>%
select(-ATOXGRH)
actual_alti_daids <- derive_var_atoxgr_dir(
input_alti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alti_daids,
compare = actual_alti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Amylase, High
### Grade 4: >= 5.0 x ULN
### Grade 3: 3.0 to < 5.0 x ULN
### Grade 2: 1.5 to < 3.0 x ULN
### Grade 1: 1.1 to < 1.5 x ULN
## Test 87: DAIDS Amylase, High ----
test_that("derive_var_atoxgr Test 87: DAIDS Amylase, High", {
expected_amyli_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"Amylase, High", 301, 60, "4", 3,
"Amylase, High", 300, 60, "4", 4,
"Amylase, High", 299, 60, "3", 5,
"Amylase, High", 180, 60, "3", 6,
"Amylase, High", 179, 60, "2", 7,
"Amylase, High", 90, 60, "2", 8,
"Amylase, High", 89, 60, "1", 9,
"Amylase, High", 66, 60, "1", 10,
"Amylase, High", 65, 60, "0", 11,
# ANRHI missing cannot grade
"Amylase, High", 65, NA, NA, 12,
# AVAL missing cannot grade
"Amylase, High", NA, 60, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_amyli_daids <- expected_amyli_daids %>%
select(-ATOXGRH)
actual_amyli_daids <- derive_var_atoxgr_dir(
input_amyli_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_amyli_daids,
compare = actual_amyli_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### AST, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 88: DAIDS AST, High ----
test_that("derive_var_atoxgr Test 88: DAIDS AST, High", {
expected_asti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"AST, High", 601, 60, "4", 3,
"AST, High", 600, 60, "4", 4,
"AST, High", 599, 60, "3", 5,
"AST, High", 300, 60, "3", 6,
"AST, High", 299, 60, "2", 7,
"AST, High", 150, 60, "2", 8,
"AST, High", 149, 60, "1", 9,
"AST, High", 76, 60, "1", 10,
"AST, High", 75, 60, "1", 11,
"AST, High", 74, 60, "0", 12,
# ANRHI missing cannot grade
"AST, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"AST, High", NA, 60, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_asti_daids <- expected_asti_daids %>%
select(-ATOXGRH)
actual_asti_daids <- derive_var_atoxgr_dir(
input_asti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_asti_daids,
compare = actual_asti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Bicarbonate, Low
### Grade 4: < 8.0 mmol/L
### Grade 3: 8.0 -< 11.0 mmol/L
### Grade 2: 11.0 -< 16.0 mmol/L
### Grade 1: 16.0 mmol/L -< LLN
## Test 89: DAIDS Bicarbonate, Low ----
test_that("derive_var_atoxgr Test 89: DAIDS Bicarbonate, Low", {
expected_bicarbd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 22, 20, "mmol/L", NA, 1,
NA_character_, 22, 20, "mmol/L", NA, 2,
# ANRLO not missing
"Bicarbonate, Low", 7.9, 20, "mmol/L", "4", 3,
"Bicarbonate, Low", 8, 20, "mmol/L", "3", 4,
"Bicarbonate, Low", 10.9, 20, "mmol/L", "3", 5,
"Bicarbonate, Low", 11, 20, "mmol/L", "2", 6,
"Bicarbonate, Low", 15.9, 20, "mmol/L", "2", 7,
"Bicarbonate, Low", 16, 20, "mmol/L", "1", 8,
"Bicarbonate, Low", 19, 20, "mmol/L", "1", 9,
"Bicarbonate, Low", 20, 20, "mmol/L", "0", 10,
# ANRLO missing - can grade 2-4
"Bicarbonate, Low", 7.9, NA, "mmol/L", "4", 11,
"Bicarbonate, Low", 8, NA, "mmol/L", "3", 12,
"Bicarbonate, Low", 10.9, NA, "mmol/L", "3", 13,
"Bicarbonate, Low", 11, NA, "mmol/L", "2", 14,
"Bicarbonate, Low", 15.9, NA, "mmol/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Bicarbonate, Low", 16, NA, "mmol/L", NA, 16,
"Bicarbonate, Low", 19, NA, "mmol/L", NA, 17,
"Bicarbonate, Low", 20, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Bicarbonate, Low", 20, 20, NA, NA, 19,
# AVAL missing cannot grade
"Bicarbonate, Low", NA, 20, "mmol/L", NA, 20,
)
input_bicarbd_daids <- expected_bicarbd_daids %>%
select(-ATOXGRL)
actual_bicarbd_daids <- derive_var_atoxgr_dir(
input_bicarbd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bicarbd_daids,
compare = actual_bicarbd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Direct Bilirubin, High
### 17.1 used as conversion from "mg/dL" to "umol/L"
### > 28 days of age
### Grade 4: > ULN
expected_dbiligt28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7, 8, "umol/L", NA, 1,
NA_character_, 7, 8, "umol/L", NA, 2,
# ANRHI not missing
"Direct Bilirubin, High", 8.1, 8, "umol/L", "4", 3,
"Direct Bilirubin, High", 8, 8, "umol/L", "0", 4,
"Direct Bilirubin, High", 7.9, 8, "umol/L", "0", 5,
# ANRHI missing cannot still grade 0 or 4
"Direct Bilirubin, High", 8.1, NA, "umol/L", NA, 6,
"Direct Bilirubin, High", 8, NA, "umol/L", NA, 7,
"Direct Bilirubin, High", 7.9, NA, "umol/L", NA, 8,
# AVAL missing cannot grade
"Direct Bilirubin, High", NA, 8, "umol/L", NA, 9,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-30")
)
### <= 28 days of age
### Grade 4: > 2 mg/dL (> 34.2 umol/L)
### Grade 3: > 1.5 to <= 2 mg/dL (> 25.65 to <= 34.2 umol/L)
### Grade 2: > 1 to <= 1.5 mg/dL (> 17.1 to <= 25.65 umol/L)
### Grade 1: ULN to <= 1 mg/dL (ULN to <= 17.1 umol/L)
expected_dbilile28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7, 8, "umol/L", NA, 10,
NA_character_, 7, 8, "umol/L", NA, 11,
# ANRHI not missing
"Direct Bilirubin, High", 34.3, 8, "umol/L", "4", 12,
"Direct Bilirubin, High", 34.2, 8, "umol/L", "3", 13,
"Direct Bilirubin, High", 25.66, 8, "umol/L", "3", 14,
"Direct Bilirubin, High", 25.65, 8, "umol/L", "2", 15,
"Direct Bilirubin, High", 17.19, 8, "umol/L", "2", 16,
"Direct Bilirubin, High", 17.1, 8, "umol/L", "1", 17,
"Direct Bilirubin, High", 8, 8, "umol/L", "1", 18,
"Direct Bilirubin, High", 7.9, 8, "umol/L", "0", 19,
# ANRHI missing can still grade 2 - 4
"Direct Bilirubin, High", 34.3, NA, "umol/L", "4", 20,
"Direct Bilirubin, High", 34.2, NA, "umol/L", "3", 21,
"Direct Bilirubin, High", 25.66, NA, "umol/L", "3", 22,
"Direct Bilirubin, High", 25.65, NA, "umol/L", "2", 23,
"Direct Bilirubin, High", 17.19, NA, "umol/L", "2", 24,
# ANRHI missing cannot still grade 0 - 1
"Direct Bilirubin, High", 17.1, NA, "umol/L", NA, 25,
"Direct Bilirubin, High", 8, NA, "umol/L", NA, 26,
"Direct Bilirubin, High", 7.9, NA, "umol/L", NA, 27,
# AVAL missing cannot grade
"Direct Bilirubin, High", NA, 8, "umol/L", NA, 28,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-29")
)
### add subjects with missing LBDT or BRTHDT
expected_dbilinoage_daids <- expected_dbilile28d_daids %>%
filter(TESTNUM %in% c(18, 19)) %>%
mutate(
LBDT = if_else(TESTNUM == 18, NA, LBDT),
BRTHDT = if_else(TESTNUM == 19, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 18, 29, 30)
)
### put all data together
expected_dbili_daids <- expected_dbilinoage_daids %>%
bind_rows(
expected_dbilile28d_daids,
expected_dbiligt28d_daids
)
## Test 90: DAIDS Direct Bilirubin, High ----
test_that("derive_var_atoxgr Test 90: DAIDS Direct Bilirubin, High", {
input_dbili_daids <- expected_dbili_daids %>%
select(-ATOXGRH)
actual_dbili_daids <- derive_var_atoxgr_dir(
input_dbili_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_dbili_daids,
compare = actual_dbili_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Total Bilirubin, High
### > 28 days of age
### Grade 4: >= 5.0 x ULN
### Grade 3: 2.6 to < 5.0 x ULN
### Grade 2: 1.6 to < 2.6 x ULN
### Grade 1: 1.1 to < 1.6 x ULN
expected_tbiligt28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9, 10, "umol/L", NA, 1,
NA_character_, 9, 10, "umol/L", NA, 2,
# ANRHI not missing
"Total Bilirubin, High", 50, 10, "umol/L", "4", 3,
"Total Bilirubin, High", 49, 10, "umol/L", "3", 4,
"Total Bilirubin, High", 26, 10, "umol/L", "3", 5,
"Total Bilirubin, High", 25.9, 10, "umol/L", "2", 6,
"Total Bilirubin, High", 16, 10, "umol/L", "2", 7,
"Total Bilirubin, High", 15.9, 10, "umol/L", "1", 8,
"Total Bilirubin, High", 11, 10, "umol/L", "1", 9,
"Total Bilirubin, High", 10.9, 10, "umol/L", "0", 10,
# Unit missing can grade - grade based on comparison of AVAL with ANRHI
"Total Bilirubin, High", 10.9, 10, NA, "0", 11,
# ANRHI missing - cannot grade
"Total Bilirubin, High", 10.9, NA, "umol/L", NA, 12,
# AVAL missing cannot grade
"Total Bilirubin, High", NA, 10, "umol/L", NA, 13,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-30")
)
### make Age <= 28 all results NA for ATOXGRH
expected_tbilile28d_daids <- expected_tbiligt28d_daids %>%
mutate(
LBDT = lubridate::ymd("2023-01-29"),
ATOXGRH = NA_character_,
TESTNUM = TESTNUM + 13
)
### make Age missing results NA for ATOXGRH
expected_tbilinoage_daids <- expected_tbiligt28d_daids %>%
filter(TESTNUM %in% c(10, 11)) %>%
mutate(
LBDT = if_else(TESTNUM == 10, NA, LBDT),
BRTHDT = if_else(TESTNUM == 11, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 10, 27, 28)
)
expected_tbili_daids <- expected_tbilinoage_daids %>%
bind_rows(
expected_tbiligt28d_daids,
expected_tbilile28d_daids
)
## Test 91: DAIDS Total Bilirubin, High ----
test_that("derive_var_atoxgr Test 91: DAIDS Total Bilirubin, High", {
input_tbili_daids <- expected_tbili_daids %>%
select(-ATOXGRH)
actual_tbili_daids <- derive_var_atoxgr_dir(
input_tbili_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_tbili_daids,
compare = actual_tbili_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Calcium, High
### >= 7 days of age
### Grade 4: >= 3.38 mmol/L
### Grade 3: 3.13 -< 3.38 mmol/L
### Grade 2: 2.88 -< 3.13 mmol/L
### Grade 1: 2.65 -< 2.88 mmol/L
expected_calcige7d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 1,
NA_character_, 3.5, "mmol/L", NA, 2,
# ANRHI not missing
"Calcium, High", 3.38, "mmol/L", "4", 3,
"Calcium, High", 3.37, "mmol/L", "3", 4,
"Calcium, High", 3.13, "mmol/L", "3", 5,
"Calcium, High", 3.12, "mmol/L", "2", 6,
"Calcium, High", 2.88, "mmol/L", "2", 7,
"Calcium, High", 2.87, "mmol/L", "1", 8,
"Calcium, High", 2.65, "mmol/L", "1", 9,
"Calcium, High", 2.64, "mmol/L", "0", 10,
# Unit missing cannot grade
"Calcium, High", 2.5, NA, NA, 11,
# AVAL missing cannot grade
"Calcium, High", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 7 days of age
### Grade 4: >= 3.38 mmol/L
### Grade 3: 3.23 -< 3.38 mmol/L
### Grade 2: 3.1 -< 3.23 mmol/L
### Grade 1: 2.88 -< 3.1 mmol/L
expected_calcilt7d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 13,
NA_character_, 3.5, "mmol/L", NA, 14,
# ANRHI not missing
"Calcium, High", 3.38, "mmol/L", "4", 15,
"Calcium, High", 3.37, "mmol/L", "3", 16,
"Calcium, High", 3.23, "mmol/L", "3", 17,
"Calcium, High", 3.22, "mmol/L", "2", 18,
"Calcium, High", 3.1, "mmol/L", "2", 19,
"Calcium, High", 3.09, "mmol/L", "1", 20,
"Calcium, High", 2.88, "mmol/L", "1", 21,
"Calcium, High", 2.87, "mmol/L", "0", 22,
# Unit missing cannot grade
"Calcium, High", 3.5, NA, NA, 23,
# AVAL missing cannot grade
"Calcium, High", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_calcinoage_daids <- expected_calcige7d_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_calci_daids <- expected_calcinoage_daids %>%
bind_rows(
expected_calcige7d_daids,
expected_calcilt7d_daids
)
## Test 92: DAIDS Calcium, High ----
test_that("derive_var_atoxgr Test 92: DAIDS Calcium, High", {
input_calci_daids <- expected_calci_daids %>%
select(-ATOXGRH)
actual_calci_daids <- derive_var_atoxgr_dir(
input_calci_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci_daids,
compare = actual_calci_daids,
keys = c("TESTNUM")
)
})
### Calcium (Ionized), High
### Grade 4: >= 1.8 mmol/L
### Grade 3: 1.6 -< 1.8 mmol/L
### Grade 2: 1.5 -< 1.6 mmol/L
### Grade 1: >ULN -< 1.5 mmol/L
## Test 93: DAIDS Calcium (Ionized), High ----
test_that("derive_var_atoxgr Test 93: DAIDS Calcium (Ionized), High", {
expected_calioni_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.8, 1.1, 1.4, "mmol/L", NA, 1,
NA_character_, 1.79, 1.1, 1.4, "mmol/L", NA, 2,
# ANRHI not missing
"Calcium (Ionized), High", 1.8, 1.1, 1.4, "mmol/L", "4", 3,
"Calcium (Ionized), High", 1.79, 1.1, 1.4, "mmol/L", "3", 4,
"Calcium (Ionized), High", 1.6, 1.1, 1.4, "mmol/L", "3", 5,
"Calcium (Ionized), High", 1.59, 1.1, 1.4, "mmol/L", "2", 6,
"Calcium (Ionized), High", 1.5, 1.1, 1.4, "mmol/L", "2", 7,
"Calcium (Ionized), High", 1.49, 1.1, 1.4, "mmol/L", "1", 8,
"Calcium (Ionized), High", 1.41, 1.1, 1.4, "mmol/L", "1", 9,
"Calcium (Ionized), High", 1.4, 1.1, 1.4, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Calcium (Ionized), High", 1.8, 1.1, NA, "mmol/L", "4", 11,
"Calcium (Ionized), High", 1.79, 1.1, NA, "mmol/L", "3", 12,
"Calcium (Ionized), High", 1.6, 1.1, NA, "mmol/L", "3", 13,
"Calcium (Ionized), High", 1.59, 1.1, NA, "mmol/L", "2", 14,
"Calcium (Ionized), High", 1.5, 1.1, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Calcium (Ionized), High", 1.49, 1.1, NA, "mmol/L", NA, 16,
"Calcium (Ionized), High", 1.41, 1.1, NA, "mmol/L", NA, 17,
"Calcium (Ionized), High", 1.4, 1.1, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Calcium (Ionized), High", 1.3, 1.1, 1.4, NA, NA, 19,
# AVAL missing cannot grade
"Calcium (Ionized), High", NA, 1.1, 1.4, "mmol/L", NA, 20,
)
input_calioni_daids <- expected_calioni_daids %>%
select(-ATOXGRH)
actual_calioni_daids <- derive_var_atoxgr_dir(
input_calioni_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni_daids,
compare = actual_calioni_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Calcium, Low
### >= 7 days of age
### Grade 4: < 1.53 mmol/L
### Grade 3: 1.53 -< 1.75 mmol/L
### Grade 2: 1.75 -< 1.95 mmol/L
### Grade 1: 1.95 -< 2.10 mmol/L
expected_calcdge7d_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2.2, "mmol/L", NA, 1,
NA_character_, 2.2, "mmol/L", NA, 2,
# ANRLO not missing
"Calcium, Low", 1.52, "mmol/L", "4", 3,
"Calcium, Low", 1.53, "mmol/L", "3", 4,
"Calcium, Low", 1.74, "mmol/L", "3", 5,
"Calcium, Low", 1.75, "mmol/L", "2", 6,
"Calcium, Low", 1.94, "mmol/L", "2", 7,
"Calcium, Low", 1.95, "mmol/L", "1", 8,
"Calcium, Low", 2.09, "mmol/L", "1", 9,
"Calcium, Low", 2.1, "mmol/L", "0", 10,
# Unit missing cannot grade
"Calcium, Low", 2.5, NA, NA, 11,
# AVAL missing cannot grade
"Calcium, Low", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 7 days of age
### Grade 4: < 1.38 mmol/L
### Grade 3: 1.38 -< 1.5 mmol/L
### Grade 2: 1.5 -< 1.63 mmol/L
### Grade 1: 1.63 -< 1.88 mmol/L
expected_calcdlt7d_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2.2, "mmol/L", NA, 13,
NA_character_, 2.2, "mmol/L", NA, 14,
# ANRLO not missing
"Calcium, Low", 1.37, "mmol/L", "4", 15,
"Calcium, Low", 1.38, "mmol/L", "3", 16,
"Calcium, Low", 1.49, "mmol/L", "3", 17,
"Calcium, Low", 1.5, "mmol/L", "2", 18,
"Calcium, Low", 1.62, "mmol/L", "2", 19,
"Calcium, Low", 1.63, "mmol/L", "1", 20,
"Calcium, Low", 1.87, "mmol/L", "1", 21,
"Calcium, Low", 1.88, "mmol/L", "0", 22,
# Unit missing cannot grade
"Calcium, Low", 2.2, NA, NA, 23,
# AVAL missing cannot grade
"Calcium, Low", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_calcdnoage_daids <- expected_calcdge7d_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_calcd_daids <- expected_calcdnoage_daids %>%
bind_rows(
expected_calcdge7d_daids,
expected_calcdlt7d_daids
)
## Test 94: DAIDS Calcium, Low ----
test_that("derive_var_atoxgr Test 94: DAIDS Calcium, Low", {
input_calcd_daids <- expected_calcd_daids %>%
select(-ATOXGRL)
actual_calcd_daids <- derive_var_atoxgr_dir(
input_calcd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd_daids,
compare = actual_calcd_daids,
keys = c("TESTNUM")
)
})
### Calcium (Ionized), Low
### Grade 4: <0.8 mmol/L
### Grade 3: 0.8 -< 0.9 mmol/L
### Grade 2: 0.9 -< 1.0 mmol/L
### Grade 1: 1.0 mmol/L -< LLN
## Test 95: DAIDS Calcium (Ionized), Low ----
test_that("derive_var_atoxgr Test 95: DAIDS Calcium (Ionized), Low", {
expected_caliond_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 0.79, 1.1, 100, "mmol/L", NA, 1,
NA_character_, 0.79, 1.1, 100, "mmol/L", NA, 2,
# ANRLO not missing
"Calcium (Ionized), Low", 0.79, 1.1, 100, "mmol/L", "4", 3,
"Calcium (Ionized), Low", 0.8, 1.1, 100, "mmol/L", "3", 4,
"Calcium (Ionized), Low", 0.89, 1.1, 100, "mmol/L", "3", 5,
"Calcium (Ionized), Low", 0.9, 1.1, 100, "mmol/L", "2", 6,
"Calcium (Ionized), Low", 0.99, 1.1, 100, "mmol/L", "2", 7,
"Calcium (Ionized), Low", 1, 1.1, 100, "mmol/L", "1", 8,
"Calcium (Ionized), Low", 1.09, 1.1, 100, "mmol/L", "1", 9,
"Calcium (Ionized), Low", 1.1, 1.1, 100, "mmol/L", "0", 10,
# ANRLO missing - can grade 2-4
"Calcium (Ionized), Low", 0.79, NA, 100, "mmol/L", "4", 11,
"Calcium (Ionized), Low", 0.8, NA, 100, "mmol/L", "3", 12,
"Calcium (Ionized), Low", 0.89, NA, 100, "mmol/L", "3", 13,
"Calcium (Ionized), Low", 0.9, NA, 100, "mmol/L", "2", 14,
"Calcium (Ionized), Low", 0.99, NA, 100, "mmol/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Calcium (Ionized), Low", 1, NA, 100, "mmol/L", NA, 16,
"Calcium (Ionized), Low", 1.09, NA, 100, "mmol/L", NA, 17,
"Calcium (Ionized), Low", 1.1, NA, 100, "mmol/L", NA, 18,
# Unit missing cannot grade
"Calcium (Ionized), Low", 1.1, 1.1, 100, NA, NA, 19,
# AVAL missing cannot grade
"Calcium (Ionized), Low", NA, 1.1, 100, "mmol/L", NA, 20,
)
input_caliond_daids <- expected_caliond_daids %>%
select(-ATOXGRL)
actual_caliond_daids <- derive_var_atoxgr_dir(
input_caliond_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond_daids,
compare = actual_caliond_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Creatine Kinase, High
### Grade 4: >= 20.0 x ULN
### Grade 3: 10.0 -< 20.0 x ULN
### Grade 2: 6 -< 10.0 x ULN
### Grade 1: 3 -< 6 x ULN
## Test 96: DAIDS Creatine Kinase, High ----
test_that("derive_var_atoxgr Test 96: DAIDS Creatine Kinase, High", {
expected_cki_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 10, 5, NA_character_, NA, 1,
NA_character_, 10, 5, NA_character_, NA, 2,
"Creatine Kinase, High", 100, 5, NA_character_, "4", 3,
"Creatine Kinase, High", 99, 5, NA_character_, "3", 4,
"Creatine Kinase, High", 50, 5, NA_character_, "3", 5,
"Creatine Kinase, High", 49, 5, NA_character_, "2", 6,
"Creatine Kinase, High", 30, 5, NA_character_, "2", 7,
"Creatine Kinase, High", 29, 5, NA_character_, "1", 8,
"Creatine Kinase, High", 15, 5, NA_character_, "1", 9,
"Creatine Kinase, High", 14, 5, NA_character_, "0", 10,
# ANRHI missing - cannot grade
"Creatine Kinase, High", 4, NA, NA_character_, NA, 11,
# AVAL missing cannot grade
"Creatine Kinase, High", NA, NA, NA_character_, NA, 12,
)
input_cki_daids <- expected_cki_daids %>%
select(-ATOXGRH)
actual_cki_daids <- derive_var_atoxgr_dir(
input_cki_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cki_daids,
compare = actual_cki_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Creatinine, High
### Grade 4: >= 3.5 x ULN or >= 2 X BASE
### Grade 3: >1.8 -< 3.5 x ULN or 1.5 -< 2 x BASE
### Grade 2: >1.3 - 1.8 x ULN or 1.3 - < 1.5 x BASE
### Grade 1: 1.1 - 1.3 x ULN
## Test 97: DAIDS Creatinine, High ----
test_that("derive_var_atoxgr Test 97: DAIDS Creatinine, High", {
expected_creati_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~BASE, ~ATOXGRH, ~TESTNUM,
"Not a term", 10, 10, 34, NA, 1,
NA_character_, 10, 10, 34, NA, 2,
"Creatinine, High", 35, 10, 34, "4", 3,
"Creatinine, High", 10, 10, 5, "4", 4,
"Creatinine, High", 34, 10, 34, "3", 5,
"Creatinine, High", 19, 10, 20, "3", 6,
"Creatinine, High", 9, 10, 5, "3", 7,
"Creatinine, High", 7.5, 10, 5, "3", 8,
"Creatinine, High", 18, 10, 34, "2", 9,
"Creatinine, High", 14, 10, 20, "2", 10,
"Creatinine, High", 7.4, 10, 5, "2", 11,
"Creatinine, High", 6.5, 10, 5, "2", 12,
"Creatinine, High", 13, 10, 34, "1", 13,
"Creatinine, High", 11, 10, 20, "1", 14,
"Creatinine, High", 10, 10, 20, "0", 15,
# ANRHI missing - cannot grade
"Creatinine, High", 10, NA, 20, NA, 16,
# AVAL missing cannot grade
"Creatinine, High", NA, 10, 20, NA, 18,
) %>%
mutate(AVALU = NA_character_)
input_creati_daids <- expected_creati_daids %>%
select(-ATOXGRH)
actual_creati_daids <- derive_var_atoxgr_dir(
input_creati_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creati_daids,
compare = actual_creati_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose Fasting, High
### Grade 4: >= 27.75 mmol/L
### Grade 3: 13.89 -< 27.75 mmol/L
### Grade 2: 6.95 -< 13.89 mmol/L
### Grade 1: 6.11 -< 6.95 mmol/L
## Test 98: DAIDS Glucose Fasting, High ----
test_that("derive_var_atoxgr Test 98: DAIDS Glucose Fasting, High", {
expected_glucfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 9.5, "mmol/L", NA, 2,
"Glucose Fasting, High", 27.75, "mmol/L", "4", 3,
"Glucose Fasting, High", 27.74, "mmol/L", "3", 4,
"Glucose Fasting, High", 13.89, "mmol/L", "3", 5,
"Glucose Fasting, High", 13.88, "mmol/L", "2", 6,
"Glucose Fasting, High", 6.95, "mmol/L", "2", 7,
"Glucose Fasting, High", 6.94, "mmol/L", "1", 8,
"Glucose Fasting, High", 6.11, "mmol/L", "1", 9,
"Glucose Fasting, High", 6.1, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose Fasting, High", 7, NA, NA, 11,
# AVAL missing cannot grade
"Glucose Fasting, High", NA, "mmol/L", NA, 12,
)
input_glucfi_daids <- expected_glucfi_daids %>%
select(-ATOXGRH)
actual_glucfi_daids <- derive_var_atoxgr_dir(
input_glucfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucfi_daids,
compare = actual_glucfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose Nonfasting, High
### Grade 4: >= 27.75 mmol/L
### Grade 3: 13.89 -< 27.75 mmol/L
### Grade 2: 8.89 -< 13.89 mmol/L
### Grade 1: 6.44 -< 8.89 mmol/L
## Test 99: DAIDS Glucose Nonfasting, High ----
test_that("derive_var_atoxgr Test 99: DAIDS Glucose Nonfasting, High", {
expected_glucnfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 9.5, "mmol/L", NA, 2,
"Glucose Nonfasting, High", 27.75, "mmol/L", "4", 3,
"Glucose Nonfasting, High", 27.74, "mmol/L", "3", 4,
"Glucose Nonfasting, High", 13.89, "mmol/L", "3", 5,
"Glucose Nonfasting, High", 13.88, "mmol/L", "2", 6,
"Glucose Nonfasting, High", 8.89, "mmol/L", "2", 7,
"Glucose Nonfasting, High", 8.88, "mmol/L", "1", 8,
"Glucose Nonfasting, High", 6.44, "mmol/L", "1", 9,
"Glucose Nonfasting, High", 6.43, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose Nonfasting, High", 7, NA, NA, 11,
# AVAL missing cannot grade
"Glucose Nonfasting, High", NA, "mmol/L", NA, 12,
)
input_glucnfi_daids <- expected_glucnfi_daids %>%
select(-ATOXGRH)
actual_glucnfi_daids <- derive_var_atoxgr_dir(
input_glucnfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucnfi_daids,
compare = actual_glucnfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose, Low
### >= 1 month of age
### Grade 4: < 1.67 mmol/L
### Grade 3: 1.67 -< 2.22 mmol/L
### Grade 2: 2.22 -< 3.05 mmol/L
### Grade 1: 3.05 -< 3.55 mmol/L
expected_glucdge1m_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 4.1, "mmol/L", NA, 2,
"Glucose, Low", 1.66, "mmol/L", "4", 3,
"Glucose, Low", 1.67, "mmol/L", "3", 4,
"Glucose, Low", 2.21, "mmol/L", "3", 5,
"Glucose, Low", 2.22, "mmol/L", "2", 6,
"Glucose, Low", 3.04, "mmol/L", "2", 7,
"Glucose, Low", 3.05, "mmol/L", "1", 8,
"Glucose, Low", 3.54, "mmol/L", "1", 9,
"Glucose, Low", 3.55, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose, Low", 4, NA, NA, 11,
# AVAL missing cannot grade
"Glucose, Low", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2022-11-30"),
LBDT = lubridate::ymd("2022-12-30"),
)
### < 1 month of age
### Grade 4: < 1.67 mmol/L
### Grade 3: 1.67 -< 2.22 mmol/L
### Grade 2: 2.22 -< 2.78 mmol/L
### Grade 1: 2.78 -< 3.00 mmol/L
expected_glucdlt1m_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 13,
NA_character_, 4.1, "mmol/L", NA, 14,
"Glucose, Low", 1.66, "mmol/L", "4", 15,
"Glucose, Low", 1.67, "mmol/L", "3", 16,
"Glucose, Low", 2.21, "mmol/L", "3", 17,
"Glucose, Low", 2.22, "mmol/L", "2", 18,
"Glucose, Low", 2.77, "mmol/L", "2", 19,
"Glucose, Low", 2.78, "mmol/L", "1", 20,
"Glucose, Low", 2.99, "mmol/L", "1", 21,
"Glucose, Low", 3, "mmol/L", "0", 22,
# AVALU missing cannot grade
"Glucose, Low", 4, NA, NA, 23,
# AVAL missing cannot grade
"Glucose, Low", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2022-11-30"),
LBDT = lubridate::ymd("2022-12-29"),
)
expected_glucdnoage_daids <- expected_glucdge1m_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
ATOXGRL = NA_character_,
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_glucd_daids <- expected_glucdnoage_daids %>%
bind_rows(
expected_glucdge1m_daids,
expected_glucdlt1m_daids
)
## Test 100: DAIDS Glucose, Low ----
test_that("derive_var_atoxgr Test 100: DAIDS Glucose, Low", {
input_glucd_daids <- expected_glucd_daids %>%
select(-ATOXGRL)
actual_glucd_daids <- derive_var_atoxgr_dir(
input_glucd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucd_daids,
compare = actual_glucd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Lactate, High
### Grade 2: >= 2.0 x ULN
### Grade 1: ULN -< 2.0 x ULN
## Test 101: DAIDS Lactate, High ----
test_that("derive_var_atoxgr Test 101: DAIDS Lactate, High", {
expected_lacti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 105, 100, NA, 1,
NA_character_, 105, 100, NA, 2,
"Lactate, High", 200, 100, "2", 3,
"Lactate, High", 199, 100, "1", 4,
"Lactate, High", 100, 100, "1", 5,
"Lactate, High", 99, 100, "0", 6,
# ANRHI missing cannot grade
"Lactate, High", 200, NA, NA, 7,
# AVAL missing cannot grade
"Lactate, High", NA, 100, NA, 8,
) %>%
mutate(AVALU = NA_character_)
input_lacti_daids <- expected_lacti_daids %>%
select(-ATOXGRH)
actual_lacti_daids <- derive_var_atoxgr_dir(
input_lacti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lacti_daids,
compare = actual_lacti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Lipase, High
### Grade 4: >= 5.0 x ULN
### Grade 3: 3.0 -< 5.0 x ULN
### Grade 2: 1.5 -< 3.0 x ULN
### Grade 1: 1.1 -< 1.5 x ULN
## Test 102: DAIDS Lipase, High ----
test_that("derive_var_atoxgr Test 102: DAIDS Lipase, High", {
expected_lipi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 100, NA, 1,
NA_character_, 60, 100, NA, 2,
"Lipase, High", 500, 100, "4", 3,
"Lipase, High", 499, 100, "3", 4,
"Lipase, High", 300, 100, "3", 5,
"Lipase, High", 299, 100, "2", 6,
"Lipase, High", 150, 100, "2", 7,
"Lipase, High", 149, 100, "1", 8,
"Lipase, High", 110, 100, "1", 9,
"Lipase, High", 109, 100, "0", 10,
# ANRHI missing cannot grade
"Lipase, High", 200, NA, NA, 11,
# AVAL missing cannot grade
"Lipase, High", NA, 100, NA, 12,
) %>%
mutate(AVALU = NA_character_)
input_lipi_daids <- expected_lipi_daids %>%
select(-ATOXGRH)
actual_lipi_daids <- derive_var_atoxgr_dir(
input_lipi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lipi_daids,
compare = actual_lipi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Cholesterol, Fasting, High
### >= 18 years of age
### Grade 3: >= 7.77 mmol/L
### Grade 2: 6.19 -< 7.77 mmol/L
### Grade 1: 5.18 -< 6.19 mmol/L
expected_cholfige18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 1,
NA_character_, 3.5, "mmol/L", NA, 2,
"Cholesterol, Fasting, High", 7.77, "mmol/L", "3", 3,
"Cholesterol, Fasting, High", 7.76, "mmol/L", "2", 4,
"Cholesterol, Fasting, High", 6.19, "mmol/L", "2", 5,
"Cholesterol, Fasting, High", 6.18, "mmol/L", "1", 6,
"Cholesterol, Fasting, High", 5.18, "mmol/L", "1", 7,
"Cholesterol, Fasting, High", 5.17, "mmol/L", "0", 8,
# Unit missing cannot grade
"Cholesterol, Fasting, High", 3.5, NA, NA, 9,
# AVAL missing cannot grade
"Cholesterol, Fasting, High", NA, "mmol/L", NA, 10,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 18 years of age
### Grade 3: >= 7.77 mmol/L
### Grade 2: 5.15 -< 7.77 mmol/L
### Grade 1: 4.4 -< 5.15 mmol/L
expected_cholfilt18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 13,
NA_character_, 3.5, "mmol/L", NA, 14,
"Cholesterol, Fasting, High", 7.77, "mmol/L", "3", 15,
"Cholesterol, Fasting, High", 7.76, "mmol/L", "2", 16,
"Cholesterol, Fasting, High", 5.15, "mmol/L", "2", 17,
"Cholesterol, Fasting, High", 5.14, "mmol/L", "1", 18,
"Cholesterol, Fasting, High", 4.4, "mmol/L", "1", 19,
"Cholesterol, Fasting, High", 4.39, "mmol/L", "0", 20,
# Unit missing cannot grade
"Cholesterol, Fasting, High", 3.5, NA, NA, 21,
# AVAL missing cannot grade
"Cholesterol, Fasting, High", NA, "mmol/L", NA, 22,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_cholfinoage_daids <- expected_cholfige18y_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_cholfi_daids <- expected_cholfinoage_daids %>%
bind_rows(
expected_cholfige18y_daids,
expected_cholfilt18y_daids
)
## Test 103: DAIDS Cholesterol, Fasting, High ----
test_that("derive_var_atoxgr Test 103: DAIDS Cholesterol, Fasting, High", {
input_cholfi_daids <- expected_cholfi_daids %>%
select(-ATOXGRH)
actual_cholfi_daids <- derive_var_atoxgr_dir(
input_cholfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cholfi_daids,
compare = actual_cholfi_daids,
keys = c("TESTNUM")
)
})
### LDL, Fasting, High
### >= 18 years of age
### Grade 3: >= 4.90 mmol/L
### Grade 2: 4.12 -< 4.90 mmol/L
### Grade 1: 3.17 -< 4.12 mmol/L
expected_ldlfige18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.1, "mmol/L", NA, 1,
NA_character_, 3.1, "mmol/L", NA, 2,
"LDL, Fasting, High", 4.9, "mmol/L", "3", 3,
"LDL, Fasting, High", 4.89, "mmol/L", "2", 4,
"LDL, Fasting, High", 4.12, "mmol/L", "2", 5,
"LDL, Fasting, High", 4.11, "mmol/L", "1", 6,
"LDL, Fasting, High", 3.37, "mmol/L", "1", 7,
"LDL, Fasting, High", 3.36, "mmol/L", "0", 8,
# Unit missing cannot grade
"LDL, Fasting, High", 3.1, NA, NA, 9,
# AVAL missing cannot grade
"LDL, Fasting, High", NA, "mmol/L", NA, 10,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-08")
)
### > 2 to < 18 years of age
### Grade 3: >= 4.90 mmol/L
### Grade 2: 3.34 -< 4.90 mmol/L
### Grade 1: 2.85 -< 3.34 mmol/L
expected_ldlfilt18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 2.8, "mmol/L", NA, 11,
NA_character_, 2.8, "mmol/L", NA, 12,
"LDL, Fasting, High", 4.9, "mmol/L", "3", 13,
"LDL, Fasting, High", 4.89, "mmol/L", "2", 14,
"LDL, Fasting, High", 3.34, "mmol/L", "2", 15,
"LDL, Fasting, High", 3.33, "mmol/L", "1", 16,
"LDL, Fasting, High", 2.85, "mmol/L", "1", 17,
"LDL, Fasting, High", 2.84, "mmol/L", "0", 18,
# Unit missing cannot grade
"LDL, Fasting, High", 3.5, NA, NA, 19,
# AVAL missing cannot grade
"LDL, Fasting, High", NA, "mmol/L", NA, 20,
) %>%
mutate(
BRTHDT = lubridate::ymd("2020-01-07"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_ldlfinoage_daids <- expected_ldlfige18y_daids %>%
filter(TESTNUM %in% c(7, 8)) %>%
mutate(
LBDT = if_else(TESTNUM == 7, NA, LBDT),
BRTHDT = if_else(TESTNUM == 8, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 7, 25, 26)
)
expected_ldlfile2y_daids <- expected_ldlfige18y_daids %>%
filter(TESTNUM %in% c(7, 8)) %>%
mutate(
BRTHDT = if_else(TESTNUM == 7, lubridate::ymd("2021-01-07"), lubridate::ymd("2022-01-07")),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 7, 27, 28)
)
expected_ldlfi_daids <- expected_ldlfile2y_daids %>%
bind_rows(
expected_ldlfinoage_daids,
expected_ldlfige18y_daids,
expected_ldlfilt18y_daids
)
## Test 104: DAIDS LDL, Fasting, High ----
test_that("derive_var_atoxgr Test 104: DAIDS LDL, Fasting, High", {
input_ldlfi_daids <- expected_ldlfi_daids %>%
select(-ATOXGRH)
actual_ldlfi_daids <- derive_var_atoxgr_dir(
input_ldlfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ldlfi_daids,
compare = actual_ldlfi_daids,
keys = c("TESTNUM")
)
})
### Triglycerides, Fasting, High
### Grade 4: > 11.4 mmol/L
### Grade 3: >5.7 - 11.4 mmol/L
### Grade 2: >3.42 - 5.7 mmol/L
### Grade 1: 1.71 - 3.42 mmol/L
## Test 105: DAIDS Triglycerides, Fasting, High ----
test_that("derive_var_atoxgr Test 105: DAIDS Triglycerides, Fasting, High", {
expected_trigfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.5, "mmol/L", NA, 1,
NA_character_, 1.5, "mmol/L", NA, 2,
"Triglycerides, Fasting, High", 11.5, "mmol/L", "4", 3,
"Triglycerides, Fasting, High", 11.4, "mmol/L", "3", 4,
"Triglycerides, Fasting, High", 5.8, "mmol/L", "3", 5,
"Triglycerides, Fasting, High", 5.7, "mmol/L", "2", 6,
"Triglycerides, Fasting, High", 3.43, "mmol/L", "2", 7,
"Triglycerides, Fasting, High", 3.42, "mmol/L", "1", 8,
"Triglycerides, Fasting, High", 1.71, "mmol/L", "1", 9,
"Triglycerides, Fasting, High", 1.7, "mmol/L", "0", 10,
# Unit missing cannot grade
"Triglycerides, Fasting, High", 1.5, NA, NA, 11,
# AVAL missing cannot grade
"Triglycerides, Fasting, High", NA, "mmol/L", NA, 12,
)
input_trigfi_daids <- expected_trigfi_daids %>%
select(-ATOXGRH)
actual_trigfi_daids <- derive_var_atoxgr_dir(
input_trigfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigfi_daids,
compare = actual_trigfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Magnesium, Low
### Grade 4: <0.3 mmol/L
### Grade 3: 0.3 -< 0.45 mmol/L
### Grade 2: 0.45 -< 0.6 mmol/L
### Grade 1: 0.6 -< 0.7 mmol/L
## Test 106: DAIDS Magnesium, Low ----
test_that("derive_var_atoxgr Test 106: DAIDS Magnesium, Low", {
expected_magd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 0.5, "mmol/L", NA, 1,
NA_character_, 0.5, "mmol/L", NA, 2,
"Magnesium, Low", 0.29, "mmol/L", "4", 3,
"Magnesium, Low", 0.3, "mmol/L", "3", 4,
"Magnesium, Low", 0.44, "mmol/L", "3", 5,
"Magnesium, Low", 0.45, "mmol/L", "2", 6,
"Magnesium, Low", 0.59, "mmol/L", "2", 7,
"Magnesium, Low", 0.6, "mmol/L", "1", 8,
"Magnesium, Low", 0.69, "mmol/L", "1", 9,
"Magnesium, Low", 0.7, "mmol/L", "0", 10,
# Unit missing cannot grade
"Magnesium, Low", 0.5, NA, NA, 11,
# AVAL missing cannot grade
"Magnesium, Low", NA, "mmol/L", NA, 12,
)
input_magd_daids <- expected_magd_daids %>%
select(-ATOXGRL)
actual_magd_daids <- derive_var_atoxgr_dir(
input_magd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magd_daids,
compare = actual_magd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Phosphate, Low
### > 14 years of age
### Grade 4: < 0.32 mmol/L
### Grade 3: 0.32 to < 0.45 mmol/L
### Grade 2: 0.45 to < 0.65 mmol/L
### Grade 1: 0.65 mmol/L to < LLN mmol/L
expected_phosd_daids_gt14y <- tibble::tribble(
~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.9, 0.8, "MM3", NA, 1,
0.31, 0.8, "mmol/L", "4", 2,
0.32, 0.8, "mmol/L", "3", 3,
0.44, 0.8, "mmol/L", "3", 4,
0.45, 0.8, "mmol/L", "2", 5,
0.64, 0.8, "mmol/L", "2", 6,
0.65, 0.8, "mmol/L", "1", 7,
0.79, 0.8, "mmol/L", "1", 8,
0.8, 0.8, "mmol/L", "0", 9,
# missing ANRLO - can grade 2 - 4
0.31, 0.8, "mmol/L", "4", 10,
0.32, 0.8, "mmol/L", "3", 11,
0.44, 0.8, "mmol/L", "3", 12,
0.45, 0.8, "mmol/L", "2", 13,
0.64, 0.8, "mmol/L", "2", 14,
# missing ANRLO - can grade 0 - 1
0.65, 0.8, "mmol/L", "1", 15,
0.79, 0.8, "mmol/L", "1", 16,
0.8, 0.8, "mmol/L", "0", 17,
# missing AVAL
NA, 0.8, "mmol/L", NA, 18,
# missing UNIT
1, 0.8, NA, NA, 19,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2008-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### 1 to 14 years of age
### Grade 4: < 0.48 mmol/L
### Grade 3: 0.48 to < 0.81 mmol/L
### Grade 2: 0.81 to < 0.97 mmol/L
### Grade 1: 0.97 to <1.13 mmol/L
expected_phosd_daids_le14y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.2, "MM3", NA, 20,
0.47, "mmol/L", "4", 21,
0.48, "mmol/L", "3", 22,
0.8, "mmol/L", "3", 23,
0.81, "mmol/L", "2", 24,
0.96, "mmol/L", "2", 25,
0.97, "mmol/L", "1", 26,
1.12, "mmol/L", "1", 27,
1.13, "mmol/L", "0", 28,
NA, "mmol/L", NA, 29,
1, NA, NA, 30,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2022-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### < 1 year of age
### Grade 4: < 0.48 mmol/L
### Grade 3: 0.48 to < 0.81 mmol/L
### Grade 2: 0.81 to < 1.13 mmol/L
### Grade 1: 1.13 to < 1.45 mmol/L
expected_phosd_daids_lt1y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.5, "MM3", NA, 31,
0.47, "mmol/L", "4", 32,
0.48, "mmol/L", "3", 33,
0.8, "mmol/L", "3", 34,
0.81, "mmol/L", "2", 35,
1.12, "mmol/L", "2", 36,
1.13, "mmol/L", "1", 37,
1.44, "mmol/L", "1", 38,
1.45, "mmol/L", "0", 39,
NA, "mmol/L", NA, 40,
1.5, NA, NA, 41,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-02")
)
# Set lab date or birth date to missing
expected_phosd_daids_noage <- expected_phosd_daids_gt14y %>%
filter(TESTNUM %in% c(8, 9)) %>%
mutate(
LBDT = if_else(TESTNUM == 8, NA, LBDT),
BRTHDT = if_else(TESTNUM == 9, NA, BRTHDT),
ATOXGRL = NA,
TESTNUM = if_else(TESTNUM == 8, 42, 43)
)
expected_phosd_daids <- expected_phosd_daids_gt14y %>%
bind_rows(
expected_phosd_daids_le14y,
expected_phosd_daids_lt1y,
expected_phosd_daids_noage
)
## Test 107: DAIDS Phosphate, Low ----
test_that("derive_var_atoxgr Test 107: DAIDS Phosphate, Low", {
input_phosd_daids <- expected_phosd_daids %>%
select(-ATOXGRL)
actual_phosd_daids <- derive_var_atoxgr_dir(
input_phosd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_phosd_daids,
compare = actual_phosd_daids,
keys = c("TESTNUM")
)
})
### Potassium, High
### Grade 4: >= 7 mmol/L
### Grade 3: 6.5 -< 7 mmol/L
### Grade 2: 6 -< 6.5 mmol/L
### Grade 1: 5.6 -< 6 mmol/L
## Test 108: DAIDS Potassium, High ----
test_that("derive_var_atoxgr Test 108: DAIDS Potassium, High", {
expected_poti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 5, "mmol/L", NA, 1,
NA_character_, 5, "mmol/L", NA, 2,
"Potassium, High", 7, "mmol/L", "4", 3,
"Potassium, High", 6.9, "mmol/L", "3", 4,
"Potassium, High", 6.5, "mmol/L", "3", 5,
"Potassium, High", 6.4, "mmol/L", "2", 6,
"Potassium, High", 6, "mmol/L", "2", 7,
"Potassium, High", 5.9, "mmol/L", "1", 8,
"Potassium, High", 5.6, "mmol/L", "1", 9,
"Potassium, High", 5.5, "mmol/L", "0", 10,
# Unit missing cannot grade
"Potassium, High", 5, NA, NA, 11,
# AVAL missing cannot grade
"Potassium, High", NA, "mmol/L", NA, 12,
)
input_poti_daids <- expected_poti_daids %>%
select(-ATOXGRH)
actual_poti_daids <- derive_var_atoxgr_dir(
input_poti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_poti_daids,
compare = actual_poti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Potassium, Low
### Grade 4: <2 mmol/L
### Grade 3: 2 -< 2.5 mmol/L
### Grade 2: 2.5 -< 3 mmol/L
### Grade 1: 3 -< 3.4 mmol/L
## Test 109: DAIDS Potassium, Low ----
test_that("derive_var_atoxgr Test 109: DAIDS Potassium, Low", {
expected_potd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 3, "mmol/L", NA, 1,
NA_character_, 3, "mmol/L", NA, 2,
"Potassium, Low", 1.9, "mmol/L", "4", 3,
"Potassium, Low", 2, "mmol/L", "3", 4,
"Potassium, Low", 2.4, "mmol/L", "3", 5,
"Potassium, Low", 2.5, "mmol/L", "2", 6,
"Potassium, Low", 2.9, "mmol/L", "2", 7,
"Potassium, Low", 3, "mmol/L", "1", 8,
"Potassium, Low", 3.3, "mmol/L", "1", 9,
"Potassium, Low", 3.4, "mmol/L", "0", 10,
# Unit missing cannot grade
"Potassium, Low", 3, NA, NA, 11,
# AVAL missing cannot grade
"Potassium, Low", NA, "mmol/L", NA, 12,
)
input_potd_daids <- expected_potd_daids %>%
select(-ATOXGRL)
actual_potd_daids <- derive_var_atoxgr_dir(
input_potd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_potd_daids,
compare = actual_potd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Sodium, High
### Grade 4: >= 160 mmol/L
### Grade 3: 154 -< 160 mmol/L
### Grade 2: 150 -< 154 mmol/L
### Grade 1: 146 -< 150 mmol/L
## Test 110: DAIDS Sodium, High ----
test_that("derive_var_atoxgr Test 110: DAIDS Sodium, High", {
expected_sodi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 146, "mmol/L", NA, 1,
NA_character_, 146, "mmol/L", NA, 2,
"Sodium, High", 160, "mmol/L", "4", 3,
"Sodium, High", 159, "mmol/L", "3", 4,
"Sodium, High", 154, "mmol/L", "3", 5,
"Sodium, High", 153, "mmol/L", "2", 6,
"Sodium, High", 150, "mmol/L", "2", 7,
"Sodium, High", 149, "mmol/L", "1", 8,
"Sodium, High", 146, "mmol/L", "1", 9,
"Sodium, High", 145, "mmol/L", "0", 10,
# Unit missing cannot grade
"Sodium, High", 140, NA, NA, 11,
# AVAL missing cannot grade
"Sodium, High", NA, "mmol/L", NA, 12,
)
input_sodi_daids <- expected_sodi_daids %>%
select(-ATOXGRH)
actual_sodi_daids <- derive_var_atoxgr_dir(
input_sodi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_sodi_daids,
compare = actual_sodi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Sodium, Low
### Grade 4: <= 120 mmol/L
### Grade 3: >120 -< 125 mmol/L
### Grade 2: 125 -< 130 mmol/L
### Grade 1: 130 -< 135 mmol/L
## Test 111: DAIDS Sodium, Low ----
test_that("derive_var_atoxgr Test 111: DAIDS Sodium, Low", {
expected_sodd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 119, "mmol/L", NA, 1,
NA_character_, 119, "mmol/L", NA, 2,
"Sodium, Low", 120, "mmol/L", "4", 3,
"Sodium, Low", 121, "mmol/L", "3", 4,
"Sodium, Low", 124, "mmol/L", "3", 5,
"Sodium, Low", 125, "mmol/L", "2", 6,
"Sodium, Low", 129, "mmol/L", "2", 7,
"Sodium, Low", 130, "mmol/L", "1", 8,
"Sodium, Low", 134, "mmol/L", "1", 9,
"Sodium, Low", 135, "mmol/L", "0", 10,
# Unit missing cannot grade
"Sodium, Low", 140, NA, NA, 11,
# AVAL missing cannot grade
"Sodium, Low", NA, "mmol/L", NA, 12,
)
input_sodd_daids <- expected_sodd_daids %>%
select(-ATOXGRL)
actual_sodd_daids <- derive_var_atoxgr_dir(
input_sodd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_sodd_daids,
compare = actual_sodd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Uric Acid, High
### Grade 4: >= 890 umol/L (0.89 mmol/L)
### Grade 3: 710 -< 890 umol/L (0.71 - <0.89 mmol/L)
### Grade 2: 590 -< 710 umol/L (0.59 - <0.71 mmol/L)
### Grade 1: 450 -< 590 umol/L (0.45 - <0.59 mmol/L)
## Test 112: DAIDS Uric Acid, High ----
test_that("derive_var_atoxgr Test 112: DAIDS Uric Acid, High", {
expected_urici_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 591, "umol/L", NA, 1,
NA_character_, 591, "umol/L", NA, 2,
"Uric Acid, High", 890, "umol/L", "4", 3,
"Uric Acid, High", 889, "umol/L", "3", 4,
"Uric Acid, High", 710, "umol/L", "3", 5,
"Uric Acid, High", 709, "umol/L", "2", 6,
"Uric Acid, High", 590, "umol/L", "2", 7,
"Uric Acid, High", 589, "umol/L", "1", 8,
"Uric Acid, High", 450, "umol/L", "1", 9,
"Uric Acid, High", 449, "umol/L", "0", 10,
# Unit missing cannot grade
"Uric Acid, High", 200, NA, NA, 11,
# AVAL missing cannot grade
"Uric Acid, High", NA, "umol/L", NA, 12,
)
input_urici_daids <- expected_urici_daids %>%
select(-ATOXGRH)
actual_urici_daids <- derive_var_atoxgr_dir(
input_urici_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici_daids,
compare = actual_urici_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Absolute CD4+ Count, Low
### > 5 years of age
### Grade 4: < 0.1 10^9/L
### Grade 3: 0.1 to < 0.2 10^9/L
### Grade 2: 0.2 to < 0.3 10^9/L
### Grade 1: 0.3 to < 0.4 10^9/L
## Test 113: DAIDS Absolute Lymphocyte Count, Low ----
test_that("derive_var_atoxgr Test 113: DAIDS Absolute Lymphocyte Count, Low", {
expected_cd4d_daids_gt5y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.1, "MM3", NA, 1,
0.09, "10^9/L", "4", 2,
0.1, "10^9/L", "3", 3,
0.19, "10^9/L", "3", 4,
0.2, "10^9/L", "2", 5,
0.29, "10^9/L", "2", 6,
0.3, "10^9/L", "1", 7,
0.39, "10^9/L", "1", 8,
0.4, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute CD4+ Count, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2029-07-01")
)
# no criteria for age <= 5 years set grade to missing
expected_cd4d_daids_le5y <- expected_cd4d_daids_gt5y %>%
mutate(
LBDT = lubridate::ymd("2028-07-01"),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
# add missing LBDT and BRTHDT
expected_cd4d_daids_noage <- expected_cd4d_daids_gt5y %>%
filter(TESTNUM %in% c(5, 6)) %>%
mutate(
LBDT = if_else(TESTNUM == 5, NA, LBDT),
BRTHDT = if_else(TESTNUM == 6, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 5, 23, 24)
)
expected_cd4d_daids <- expected_cd4d_daids_gt5y %>%
bind_rows(
expected_cd4d_daids_le5y,
expected_cd4d_daids_noage
)
input_cd4d_daids <- expected_cd4d_daids %>%
select(-ATOXGRL)
actual_cd4d_daids <- derive_var_atoxgr_dir(
input_cd4d_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4d_daids,
compare = actual_cd4d_daids,
keys = c("TESTNUM")
)
})
### Absolute Lymphocyte Count, Low
### > 5 years of age
### Grade 4: < 0.35 10^9/L
### Grade 3: 0.35 to < 0.5 10^9/L
### Grade 2: 0.5 to < 0.6 10^9/L
### Grade 1: 0.6 to < 0.65 10^9/L
## Test 114: DAIDS Absolute Lymphocyte Count, Low ----
test_that("derive_var_atoxgr Test 114: DAIDS Absolute Lymphocyte Count, Low", {
expected_lymphd_daids_gt5y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.35, "MM3", NA, 1,
0.34, "10^9/L", "4", 2,
0.35, "10^9/L", "3", 3,
0.49, "10^9/L", "3", 4,
0.5, "10^9/L", "2", 5,
0.59, "10^9/L", "2", 6,
0.6, "10^9/L", "1", 7,
0.64, "10^9/L", "1", 8,
0.65, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute Lymphocyte Count, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2029-07-01")
)
# no criteria for age <= 5 years set grade to missing
expected_lymphd_daids_le5y <- expected_lymphd_daids_gt5y %>%
mutate(
LBDT = lubridate::ymd("2028-07-01"),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
# add missing LBDT and BRTHDT
expected_lymphd_daids_noage <- expected_lymphd_daids_gt5y %>%
filter(TESTNUM %in% c(5, 6)) %>%
mutate(
LBDT = if_else(TESTNUM == 5, NA, LBDT),
BRTHDT = if_else(TESTNUM == 6, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 5, 23, 24)
)
expected_lymphd_daids <- expected_lymphd_daids_gt5y %>%
bind_rows(
expected_lymphd_daids_le5y,
expected_lymphd_daids_noage
)
input_lymphd_daids <- expected_lymphd_daids %>%
select(-ATOXGRL)
actual_lymphd_daids <- derive_var_atoxgr_dir(
input_lymphd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymphd_daids,
compare = actual_lymphd_daids,
keys = c("TESTNUM")
)
})
### Absolute Neutrophil Count (ANC), Low
### > 7 days of age
### Grade 4: < 0.4 10^9/L
### Grade 3: 0.4 to < 0.6 10^9/L
### Grade 2: 0.6 to < 0.8 10^9/L
### Grade 1: 0.8 to 1 10^9/L
expected_ancd_daids_gt7d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.3, "MM3", NA, 1,
0.399, "10^9/L", "4", 2,
0.4, "10^9/L", "3", 3,
0.599, "10^9/L", "3", 4,
0.6, "10^9/L", "2", 5,
0.799, "10^9/L", "2", 6,
0.8, "10^9/L", "1", 7,
1, "10^9/L", "1", 8,
1.01, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-09")
)
### 2 to 7 days of age
### Grade 4: < 0.75 10^9/L
### Grade 3: 0.75 to < 1.0 10^9/L
### Grade 2: 1.0 to < 1.25 10^9/L
### Grade 1: 1.25 to 1.5 10^9/L
expected_ancd_daids_ge2d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.7, "MM3", NA, 12,
0.749, "10^9/L", "4", 13,
0.75, "10^9/L", "3", 14,
0.999, "10^9/L", "3", 15,
1, "10^9/L", "2", 16,
1.249, "10^9/L", "2", 17,
1.25, "10^9/L", "1", 18,
1.5, "10^9/L", "1", 19,
1.51, "10^9/L", "0", 20,
NA, "10^9/L", NA, 21,
1, NA, NA, 22,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-03")
)
### <= 1 day of age
### Grade 4: < 1.50 10^9/L
### Grade 3: 1.50 to < 3.0 10^9/L
### Grade 2: 3.0 to < 4.0 10^9/L
### Grade 1: 4.0 to 5.0 10^9/L
expected_ancd_daids_le1d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.5, "MM3", NA, 23,
1.499, "10^9/L", "4", 24,
1.5, "10^9/L", "3", 25,
2.999, "10^9/L", "3", 26,
3, "10^9/L", "2", 27,
3.999, "10^9/L", "2", 28,
4, "10^9/L", "1", 29,
5, "10^9/L", "1", 30,
5.01, "10^9/L", "0", 31,
NA, "10^9/L", NA, 32,
5, NA, NA, 33,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-02")
)
expected_ancd_daids <- expected_ancd_daids_gt7d %>%
bind_rows(
expected_ancd_daids_ge2d,
expected_ancd_daids_le1d
)
# Set lab date/birth date to missing
expected_ancd_daids_noage <- expected_ancd_daids %>%
filter(TESTNUM %in% c(20, 31)) %>%
mutate(
LBDT = if_else(TESTNUM == 20, NA, LBDT),
BRTHDT = if_else(TESTNUM == 31, NA, BRTHDT),
ATOXGRL = NA,
TESTNUM = case_when(
TESTNUM == 20 ~ 34,
TESTNUM == 31 ~ 35
)
)
expected_ancd_daids <- expected_ancd_daids %>%
bind_rows(expected_ancd_daids_noage)
input_ancd_daids <- expected_ancd_daids %>%
select(-ATOXGRL)
## Test 115: DAIDS ANC Low ----
test_that("derive_var_atoxgr Test 115: DAIDS ANC Low", {
actual_ancd_daids <- derive_var_atoxgr_dir(
input_ancd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ancd_daids,
compare = actual_ancd_daids,
keys = c("TESTNUM")
)
})
### Fibrinogen Decreased
### Grade 4: <0.5 g/L OR < 0.25 x LLN
### Grade 3: 0.5 to <0.75 g/L OR 0.25 to < 0.50 x LLN
### Grade 2: 0.75 to <1 g/L OR ≥ 0.50 to < 0.75 x LLN
### Grade 1: 1 to < 2 g/L OR 0.75 to < 1.00 x LLN
## Test 116: DAIDS Fibrinogen Decreased ----
test_that("derive_var_atoxgr Test 116: DAIDS Fibrinogen Decreased", {
expected_fibd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2, 1, "g/L", NA, 1,
NA_character_, 2, 1, "g/L", NA, 2,
"Fibrinogen Decreased", 2, 1, "g/dL", NA, 3,
# test first half of criteria
"Fibrinogen Decreased", 0.49, 1, "g/L", "4", 4,
"Fibrinogen Decreased", 0.5, 1, "g/L", "3", 5,
"Fibrinogen Decreased", 0.74, 1, "g/L", "3", 6,
"Fibrinogen Decreased", 0.75, 1, "g/L", "2", 7,
"Fibrinogen Decreased", 0.99, 1, "g/L", "2", 8,
"Fibrinogen Decreased", 1, 1, "g/L", "1", 9,
"Fibrinogen Decreased", 1.99, 1, "g/L", "1", 10,
"Fibrinogen Decreased", 2, 1, "g/L", "0", 11,
# test second half of criteria
"Fibrinogen Decreased", 0.74, 3, "g/L", "4", 12,
"Fibrinogen Decreased", 0.75, 3, "g/L", "3", 13,
"Fibrinogen Decreased", 1.49, 3, "g/L", "3", 14,
"Fibrinogen Decreased", 1.5, 3, "g/L", "2", 15,
"Fibrinogen Decreased", 2.24, 3, "g/L", "2", 16,
"Fibrinogen Decreased", 2.25, 3, "g/L", "1", 17,
"Fibrinogen Decreased", 2.99, 3, "g/L", "1", 18,
"Fibrinogen Decreased", 3, 3, "g/L", "0", 19,
# TEST for missing values
"Fibrinogen Decreased", 0.49, NA, "g/L", "4", 20,
"Fibrinogen Decreased", 0.5, NA, "g/L", NA, 21,
"Fibrinogen Decreased", 2, 1, NA, NA, 22,
"Fibrinogen Decreased", NA, 1, "g/L", NA, 23,
)
input_fibd_daids <- expected_fibd_daids %>%
select(-ATOXGRL)
actual_fibd_daids <- derive_var_atoxgr_dir(
input_fibd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fibd_daids,
compare = actual_fibd_daids,
keys = c("TESTNUM")
)
})
### Hemoglobin, Low
### >= 13 years of age (male only)
### Grade 4: < 70 g/L
### Grade 3: 70 to < 90 g/L
### Grade 2: 90 to < 100 g/L
### Grade 1: 100 to 109 g/L
expected_hgbd_daids_ge13ym <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~SEX, ~TESTNUM,
"Hemoglobin, Low", 69, "MM3", NA, "M", 1,
"Hemoglobin, Low", 69, "g/L", "4", "M", 2,
"Hemoglobin, Low", 70, "g/L", "3", "M", 3,
"Hemoglobin, Low", 89, "g/L", "3", "M", 4,
"Hemoglobin, Low", 90, "g/L", "2", "M", 5,
"Hemoglobin, Low", 99, "g/L", "2", "M", 6,
"Hemoglobin, Low", 100, "g/L", "1", "M", 7,
"Hemoglobin, Low", 109, "g/L", "1", "M", 8,
"Hemoglobin, Low", 110, "g/L", "0", "M", 9,
"Hemoglobin, Low", NA, "g/L", NA, "M", 10,
"Hemoglobin, Low", 110, NA, NA, "M", 11,
"Hemoglobin, Low", 110, "g/L", NA, NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### >= 13 years of age (female only)
### Grade 4: < 65 g/L
### Grade 3: 65 to < 85 g/L
### Grade 2: 85 to < 95 g/L
### Grade 1: 95 to 104 g/L
expected_hgbd_daids_ge13yf <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~SEX, ~TESTNUM,
"Hemoglobin, Low", 64, "MM3", NA, "F", 13,
"Hemoglobin, Low", 64, "g/L", "4", "F", 14,
"Hemoglobin, Low", 65, "g/L", "3", "F", 15,
"Hemoglobin, Low", 84, "g/L", "3", "F", 16,
"Hemoglobin, Low", 85, "g/L", "2", "F", 17,
"Hemoglobin, Low", 94, "g/L", "2", "F", 18,
"Hemoglobin, Low", 95, "g/L", "1", "F", 19,
"Hemoglobin, Low", 104, "g/L", "1", "F", 20,
"Hemoglobin, Low", 105, "g/L", "0", "F", 21,
"Hemoglobin, Low", NA, "g/L", NA, "F", 22,
"Hemoglobin, Low", 110, NA, NA, "F", 23,
"Hemoglobin, Low", 110, "g/L", NA, NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### 57 days to < 13 years of age (male and female)
### Grade 4: < 65 g/L
### Grade 3: 65 to < 85 g/L
### Grade 2: 85 to < 95 g/L
### Grade 1: 95 to 104 g/L
expected_hgbd_daids_lt13y <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 64, "MM3", NA, 25,
"Hemoglobin, Low", 64, "g/L", "4", 26,
"Hemoglobin, Low", 65, "g/L", "3", 27,
"Hemoglobin, Low", 84, "g/L", "3", 28,
"Hemoglobin, Low", 85, "g/L", "2", 29,
"Hemoglobin, Low", 94, "g/L", "2", 30,
"Hemoglobin, Low", 95, "g/L", "1", 31,
"Hemoglobin, Low", 104, "g/L", "1", 32,
"Hemoglobin, Low", 105, "g/L", "0", 33,
"Hemoglobin, Low", NA, "g/L", NA, 34,
"Hemoglobin, Low", 110, NA, NA, 35,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-06-30")
)
### 36 to ≤ 56 days of age (male and female)
### Grade 4: < 60 g/L
### Grade 3: 60 to < 70 g/L
### Grade 2: 70 to < 85 g/L
### Grade 1: 85 to 96 g/L
expected_hgbd_daids_le56d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 59, "MM3", NA, 36,
"Hemoglobin, Low", 59, "g/L", "4", 37,
"Hemoglobin, Low", 60, "g/L", "3", 38,
"Hemoglobin, Low", 69, "g/L", "3", 39,
"Hemoglobin, Low", 70, "g/L", "2", 40,
"Hemoglobin, Low", 84, "g/L", "2", 41,
"Hemoglobin, Low", 85, "g/L", "1", 42,
"Hemoglobin, Low", 96, "g/L", "1", 43,
"Hemoglobin, Low", 97, "g/L", "0", 44,
"Hemoglobin, Low", NA, "g/L", NA, 45,
"Hemoglobin, Low", 110, NA, NA, 46,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-08-26")
)
### 22 to ≤ 35 days of age (male and female)
### Grade 4: < 67 g/L
### Grade 3: 67 to < 80 g/L
### Grade 2: 80 to < 95 g/L
### Grade 1: 95 to 110 g/L
expected_hgbd_daids_le35d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 66, "MM3", NA, 47,
"Hemoglobin, Low", 66, "g/L", "4", 48,
"Hemoglobin, Low", 67, "g/L", "3", 49,
"Hemoglobin, Low", 79, "g/L", "3", 50,
"Hemoglobin, Low", 80, "g/L", "2", 51,
"Hemoglobin, Low", 94, "g/L", "2", 52,
"Hemoglobin, Low", 95, "g/L", "1", 53,
"Hemoglobin, Low", 110, "g/L", "1", 54,
"Hemoglobin, Low", 111, "g/L", "0", 55,
"Hemoglobin, Low", NA, "g/L", NA, 56,
"Hemoglobin, Low", 110, NA, NA, 57,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-08-05")
)
### 8 to ≤ 21 days of age (male and female)
### Grade 4: < 80 g/L
### Grade 3: 80 to < 90 g/L
### Grade 2: 90 to < 110 g/L
### Grade 1: 110 to 130 g/L
expected_hgbd_daids_le21d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 79, "MM3", NA, 58,
"Hemoglobin, Low", 79, "g/L", "4", 59,
"Hemoglobin, Low", 80, "g/L", "3", 60,
"Hemoglobin, Low", 89, "g/L", "3", 61,
"Hemoglobin, Low", 90, "g/L", "2", 62,
"Hemoglobin, Low", 109, "g/L", "2", 63,
"Hemoglobin, Low", 110, "g/L", "1", 64,
"Hemoglobin, Low", 130, "g/L", "1", 65,
"Hemoglobin, Low", 131, "g/L", "0", 66,
"Hemoglobin, Low", NA, "g/L", NA, 67,
"Hemoglobin, Low", 110, NA, NA, 68,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-22")
)
### ≤ 7 days of age (male and female)
### Grade 4: < 90 g/L
### Grade 3: 90 to < 100 g/L
### Grade 2: 100 to < 130 g/L
### Grade 1: 130 to 140 g/L
expected_hgbd_daids_le7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 89, "MM3", NA, 69,
"Hemoglobin, Low", 89, "g/L", "4", 70,
"Hemoglobin, Low", 90, "g/L", "3", 71,
"Hemoglobin, Low", 99, "g/L", "3", 72,
"Hemoglobin, Low", 100, "g/L", "2", 73,
"Hemoglobin, Low", 129, "g/L", "2", 74,
"Hemoglobin, Low", 130, "g/L", "1", 75,
"Hemoglobin, Low", 140, "g/L", "1", 76,
"Hemoglobin, Low", 141, "g/L", "0", 77,
"Hemoglobin, Low", NA, "g/L", NA, 78,
"Hemoglobin, Low", 110, NA, NA, 79,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-08")
)
expected_hgbd_daids <- expected_hgbd_daids_ge13ym %>%
bind_rows(
expected_hgbd_daids_ge13yf,
expected_hgbd_daids_lt13y,
expected_hgbd_daids_le56d,
expected_hgbd_daids_le35d,
expected_hgbd_daids_le21d,
expected_hgbd_daids_le7d
)
# Set lab date to missing fo each type, ie SEX is M, F or missing
expected_hgbd_daids_noage <- expected_hgbd_daids %>%
filter(TESTNUM %in% c(5, 17, 29)) %>%
mutate(
LBDT = NA,
ATOXGRL = NA,
TESTNUM = case_when(
TESTNUM == 5 ~ 80,
TESTNUM == 17 ~ 81,
TESTNUM == 29 ~ 82
)
)
expected_hgbd_daids <- expected_hgbd_daids %>%
bind_rows(expected_hgbd_daids_noage)
input_hgbd_daids <- expected_hgbd_daids %>%
select(-ATOXGRL)
## Test 117: DAIDS HGB Low ----
test_that("derive_var_atoxgr Test 117: DAIDS HGB Low", {
actual_hgbd_daids <- derive_var_atoxgr_dir(
input_hgbd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbd_daids,
compare = actual_hgbd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### INR, high
### Grade 4: >=3 x ULN
### Grade 3: 2 to <3 x ULN
### Grade 2: 1.5 to < 2 x ULN
### Grade 1: 1.1 to < 1.5 x ULN
## Test 118: DAIDS INR High ----
test_that("derive_var_atoxgr Test 118: DAIDS INR High", {
expected_inri_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 80, NA_character_, NA,
NA_character_, 60, 80, NA_character_, NA,
"INR, High", 240, 80, NA_character_, "4",
"INR, High", 239, 80, NA_character_, "3",
"INR, High", 160, 80, NA_character_, "3",
"INR, High", 159, 80, NA_character_, "2",
"INR, High", 120, 80, NA_character_, "2",
"INR, High", 119, 80, NA_character_, "1",
"INR, High", 88, 80, NA_character_, "1",
"INR, High", 87, 80, NA_character_, "0",
# ANRHI missing - cannot grade
"INR, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"INR, High", NA, 80, NA_character_, NA,
)
input_inri_daids <- expected_inri_daids %>%
select(-ATOXGRH)
actual_inri_daids <- derive_var_atoxgr_dir(
input_inri_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri_daids,
compare = actual_inri_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Methemoglobin
### Grade 4: >=20.0%
### Grade 3: 15 to < 20%
### Grade 2: 10 to < 15%
### Grade 1: 5 to <10%
## Test 119: DAIDS Methemoglobin ----
test_that("derive_var_atoxgr Test 119: DAIDS Methemoglobin", {
expected_methi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH,
"Not a term", 20, "%", NA,
NA_character_, 20, "%", NA,
"Methemoglobin", 20, "%", "4",
"Methemoglobin", 19, "%", "3",
"Methemoglobin", 15, "%", "3",
"Methemoglobin", 14, "%", "2",
"Methemoglobin", 10, "%", "2",
"Methemoglobin", 9, "%", "1",
"Methemoglobin", 5, "%", "1",
"Methemoglobin", 4, "%", "0",
# Unit wrong - cannot grade
"Methemoglobin", 100, NA, NA,
# AVAL missing cannot grade
"Methemoglobin", NA, "%", NA,
)
input_methi_daids <- expected_methi_daids %>%
select(-ATOXGRH)
actual_methi_daids <- derive_var_atoxgr_dir(
input_methi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_methi_daids,
compare = actual_methi_daids,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
### PTT, high
### Grade 4: >=3 x ULN
### Grade 3: 2.33 to <3 x ULN
### Grade 2: 1.66 to < 2.33 x ULN
### Grade 1: 1.1 to < 1.66 x ULN
## Test 120: DAIDS PTT High ----
test_that("derive_var_atoxgr Test 120: DAIDS PTT High", {
expected_ptti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 80, NA_character_, NA,
NA_character_, 60, 80, NA_character_, NA,
"PTT, High", 240, 80, NA_character_, "4",
"PTT, High", 239, 80, NA_character_, "3",
"PTT, High", 186.4, 80, NA_character_, "3",
"PTT, High", 186.3, 80, NA_character_, "2",
"PTT, High", 132.8, 80, NA_character_, "2",
"PTT, High", 132.7, 80, NA_character_, "1",
"PTT, High", 88, 80, NA_character_, "1",
"PTT, High", 87, 80, NA_character_, "0",
# ANRHI missing - cannot grade
"PTT, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"PTT, High", NA, 80, NA_character_, NA,
)
input_ptti_daids <- expected_ptti_daids %>%
select(-ATOXGRH)
actual_ptti_daids <- derive_var_atoxgr_dir(
input_ptti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ptti_daids,
compare = actual_ptti_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Platelets, Decreased
### Grade 4: <25 x 10e9 /L
### Grade 3: 25 to <50 x 10e9 /L
### Grade 2: 50 to <100 - x 10e9
### Grade 1: 100 - 125 x 10e9 /L
## Test 121: DAIDS Platelets decreased ----
test_that("derive_var_atoxgr Test 121: DAIDS Platelets decreased", {
expected_plated_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 126, "10^9/L", NA, 1,
NA_character_, 120, "10^9/L", NA, 2,
"Platelets, Decreased", 115, "MM3", NA, 3,
"Platelets, Decreased", 24.9, "10^9/L", "4", 4,
"Platelets, Decreased", 25, "10^9/L", "3", 5,
"Platelets, Decreased", 49.9, "10^9/L", "3", 6,
"Platelets, Decreased", 50, "10^9/L", "2", 7,
"Platelets, Decreased", 99.9, "10^9/L", "2", 8,
"Platelets, Decreased", 100, "10^9/L", "1", 9,
"Platelets, Decreased", 124.9, "10^9/L", "1", 10,
"Platelets, Decreased", 125, "10^9/L", "0", 11,
)
input_plated_daids <- expected_plated_daids %>%
select(-ATOXGRL)
actual_plated_daids <- derive_var_atoxgr_dir(
input_plated_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plated_daids,
compare = actual_plated_daids,
keys = c("TESTNUM")
)
})
### PT, high
### Grade 4: >=3 x ULN
### Grade 3: 1.5 - <3 x ULN
### Grade 2: 1.25 - <1.5 x ULN
### Grade 1: 1.1 - <1.25 x ULN
## Test 122: DAIDS PT High ----
test_that("derive_var_atoxgr Test 122: DAIDS PT High", {
expected_pti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 100, NA_character_, NA,
NA_character_, 60, 100, NA_character_, NA,
"PT, High", 300, 100, NA_character_, "4",
"PT, High", 299, 100, NA_character_, "3",
"PT, High", 150, 100, NA_character_, "3",
"PT, High", 149, 100, NA_character_, "2",
"PT, High", 125, 100, NA_character_, "2",
"PT, High", 124, 100, NA_character_, "1",
"PT, High", 110, 100, NA_character_, "1",
"PT, High", 109, 100, NA_character_, "0",
# ANRHI missing - cannot grade
"PT, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"PT, High", NA, 100, NA_character_, NA,
)
input_pti_daids <- expected_pti_daids %>%
select(-ATOXGRH)
actual_pti_daids <- derive_var_atoxgr_dir(
input_pti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_pti_daids,
compare = actual_pti_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### White blood cell decreased (> 7 days of age)
### Grade 4: <1 x 10e9/L
### Grade 3: 1 to 1.499 x 10e9/L
### Grade 2: 1.5 to 1.999 x 10e9/L
### Grade 1: 2 to 2.499 x 10e9/L
expected_wbcd_daids_gt7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 1, "10^9/L", NA, 1,
NA_character_, 2, "10^9/L", NA, 2,
"WBC, Decreased", 0.9, "MM3", NA, 3,
"WBC, Decreased", 0.9, "10^9/L", "4", 4,
"WBC, Decreased", 1, "10^9/L", "3", 5,
"WBC, Decreased", 1.49, "10^9/L", "3", 6,
"WBC, Decreased", 1.5, "10^9/L", "2", 7,
"WBC, Decreased", 1.99, "10^9/L", "2", 8,
"WBC, Decreased", 2, "10^9/L", "1", 9,
"WBC, Decreased", 2.49, "10^9/L", "1", 10,
"WBC, Decreased", 2.5, "10^9/L", "0", 11,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-09")
)
### White blood cell decreased (<= 7 days of age)
### Grade 4: <2.500 x 10e9/L
### Grade 3: 2.5 to 3.999 x 10e9/L
### Grade 2: 4 to 5.499 x 10e9/L
### Grade 1: 5.5 to 6.999 x 10e9/L
expected_wbcd_daids_le7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"WBC, Decreased", 2.49, "MM3", NA, 12,
"WBC, Decreased", 2.49, "10^9/L", "4", 13,
"WBC, Decreased", 2.5, "10^9/L", "3", 14,
"WBC, Decreased", 3.99, "10^9/L", "3", 15,
"WBC, Decreased", 4, "10^9/L", "2", 16,
"WBC, Decreased", 5.49, "10^9/L", "2", 17,
"WBC, Decreased", 5.5, "10^9/L", "1", 18,
"WBC, Decreased", 6.99, "10^9/L", "1", 19,
"WBC, Decreased", 7, "10^9/L", "0", 20,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-08")
)
expected_wbcd_daids_noage <- expected_wbcd_daids_gt7d %>%
filter(TESTNUM %in% c(10, 11)) %>%
mutate(
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
LBDT = if_else(TESTNUM == 11, NA, LBDT),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
expected_wbcd_daids <- expected_wbcd_daids_gt7d %>%
bind_rows(
expected_wbcd_daids_le7d,
expected_wbcd_daids_noage
)
input_wbcd_daids <- expected_wbcd_daids %>%
select(-ATOXGRL)
## Test 123: DAIDS White blood cell decreased ----
test_that("derive_var_atoxgr Test 123: DAIDS White blood cell decreased", {
actual_wbcd_daids <- derive_var_atoxgr_dir(
input_wbcd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd_daids,
compare = actual_wbcd_daids,
keys = c("TESTNUM")
)
})
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## Test 1: ATOXGR cannot be graded ----
test_that("derive_var_atoxgr Test 1: ATOXGR cannot be graded", {
exp_out_1 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
"Hypophosphatemia", NA_character_, NA_character_, NA_character_, NA_character_,
NA_character_, "Hyperglycemia", NA_character_, NA_character_, NA_character_,
"Hypoglycemia", "Hyperglycemia", NA_character_, NA_character_, NA_character_,
# ATOXGRL is ungradable so cannot say ATOXGR is normal
"Hypoglycemia", "Hyperglycemia", NA_character_, "0", NA_character_,
# ATOXGRH is ungradable so cannot say ATOXGR is normal
"Hypoglycemia", "Hyperglycemia", "0", NA_character_, NA_character_,
)
input_1 <- exp_out_1 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_1,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_1
)
})
## Test 2: ATOXGR = 0 (normal) ----
test_that("derive_var_atoxgr Test 2: ATOXGR = 0 (normal)", {
exp_out_2 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", "0", "0", "0",
NA_character_, "INR Increased", NA_character_, "0", "0",
"Hypophosphatemia", NA_character_, "0", NA_character_, "0",
)
input_2 <- exp_out_2 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_2,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_2
)
})
## Test 3: ATOXGR > 0 (HYPER) ----
test_that("derive_var_atoxgr Test 3: ATOXGR > 0 (HYPER)", {
exp_out_3 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", NA_character_, "1", "1",
"Hypoglycemia", "Hyperglycemia", "0", "4", "4",
NA_character_, "INR Increased", NA_character_, "2", "2",
)
input_3 <- exp_out_3 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_3,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_3
)
})
## Test 4: ATOXGR < 0 (HYPO) ----
test_that("derive_var_atoxgr Test 4: ATOXGR < 0 (HYPO)", {
exp_out_4 <- tibble::tribble(
~ATOXDSCL, ~ATOXDSCH, ~ATOXGRL, ~ATOXGRH, ~ATOXGR,
"Hypoglycemia", "Hyperglycemia", "3", NA_character_, "-3",
"Hypoglycemia", "Hyperglycemia", "1", "0", "-1",
"Hypophosphatemia", NA_character_, "4", NA_character_, "-4",
)
input_4 <- exp_out_4 %>%
select(-ATOXGR)
expect_equal(
derive_var_atoxgr(
input_4,
lotox_description_var = ATOXDSCL,
hitox_description_var = ATOXDSCH
),
exp_out_4
)
})
# derive_var_atoxgr_dir
## Blood and lymphatic system disorders
### Anemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: <80 g/L
### Grade 2: <100 - 80g/L
### Grade 1: <LLN - 100 g/L
expected_anemia <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, 200, "G/L", NA,
NA_character_, 60, 50, 100, "G/L", NA,
"ANEMIA", 79, 140, NA, "G/L", "3",
"ANEMIA", 80, 140, NA, "G/L", "2",
"Anemia", 99, 140, NA, "G/L", "2",
"Anemia", 100, 140, NA, "G/L", "1",
# wrong UNIT - GRADE should be missing
"anemia", 100, 140, NA, "G/dL", NA,
"Anemia", 139, 140, NA, "G/L", "1",
"ANEMIA", 140, 140, NA, "g/L", "0",
# ANRLO missing AVAL not grade 2 or 3 - cannot grade
"Anemia", 140, NA, NA, "G/L", NA,
"Anemia", 139, NA, NA, "G/L", NA,
"Anemia", 100, NA, NA, "G/L", NA,
# ANRLO missing but AVAL satisfies grade 2
"Anemia", 99, NA, NA, "G/L", "2",
# ANRLO missing but AVAL satisfies grade 3
"Anemia", 79, NA, NA, "G/L", "3",
# Unit missing cannot grade
"Anemia", 140, 140, NA, NA, NA,
# AVAL missing cannot grade
"Anemia", NA, 140, NA, "G/L", NA,
)
input_anemia <- expected_anemia %>%
select(-ATOXGRL)
## Test 5: CTCAEv4 Anemia ----
test_that("derive_var_atoxgr Test 5: CTCAEv4 Anemia", {
actual_anemia_ctcv4 <- derive_var_atoxgr_dir(
input_anemia,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_anemia,
compare = actual_anemia_ctcv4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 6: CTCAEv5 Anemia ----
test_that("derive_var_atoxgr Test 6: CTCAEv5 Anemia", {
actual_anemia_ctcv5 <- derive_var_atoxgr_dir(
input_anemia,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_anemia,
compare = actual_anemia_ctcv5,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Leukocytosis
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >100,000/mm3
expected_leukocytosis <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 99, 0, NA, "10^9/L", NA,
NA, 99, 0, NA, "10^9/L", NA,
"Leukocytosis", 101, 0, 40, "10^9/L", "3",
"leukocytosis", 100, 0, 40, "10^9/L", "0",
"Leukocytosis", 99, 0, NA, "10^9/L", "0",
# wrong UNIT - GRADE should be missing
"Leukocytosis", 99, 0, 40, "10^9/M", NA,
# Unit missing cannot grade
"Leukocytosis", 99, 0, 40, NA, NA,
# AVAL missing cannot grade
"Leukocytosis", NA, 0, 40, "10^9/L", NA,
)
input_leukocytosis <- expected_leukocytosis %>%
select(-ATOXGRH)
## Test 7: CTCAEv4 Leukocytosis ----
test_that("derive_var_atoxgr Test 7: CTCAEv4 Leukocytosis", {
actual_leukocytosis <- derive_var_atoxgr_dir(
input_leukocytosis,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_leukocytosis,
compare = actual_leukocytosis,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 8: CTCAEv5 Leukocytosis ----
test_that("derive_var_atoxgr Test 8: CTCAEv5 Leukocytosis", {
actual_leukocytosis <- derive_var_atoxgr_dir(
input_leukocytosis,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_leukocytosis,
compare = actual_leukocytosis,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Investigations
### Activated partial thromboplastin time prolonged
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >2.5 x ULN
### Grade 2: >1.5 - 2.5 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_aptt <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 100, NA_character_, NA,
NA_character_, 60, 100, NA_character_, NA,
"Activated partial thromboplastin time prolonged", 251, 100, NA_character_, "3",
"Activated Partial thromboplastin time prolonged", 250, 100, NA_character_, "2",
"Activated partial Thromboplastin time prolonged", 151, 100, NA_character_, "2",
"Activated partial thromboplastin time prolonged", 150, 100, NA_character_, "1",
"Activated partial thromboplastin Time prolonged", 101, 100, NA_character_, "1",
"Activated partial thromboplastin time prolonged", 100, 100, NA_character_, "0",
# ANRHI missing - cannot grade
"Activated partial thromboplastin time prolonged", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Activated partial thromboplastin time prolonged", NA, 100, NA_character_, NA,
)
input_aptt <- expected_aptt %>%
select(-ATOXGRH)
## Test 9: CTCAEv4 Activated partial thromboplastin time prolonged ----
test_that("derive_var_atoxgr Test 9: CTCAEv4 Activated partial thromboplastin time prolonged", {
actual_aptt <- derive_var_atoxgr_dir(
input_aptt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_aptt,
compare = actual_aptt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
## Test 10: CTCAEv5 Activated partial thromboplastin time prolonged ----
test_that("derive_var_atoxgr Test 10: CTCAEv5 Activated partial thromboplastin time prolonged", {
actual_aptt <- derive_var_atoxgr_dir(
input_aptt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_aptt,
compare = actual_aptt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Alanine aminotransferase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >3.0 - 5.0 x ULN
### Grade 1: >ULN - 3.0 x ULN
expected_alt_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alanine aminotransferase Increased", 801, 40, NA_character_, "4",
"Alanine aminotransferase Increased", 800, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 201, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 200, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 121, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 120, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 41, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alanine aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alanine aminotransferase Increased", NA, 40, NA_character_, NA,
)
## Test 11: CTCAEv4 Alanine aminotransferase increased ----
test_that("derive_var_atoxgr Test 11: CTCAEv4 Alanine aminotransferase increased", {
input_alt <- expected_alt_ctcv4 %>%
select(-ATOXGRH)
actual_alt <- derive_var_atoxgr_dir(
input_alt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alt_ctcv4,
compare = actual_alt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >3.0 - 5.0 x ULN if BL was normal OR >3.0 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL if BL was abnormal
## Test 12: CTCAEv5 Alanine aminotransferase increased ----
test_that("derive_var_atoxgr Test 12: CTCAEv5 Alanine aminotransferase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_alt_ctcv5_norm <- expected_alt_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_alt_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alanine aminotransferase Increased", 801, 40, NA_character_, "4",
"Alanine aminotransferase Increased", 800, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 201, 40, NA_character_, "3",
"Alanine aminotransferase Increased", 200, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 121, 40, NA_character_, "2",
"Alanine aminotransferase Increased", 120, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 60, 40, NA_character_, "1",
"Alanine aminotransferase Increased", 59, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alanine aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alanine aminotransferase Increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_alt_ctcv5 <- expected_alt_ctcv5_norm %>%
bind_rows(expected_alt_ctcv5_abn)
input_alt <- expected_alt_ctcv5 %>%
select(-ATOXGRH)
actual_alt <- derive_var_atoxgr_dir(
input_alt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alt_ctcv5,
compare = actual_alt,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Alkaline phosphatase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_alkph_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alkaline phosphatase increased", 801, 40, NA_character_, "4",
"Alkaline phosphatase increased", 800, 40, NA_character_, "3",
"Alkaline phosphatase increased", 201, 40, NA_character_, "3",
"Alkaline phosphatase increased", 200, 40, NA_character_, "2",
"Alkaline phosphatase increased", 101, 40, NA_character_, "2",
"Alkaline phosphatase increased", 100, 40, NA_character_, "1",
"Alkaline phosphatase increased", 41, 40, NA_character_, "1",
"Alkaline phosphatase increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alkaline phosphatase increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alkaline phosphatase increased", NA, 40, NA_character_, NA,
)
## Test 13: CTCAEv4 Alkaline phosphatase increased ----
test_that("derive_var_atoxgr Test 13: CTCAEv4 Alkaline phosphatase increased", {
input_alkph <- expected_alkph_ctcv4 %>%
select(-ATOXGRH)
actual_alkph <- derive_var_atoxgr_dir(
input_alkph,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkph_ctcv4,
compare = actual_alkph,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Alkaline phosphatase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >2.5 - 5.0 x ULN if BL was normal OR >2.5 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 2.5 x ULN if BL was normal OR >2.0 - 2.5 x BL if BL was abnormal
## Test 14: CTCAEv5 Alkaline phosphatase increased ----
test_that("derive_var_atoxgr Test 14: CTCAEv5 Alkaline phosphatase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_alkph_ctcv5_norm <- expected_alkph_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_alkph_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Alkaline phosphatase increased", 801, 40, NA_character_, "4",
"Alkaline phosphatase increased", 800, 40, NA_character_, "3",
"Alkaline phosphatase increased", 201, 40, NA_character_, "3",
"Alkaline phosphatase increased", 200, 40, NA_character_, "2",
"Alkaline phosphatase increased", 101, 40, NA_character_, "2",
"Alkaline phosphatase increased", 100, 40, NA_character_, "1",
"Alkaline phosphatase increased", 80, 40, NA_character_, "1",
"Alkaline phosphatase increased", 79, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Alkaline phosphatase increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Alkaline phosphatase increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_alkph_ctcv5 <- expected_alkph_ctcv5_norm %>%
bind_rows(expected_alkph_ctcv5_abn)
input_alkph <- expected_alkph_ctcv5 %>%
select(-ATOXGRH)
actual_alkph <- derive_var_atoxgr_dir(
input_alkph,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkph_ctcv5,
compare = actual_alkph,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Aspartate aminotransferase increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >3.0 - 5.0 x ULN
### Grade 1: >ULN - 3.0 x ULN
expected_ast_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Aspartate aminotransferase Increased", 801, 40, NA_character_, "4",
"Aspartate aminotransferase Increased", 800, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 201, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 200, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 121, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 120, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 41, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Aspartate aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Aspartate aminotransferase Increased", NA, 40, NA_character_, NA,
)
## Test 15: CTCAEv4 Aspartate aminotransferase increased ----
test_that("derive_var_atoxgr Test 15: CTCAEv4 Aspartate aminotransferase increased", {
input_ast <- expected_ast_ctcv4 %>%
select(-ATOXGRH)
actual_ast <- derive_var_atoxgr_dir(
input_ast,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ast_ctcv4,
compare = actual_ast,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >3.0 - 5.0 x ULN if BL was normal OR >3.0 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL if BL was abnormal
## Test 16: CTCAEv5 Aspartate aminotransferase increased ----
test_that("derive_var_atoxgr Test 16: CTCAEv5 Aspartate aminotransferase increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_ast_ctcv5_norm <- expected_ast_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_ast_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Aspartate aminotransferase Increased", 801, 40, NA_character_, "4",
"Aspartate aminotransferase Increased", 800, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 201, 40, NA_character_, "3",
"Aspartate aminotransferase Increased", 200, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 121, 40, NA_character_, "2",
"Aspartate aminotransferase Increased", 120, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 60, 40, NA_character_, "1",
"Aspartate aminotransferase Increased", 59, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Aspartate aminotransferase Increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Aspartate aminotransferase Increased", NA, 40, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_ast_ctcv5 <- expected_ast_ctcv5_norm %>%
bind_rows(expected_ast_ctcv5_abn)
input_ast <- expected_ast_ctcv5 %>%
select(-ATOXGRH)
actual_ast <- derive_var_atoxgr_dir(
input_ast,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ast_ctcv5,
compare = actual_ast,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### Blood bilirubin increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >10.0 x ULN
### Grade 3: >3.0 - 10.0 x ULN
### Grade 2: >1.5 - 3.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_bili_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 40, NA_character_, NA,
NA_character_, 60, 40, NA_character_, NA,
"Blood bilirubin increased", 401, 40, NA_character_, "4",
"Blood bilirubin increased", 400, 40, NA_character_, "3",
"Blood bilirubin increased", 121, 40, NA_character_, "3",
"Blood bilirubin increased", 120, 40, NA_character_, "2",
"Blood bilirubin increased", 61, 40, NA_character_, "2",
"Blood bilirubin increased", 60, 40, NA_character_, "1",
"Blood bilirubin increased", 41, 40, NA_character_, "1",
"Blood bilirubin increased", 40, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Blood bilirubin increased", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"Blood bilirubin increased", NA, 40, NA_character_, NA,
)
## Test 17: CTCAEv4 Blood bilirubin increased ----
test_that("derive_var_atoxgr Test 17: CTCAEv4 Blood bilirubin increased", {
input_bili <- expected_bili_ctcv4 %>%
select(-ATOXGRH)
actual_bili <- derive_var_atoxgr_dir(
input_bili,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bili_ctcv4,
compare = actual_bili,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Blood bilirubin increased
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >10.0 x ULN if BL was normal OR >10.0 x BL if BL was abnormal
### Grade 3: >3.0 - 10.0 x ULN if BL was normal OR >3.0 - 10.0 x BL
### Grade 2: >1.5 - 3.0 x ULN if BL was normal OR >1.5 - 3.0 x BL
### Grade 1: >ULN - 1.5 x ULN if BL was normal OR >1.0 - 1.5 x BL
## Test 18: CTCAEv5 Blood bilirubin increased ----
test_that("derive_var_atoxgr Test 18: CTCAEv5 Blood bilirubin increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_bili_ctcv5_norm <- expected_bili_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with abnormal BASE then add records with normal BASE
expected_bili_ctcv5 <- expected_bili_ctcv4 %>%
# set BASE to ANRHI then make ANRHI < BASE
mutate(
BASE = ANRHI,
ANRHI = ANRHI - 1,
FLAG = "ABNORMAL"
) %>%
bind_rows(expected_bili_ctcv5_norm)
input_bili <- expected_bili_ctcv5 %>%
select(-ATOXGRH)
actual_bili <- derive_var_atoxgr_dir(
input_bili,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bili_ctcv5,
compare = actual_bili,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "FLAG", "AVALU")
)
})
### CD4 Lymphocytes decreased
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: <0.05 x 10e9 /L
### Grade 3: <0.2 x 0.05 - 10e9 /L
### Grade 2: <0.5 - 0.2 x 10e9 /L
### Grade 1: <LLN - 0.5 x 10e9 /L
expected_cd4 <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, "10^9/L", NA,
NA_character_, 60, 50, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.04, 0.8, "10^9/L", "4",
"CD4 lymphocytes decreased", 0.05, 0.8, "10^9/l", "3",
"CD4 lymphocytes decreased", 0.19, 0.8, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.2, 0.8, "10^9/L", "2",
"CD4 lymphocytes decreased", 0.49, 0.8, "10^9/L", "2",
# wrong unit - grade missing
"CD4 lymphocytes decreased", 0.49, 0.8, "10^8/L", NA,
"CD4 lymphocytes decreased", 0.5, 0.8, "10^9/L", "1",
"CD4 lymphocytes decreased", 0.79, 0.8, "10^9/L", "1",
"CD4 lymphocytes decreased", 0.8, 0.8, "10^9/L", "0",
# ANRLO missing - AVAL satisfies grade 2 - 4
"CD4 lymphocytes decreased", 0.04, NA, "10^9/L", "4",
"CD4 lymphocytes decreased", 0.05, NA, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.19, NA, "10^9/L", "3",
"CD4 lymphocytes decreased", 0.2, NA, "10^9/L", "2",
"CD4 lymphocytes decreased", 0.49, NA, "10^9/L", "2",
# ANRLO missing - AVAL does NOT satisfies grade 2 - 4
"CD4 lymphocytes decreased", 0.5, NA, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.79, NA, "10^9/L", NA,
"CD4 lymphocytes decreased", 0.8, NA, "10^9/L", NA,
# Unit missing - cannot grade
"CD4 lymphocytes decreased", 0.8, 0.8, NA, NA,
# AVAL missing cannot grade
"CD4 lymphocytes decreased", NA, 0.8, "10^9/L", NA,
)
input_cd4 <- expected_cd4 %>%
select(-ATOXGRL)
## Test 19: CTCAEv4 CD4 Lymphocytes decreased ----
test_that("derive_var_atoxgr Test 19: CTCAEv4 CD4 Lymphocytes decreased", {
actual_cd4 <- derive_var_atoxgr_dir(
input_cd4,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4,
compare = actual_cd4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "AVALU")
)
})
## Test 20: CTCAEv5 CD4 Lymphocytes decreased ----
test_that("derive_var_atoxgr Test 20: CTCAEv5 CD4 Lymphocytes decreased", {
actual_cd4 <- derive_var_atoxgr_dir(
input_cd4,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4,
compare = actual_cd4,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "AVALU")
)
})
### Cholesterol high
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: >12.92 mmol/L
### Grade 3: >10.34 - 12.92 mmol/L
### Grade 2: >7.75 - 10.34 mmol/L
### Grade 1: >ULN - 7.75 mmol/L
expected_choles <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 8, 0, 5, "mmol/L", NA,
NA_character_, 10, 0, 5, "mmol/L", NA,
"Cholesterol high", 12.93, 0, 5, "mmol/L", "4",
"Cholesterol High", 12.92, 0, 5, "mmol/L", "3",
"Cholesterol high", 10.35, 0, 5, "Mmol/L", "3",
# wrong unit - grade missing
"Cholesterol high", 10.35, 0, 5, "umol/L", NA,
"Cholesterol high", 10.34, 0, 5, "mmol/L", "2",
"Cholesterol high", 7.76, 0, 5, "mmol/L", "2",
"Cholesterol high", 7.75, 0, 5, "mmol/L", "1",
"Cholesterol high", 5.1, 0, 5, "mmol/L", "1",
"Cholesterol high", 5, 0, 5, "mmol/L", "0",
# ANRHI missing - AVAL satisfies grade 2 - 4
"Cholesterol high", 12.93, 0, NA, "mmol/L", "4",
"Cholesterol High", 12.92, 0, NA, "mmol/L", "3",
"Cholesterol high", 10.35, 0, NA, "Mmol/L", "3",
"Cholesterol high", 10.34, 0, NA, "mmol/L", "2",
"Cholesterol high", 7.76, 0, NA, "mmol/L", "2",
# ANRHI missing - AVAL does NOT satisfies grade 2 - 4
"Cholesterol high", 7.75, 0, NA, "mmol/L", NA,
"Cholesterol high", 5.1, 0, NA, "mmol/L", NA,
"Cholesterol high", 5, 0, NA, "mmol/L", NA,
# Unit missing - cannot grade
"Cholesterol high", 5, 0, 5, NA, NA,
# AVAL missing cannot grade
"Cholesterol high", NA, 0, 5, "mmol/L", NA,
)
input_choles <- expected_choles %>%
select(-ATOXGRH)
## Test 21: CTCAEv4 Cholesterol high ----
test_that("derive_var_atoxgr Test 21: CTCAEv4 Cholesterol high", {
actual_choles <- derive_var_atoxgr_dir(
input_choles,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_choles,
compare = actual_choles,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 22: CTCAEv5 Cholesterol high ----
test_that("derive_var_atoxgr Test 22: CTCAEv5 Cholesterol high", {
actual_choles <- derive_var_atoxgr_dir(
input_choles,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_choles,
compare = actual_choles,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### CPK increased
### NCICTCAEv5 same criteria as NCICTCAEv4
### Grade 4: >10.0 x ULN
### Grade 3: >5.0 - 10.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_cpk <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"CPK increased", 401, 0, 40, NA_character_, "4",
"CPK increased", 400, 0, 40, NA_character_, "3",
"CPK increased", 201, 0, 40, NA_character_, "3",
"CPK increased", 200, 0, 40, NA_character_, "2",
"CPK increased", 101, 0, 40, NA_character_, "2",
"CPK increased", 100, 0, 40, NA_character_, "1",
"CPK increased", 41, 0, 40, NA_character_, "1",
"CPK increased", 40, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"CPK increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"CPK increased", NA, 0, 40, NA_character_, NA,
)
input_cpk <- expected_cpk %>%
select(-ATOXGRH)
## Test 23: CTCAEv4 CPK increased ----
test_that("derive_var_atoxgr Test 23: CTCAEv4 CPK increased", {
actual_cpk <- derive_var_atoxgr_dir(
input_cpk,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cpk,
compare = actual_cpk,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 24: CTCAEv5 CPK increased ----
test_that("derive_var_atoxgr Test 24: CTCAEv5 CPK increased", {
actual_cpk <- derive_var_atoxgr_dir(
input_cpk,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cpk,
compare = actual_cpk,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Creatinine increased (NCICTCv4)
### NCICTCAEv5 same criteria as NCICTCAEv4 except for Grade 1
### Grade 4: >6.0 x ULN
### Grade 3: >3.0 baseline; >3.0 - 6.0 x ULN
### Grade 2: >1.5 - 3.0 x baseline; >1.5 - 3.0 x ULN
### Grade 1: >1 - 1.5 x baseline; >ULN - 1.5 x ULN
# create flag to remove obs not relevant for NCI-CTCAEv5
expected_creatn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~V4, ~V5,
"Not a term", 80, 80, 40, NA_character_, NA, "Y", "Y",
NA_character_, 60, 60, 40, NA_character_, NA, "Y", "Y",
# GRADE derived from AVAL against ANRHI
"Creatinine increased", 241, 241, 40, NA_character_, "4", "Y", "Y",
"Creatinine increased", 240, 230, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 121, 120, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 120, 119, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 61, 60, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 60, 60, 40, NA_character_, "1", "Y", "Y",
"Creatinine increased", 41, 41, 40, NA_character_, "1", "Y", "Y",
"Creatinine increased", 40, 40, 40, NA_character_, "0", "Y", "Y",
# GRADE derived from AVAL against BASE
"Creatinine increased", 42, 6, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 42, 13.9, 40, NA_character_, "3", "Y", "Y",
"Creatinine increased", 42, 14, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 42.1, 28, 40, NA_character_, "2", "Y", "Y",
"Creatinine increased", 42, 28, 42, NA_character_, "1", "Y", "N",
"Creatinine increased", 42, 41, 42, NA_character_, "1", "Y", "N",
"Creatinine increased", 42, 42, 42, NA_character_, "0", "Y", "N",
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"Creatinine increased", 42, NA, 42, NA_character_, NA, "Y", "N",
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"Creatinine increased", 42, 42, NA, NA_character_, NA, "Y", "Y",
# AVAL missing cannot grade
"Creatinine increased", NA, 0, 40, NA_character_, NA, "Y", "Y",
)
## Test 25: CTCAEv4 Creatinine increased ----
test_that("derive_var_atoxgr Test 25: CTCAEv4 Creatinine increased", {
input_creatn <- expected_creatn %>%
select(-ATOXGRH)
actual_creatn <- derive_var_atoxgr_dir(
input_creatn,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creatn,
compare = actual_creatn,
keys = c("ATOXDSCH", "AVAL", "BASE", "ANRHI", "AVALU")
)
})
### Creatinine increased (NCICTCv5)
### NCICTCAEv5 same criteria as NCICTCAEv4 except for Grade 1
### Grade 4: >6.0 x ULN
### Grade 3: >3.0 baseline; >3.0 - 6.0 x ULN
### Grade 2: >1.5 - 3.0 x baseline; >1.5 - 3.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
## Test 26: CTCAEv4 Creatinine increased ----
test_that("derive_var_atoxgr Test 26: CTCAEv4 Creatinine increased", {
expected_creatn <- expected_creatn %>%
filter(V5 == "Y")
input_creatn <- expected_creatn %>%
select(-ATOXGRH)
actual_creatn <- derive_var_atoxgr_dir(
input_creatn,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creatn,
compare = actual_creatn,
keys = c("ATOXDSCH", "AVAL", "BASE", "ANRHI", "AVALU")
)
})
### Fibrinogen decreased (NCICTCv4)
### Grade 4: <0.25 x LLN or 75% decrease from baseline or absolute value <50 mg/dL
### Grade 3: <0.5 - 0.25 x LLN or 50 - <75% decrease from baseline
### Grade 2: <0.75 - 0.5 x LLN or 25 - <50% decrease from baseline
### Grade 1: <1.0 - 0.75 x LLN or <25% decrease from baseline
## Test 27: CTCAEv4 Fibrinogen decreased ----
test_that("derive_var_atoxgr Test 27: CTCAEv4 Fibrinogen decreased", {
expected_fib <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~PCHG, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, "g/L", NA,
NA_character_, 10, 10, 40, "g/L", NA,
# Satisfies < 0.5 for grade 4 - other criteria missing
"Fibrinogen decreased", 0.49, NA, NA, "g/L", "4",
# Satisfies < 0.5 for grade 4 - satisfies grade 3 for other criteria
"Fibrinogen decreased", 0.49, 1, -51, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG missing
"Fibrinogen decreased", 0.5, 2.1, NA, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG satisfies grade 3
"Fibrinogen decreased", 0.5, 2.1, -51, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN missing
"Fibrinogen decreased", 1, NA, -75, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN satisfies grade 3
"Fibrinogen decreased", 1, 0.49, -75, "g/L", "4",
# Satisfies < 0.5*LLN for grade 3 - PCHG missing
"Fibrinogen decreased", 1, 2.1, NA, "g/L", "3",
# Satisfies < 0.5*LLN for grade 3 - PCHG satisfies grade 2
"Fibrinogen decreased", 1, 2.1, -49, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN missing
"Fibrinogen decreased", 1, NA, -50, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN satisfies grade 2
"Fibrinogen decreased", 1, 2, -50, "g/L", "3",
# Satisfies < 0.75*LLN for grade 2 - PCHG missing
"Fibrinogen decreased", 1.5, 2.1, NA, "g/L", "2",
# Satisfies < 0.75*LLN for grade 2 - PCHG satisfies grade 1
"Fibrinogen decreased", 1.5, 2.1, -10, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN missing
"Fibrinogen decreased", 1.5, NA, -25, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN satisfies grade 1
"Fibrinogen decreased", 1.5, 1.6, -25, "g/L", "2",
# Satisfies < LLN for grade 1 - PCHG missing
"Fibrinogen decreased", 2, 2.1, NA, "g/L", "1",
# Satisfies < LLN for grade 1 - PCHG satisfies grade 0
"Fibrinogen decreased", 2, 2.1, 10, "g/L", "1",
# Satisfies % decrease for grade 1 - LLN missing
"Fibrinogen decreased", 1.5, NA, -1, "g/L", "1",
# Satisfies % decrease for grade 1 - AVAL = LLN
"Fibrinogen decreased", 1.5, 1.5, -1, "g/L", "1",
# Satisfies grade 0 - AVAL >= LLN AND no % descrease
"Fibrinogen decreased", 1.5, 1.5, 0, "g/L", "0",
# AVAL >= LLN BUT PCT missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, 1.5, NA, "g/L", NA,
# PCT >= 0 BUT LLN missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, NA, 10, "g/L", NA,
# AVAL missing cannot grade
"Fibrinogen decreased", NA, 1.5, 10, "g/L", NA,
# wrong unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, "g/dL", NA,
# missing unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, NA, NA,
)
input_fib <- expected_fib %>%
select(-ATOXGRL)
actual_fib <- derive_var_atoxgr_dir(
input_fib,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fib,
compare = actual_fib,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "PCHG", "AVALU")
)
})
### Fibrinogen decreased (NCICTCv5)
### Grade 4: <0.25 x LLN OR if abnormal, 75% dec. from BL OR absolute value <50 mg/dL
### Grade 3: <0.5 - 0.25 x LLN OR if abnormal, 50 - <75% dec. from BL
### Grade 2: <0.75 - 0.5 x LLN OR if abnormal, 25 - <50% dec. from BL
### Grade 1: <1.0 - 0.75 x LLN OR if abnormal, <25% dec. from BL
## Test 28: CTCAEv5 Fibrinogen decreased ----
test_that("derive_var_atoxgr Test 28: CTCAEv5 Fibrinogen decreased", {
expected_fib <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~PCHG, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, "g/L", NA,
NA_character_, 10, 10, 40, "g/L", NA,
# Satisfies < 0.5 for grade 4 - other criteria missing
"Fibrinogen decreased", 0.49, NA, NA, "g/L", "4",
# Satisfies < 0.5 for grade 4 - satisfies grade 3 for other criteria
"Fibrinogen decreased", 0.49, 1, -51, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG missing
"Fibrinogen decreased", 0.5, 2.1, NA, "g/L", "4",
# Satisfies < 0.25*LLN for grade 4 - PCHG satisfies grade 3
"Fibrinogen decreased", 0.5, 2.1, -51, "g/L", "4",
# Satisfies <=75% decrease for grade 4 - LLN satisfies grade 3
"Fibrinogen decreased", 0.5, 1.1, -75, "g/L", "4",
# Satisfies < 0.5*LLN for grade 3 - PCHG missing
"Fibrinogen decreased", 1, 2.1, NA, "g/L", "3",
# Satisfies < 0.5*LLN for grade 3 - PCHG satisfies grade 2
"Fibrinogen decreased", 1, 2.1, -49, "g/L", "3",
# Satisfies <=50% decrease for grade 3 - LLN satisfies grade 2
"Fibrinogen decreased", 1, 2, -50, "g/L", "3",
# Satisfies < 0.75*LLN for grade 2 - PCHG missing
"Fibrinogen decreased", 1.5, 2.1, NA, "g/L", "2",
# Satisfies < 0.75*LLN for grade 2 - PCHG satisfies grade 1
"Fibrinogen decreased", 1.5, 2.1, -10, "g/L", "2",
# Satisfies <=25% for grade 2 - LLN satisfies grade 1
"Fibrinogen decreased", 1.5, 1.6, -25, "g/L", "2",
# Satisfies < LLN for grade 1 - PCHG missing
"Fibrinogen decreased", 2, 2.1, NA, "g/L", "1",
# Satisfies < LLN for grade 1 - PCHG satisfies grade 0
"Fibrinogen decreased", 2, 2.1, 10, "g/L", "1",
# Satisfies grade 0 - AVAL >= LLN AND no % descrease
"Fibrinogen decreased", 1.5, 1.5, 0, "g/L", "0",
# Satisfies % decrease for grade 1 - AVAL = LLN so not abnormal
"Fibrinogen decreased", 1.5, 1.5, -1, "g/L", "0",
# AVAL >= LLN - PCT missing but its normal so ignore PCT
"Fibrinogen decreased", 1.5, 1.5, NA, "g/L", "0",
# Satisfies <=75% decrease for grade 4 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1, NA, -75, "g/L", NA,
# Satisfies <=50% decrease for grade 3 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1, NA, -50, "g/L", NA,
# Satisfies <=25% decrease for grade 2 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1.5, NA, -25, "g/L", NA,
# Satisfies % decrease for grade 1 - LLN missing do not know its abnormal
"Fibrinogen decreased", 1.5, NA, -1, "g/L", NA,
# PCT >= 0 BUT LLN missing cannot grade as NORMAL
"Fibrinogen decreased", 1.5, NA, 10, "g/L", NA,
# AVAL missing cannot grade
"Fibrinogen decreased", NA, 1.5, 10, "g/L", NA,
# wrong unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, "g/dL", NA,
# missing unit cannot grade as it may satisfy grade 4
"Fibrinogen decreased", 1.5, 1.5, 0, NA, NA,
)
input_fib <- expected_fib %>%
select(-ATOXGRL)
actual_fib <- derive_var_atoxgr_dir(
input_fib,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fib,
compare = actual_fib,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "PCHG", "AVALU")
)
})
### GGT increased (NCICTCv4)
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN
### Grade 3: >5.0 - 20.0 x ULN
### Grade 2: >2.5 - 5.0 x ULN
### Grade 1: >ULN - 2.5 x ULN
expected_ggt_ctcv4 <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"GGT increased", 801, 0, 40, NA_character_, "4",
"GGT increased", 800, 0, 40, NA_character_, "3",
"GGT increased", 201, 0, 40, NA_character_, "3",
"GGT increased", 200, 0, 40, NA_character_, "2",
"GGT increased", 101, 0, 40, NA_character_, "2",
"GGT increased", 100, 0, 40, NA_character_, "1",
"GGT increased", 41, 0, 40, NA_character_, "1",
"GGT increased", 40, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"GGT increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"GGT increased", NA, 0, NA, NA_character_, NA,
)
## Test 29: CTCAEv4 GGT increased ----
test_that("derive_var_atoxgr Test 29: CTCAEv4 GGT increased", {
input_ggt <- expected_ggt_ctcv4 %>%
select(-ATOXGRH)
actual_ggt <- derive_var_atoxgr_dir(
input_ggt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ggt_ctcv4,
compare = actual_ggt,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### GGT increased (NCICTCv5)
### NCICTCAEv5 same criteria as NCICTCAEv4 when BASELINE is normal
### Grade 4: >20.0 x ULN if BL was normal OR >20.0 x BL if BL was abnormal
### Grade 3: >5.0 - 20.0 x ULN if BL was normal OR >5.0 - 20.0 x BL if BL was abnormal
### Grade 2: >2.5 - 5.0 x ULN if BL was normal OR >2.5 - 5.0 x BL if BL was abnormal
### Grade 1: >ULN - 2.5 x ULN if BL was normal OR >2.0 - 2.5 x BL if BL was abnormal
## Test 30: CTCAEv5 GGT increased ----
test_that("derive_var_atoxgr Test 30: CTCAEv5 GGT increased", {
# V5 and V4 criteria identical when BASELINE normal
expected_ggt_ctcv5_norm <- expected_ggt_ctcv4 %>%
# set BASE to be normal and create FLAG
mutate(
BASE = ANRHI,
FLAG = "NORMAL"
)
# create records with baseline abnormal and apply criteria
expected_ggt_ctcv5_abn <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~BASE, ~AVALU, ~ATOXGRH,
"Not a term", 80, 0, 40, NA_character_, NA,
NA_character_, 60, 0, 40, NA_character_, NA,
"GGT increased", 801, 0, 40, NA_character_, "4",
"GGT increased", 800, 0, 40, NA_character_, "3",
"GGT increased", 201, 0, 40, NA_character_, "3",
"GGT increased", 200, 0, 40, NA_character_, "2",
"GGT increased", 101, 0, 40, NA_character_, "2",
"GGT increased", 100, 0, 40, NA_character_, "1",
"GGT increased", 81, 0, 40, NA_character_, "1",
"GGT increased", 80, 0, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"GGT increased", 100, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"GGT increased", NA, 0, NA, NA_character_, NA,
) %>%
# set BASE to be abnormal and create FLAG
mutate(
ANRHI = BASE - 1,
FLAG = "ABNORMAL"
)
# combine records with baseline normal and abnormal
expected_ggt_ctcv5 <- expected_ggt_ctcv5_norm %>%
bind_rows(expected_ggt_ctcv5_abn)
input_ggt <- expected_ggt_ctcv5 %>%
select(-ATOXGRH)
actual_ggt <- derive_var_atoxgr_dir(
input_ggt,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ggt_ctcv5,
compare = actual_ggt,
keys = c("ATOXDSCH", "AVAL", "ANRLO", "ANRHI", "FLAG", "AVALU")
)
})
### Haptoglobin decreased (NCICTCv4)
# Same as NCICTCv5
### Grade 1: <LLN
expected_hapt <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 9, 10, 40, NA_character_, NA,
NA_character_, 10, 10, 40, NA_character_, NA,
"Haptoglobin decreased", 9, 10, 40, NA_character_, "1",
"Haptoglobin decreased", 10, 10, 40, NA_character_, "0",
"Haptoglobin decreased", 11, 10, 40, NA_character_, "0",
# ANRHI missing - cannot grade
"Haptoglobin decreased", NA, 10, 40, NA_character_, NA,
# AVAL missing cannot grade
"Haptoglobin decreased", 10, NA, NA, NA_character_, NA,
)
input_hapt <- expected_hapt %>%
select(-ATOXGRL)
## Test 31: CTCAEv4 Haptoglobin decreased ----
test_that("derive_var_atoxgr Test 31: CTCAEv4 Haptoglobin decreased", {
actual_hapt <- derive_var_atoxgr_dir(
input_hapt,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hapt,
compare = actual_hapt,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 32: CTCAEv5 Haptoglobin decreased ----
test_that("derive_var_atoxgr Test 32: CTCAEv5 Haptoglobin decreased", {
actual_hapt <- derive_var_atoxgr_dir(
input_hapt,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hapt,
compare = actual_hapt,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hemoglobin increased
# NCICTCAEv5 same as NCICTCAEv4 when BASE is normal
### Grade 3: Increase in >4 gm/dL above ULN or above baseline if baseline is above ULN
### Grade 2: Increase in >2 - 4 gm/dL above ULN or above baseline if baseline is above ULN
### Grade 1: Increase in >0 - 2 gm/dL above ULN or above baseline if baseline is above ULN
expected_hgbi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM, ~V5,
"Not a term", 80, 120, 200, "g/L", NA, 1, "Y",
NA_character_, 60, 50, 100, "g/L", NA, 2, "Y",
# BASE greater than ANRHI
"Hemoglobin increased", 106, 65, 60, "g/L", "3", 3, "N",
"Hemoglobin increased", 105, 65, 60, "g/L", "2", 4, "N",
"Hemoglobin increased", 86, 65, 60, "g/L", "2", 5, "N",
"Hemoglobin increased", 85, 65, 60, "g/L", "1", 6, "N",
"Hemoglobin increased", 66, 65, 60, "g/L", "1", 7, "N",
"Hemoglobin increased", 65, 65, 60, "g/L", "0", 8, "N",
"Hemoglobin increased", NA, 65, 60, "g/L", NA, 9, "N",
# BASE less than or equal to ANRHI
"Hemoglobin increased", 106, 60, 65, "g/L", "3", 10, "Y",
"Hemoglobin increased", 105, 60, 65, "g/L", "2", 11, "Y",
"Hemoglobin increased", 86, 60, 65, "g/L", "2", 12, "Y",
"Hemoglobin increased", 85, 60, 65, "g/L", "1", 13, "Y",
"Hemoglobin increased", 66, 60, 65, "g/L", "1", 14, "Y",
"Hemoglobin increased", 65, 60, 65, "g/L", "0", 15, "Y",
"Hemoglobin increased", NA, 60, 65, "g/L", NA, 16, "Y",
# BASE missing
"Hemoglobin increased", 106, NA, 65, "g/L", "3", 17, "N",
"Hemoglobin increased", 105, NA, 65, "g/L", "2", 18, "N",
"Hemoglobin increased", 86, NA, 65, "g/L", "2", 19, "N",
"Hemoglobin increased", 85, NA, 65, "g/L", "1", 20, "N",
"Hemoglobin increased", 66, NA, 65, "g/L", "1", 21, "N",
"Hemoglobin increased", 65, NA, 65, "g/L", "0", 22, "N",
"Hemoglobin increased", NA, NA, 65, "g/L", NA, 23, "N",
# Unit missing cannot grade
"Hemoglobin increased", 200, 61, 65, NA, NA, 24, "Y",
# ANRHI missing - cannot grade
"Hemoglobin increased", 200, 60, NA, "g/L", NA, 25, "Y",
# AVAL missing cannot grade
"Hemoglobin increased", NA, 60, 65, "g/L", NA, 26, "Y",
)
## Test 33: CTCAEv4 Hemoglobin increased ----
test_that("derive_var_atoxgr Test 33: CTCAEv4 Hemoglobin increased", {
input_hgbi <- expected_hgbi %>%
select(-ATOXGRH)
actual_hgbi <- derive_var_atoxgr_dir(
input_hgbi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbi,
compare = actual_hgbi,
keys = c("TESTNUM")
)
})
## Test 34: CTCAEv5 Hemoglobin increased ----
test_that("derive_var_atoxgr Test 34: CTCAEv5 Hemoglobin increased", {
expected_hgbi <- expected_hgbi %>%
filter(V5 == "Y")
input_hgbi <- expected_hgbi %>%
select(-ATOXGRH)
actual_hgbi <- derive_var_atoxgr_dir(
input_hgbi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbi,
compare = actual_hgbi,
keys = c("TESTNUM")
)
})
### INR increased (NCICTCV4)
### NCICTCV5 different for grade 1
### Grade 3: >2.5 x ULN; >2.5 times above baseline if on anticoagulation
### Grade 2: >1.5 - 2.5 x ULN; >1.5 - 2.5 times above baseline if on anticoagulation
### Grade 1: >1 - 1.5 x ULN; >1 - 1.5 times above baseline if on anticoagulation
## Test 35: CTCAEv4 INR increased ----
test_that("derive_var_atoxgr Test 35: CTCAEv4 INR increased", {
expected_inri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 120, 200, NA_character_, NA, 1,
NA_character_, 60, 50, 100, NA_character_, NA, 2,
# GRADE derived from AVAL against ANRHI
"INR IncreaSed", 251, 200, 100, NA_character_, "3", 3,
"INR Increased", 250, 199, 100, NA_character_, "2", 4,
"INR Increased", 151, 150, 100, NA_character_, "2", 5,
"INR Increased", 150, 150, 100, NA_character_, "1", 6,
"INR Increased", 101, 150, 100, NA_character_, "1", 7,
"INR Increased", 100, 100, 100, NA_character_, "0", 8,
# GRADE derived from AVAL against BASE
"INR IncreaSed", 251, 100, 200, NA_character_, "3", 9,
"INR Increased", 250, 100, 199, NA_character_, "2", 10,
"INR Increased", 151, 100, 150, NA_character_, "2", 11,
"INR Increased", 150, 100, 150, NA_character_, "1", 12,
"INR Increased", 101, 100, 150, NA_character_, "1", 13,
"INR Increased", 100, 100, 100, NA_character_, "0", 14,
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"INR Increased", 100, NA, 100, NA_character_, NA, 15,
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"INR Increased", 100, 100, NA, NA_character_, NA, 16,
# AVAL missing cannot grade
"INR Increased", NA, 100, 100, NA_character_, NA, 17,
)
input_inri <- expected_inri %>%
select(-ATOXGRH)
actual_inri <- derive_var_atoxgr_dir(
input_inri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri,
compare = actual_inri,
keys = c("TESTNUM")
)
})
### INR increased (NCICTCV4)
### NCICTCV5 different for grade 1
### Grade 3: >2.5 x ULN; >2.5 times above baseline if on anticoagulation
### Grade 2: >1.5 - 2.5 x ULN; >1.5 - 2.5 times above baseline if on anticoagulation
### Grade 1: >1.2 - 1.5 x ULN; >1 - 1.5 times above baseline if on anticoagulation
## Test 36: CTCAEv5 INR increased ----
test_that("derive_var_atoxgr Test 36: CTCAEv5 INR increased", {
expected_inri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~BASE, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 120, 200, NA_character_, NA, 1,
NA_character_, 60, 50, 100, NA_character_, NA, 2,
# GRADE derived from AVAL against ANRHI
"INR IncreaSed", 251, 200, 100, NA_character_, "3", 3,
"INR Increased", 250, 199, 100, NA_character_, "2", 4,
"INR Increased", 151, 150, 100, NA_character_, "2", 5,
"INR Increased", 150, 150, 100, NA_character_, "1", 6,
"INR Increased", 121, 150, 100, NA_character_, "1", 7,
"INR Increased", 120, 120, 100, NA_character_, "0", 8,
# GRADE derived from AVAL against BASE
"INR IncreaSed", 251, 100, 200, NA_character_, "3", 9,
"INR Increased", 250, 100, 199, NA_character_, "2", 10,
"INR Increased", 151, 100, 150, NA_character_, "2", 11,
"INR Increased", 150, 100, 150, NA_character_, "1", 12,
"INR Increased", 101, 100, 150, NA_character_, "1", 13,
"INR Increased", 100, 100, 100, NA_character_, "0", 14,
# BASE missing - AVAL <= ANRLO cannot grade as NORMAL
"INR Increased", 100, NA, 100, NA_character_, NA, 15,
# ANRHI missing - AVAL <= BASE cannot grade as NORMAL
"INR Increased", 100, 100, NA, NA_character_, NA, 16,
# AVAL missing cannot grade
"INR Increased", NA, 100, 100, NA_character_, NA, 17,
)
input_inri <- expected_inri %>%
select(-ATOXGRH)
actual_inri <- derive_var_atoxgr_dir(
input_inri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri,
compare = actual_inri,
keys = c("TESTNUM")
)
})
### Lipase increased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >5.0 x ULN
### Grade 3: >2.0 - 5.0 x ULN
### Grade 2: >1.5 - 2.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_lip <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, NA_character_, NA,
NA_character_, 60, 50, 100, NA_character_, NA,
"Lipase IncreaSed", 501, 0, 100, NA_character_, "4",
"Lipase Increased", 500, 0, 100, NA_character_, "3",
"Lipase Increased", 201, 0, 100, NA_character_, "3",
"Lipase Increased", 200, 0, 100, NA_character_, "2",
"Lipase Increased", 151, 0, 100, NA_character_, "2",
"Lipase Increased", 150, 0, 100, NA_character_, "1",
"Lipase Increased", 101, 0, 100, NA_character_, "1",
"Lipase Increased", 100, 0, 100, NA_character_, "0",
# ANRHI missing cannot grade
"Lipase Increased", 200, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"Lipase Increased", NA, 0, 100, NA_character_, NA,
)
input_lip <- expected_lip %>%
select(-ATOXGRH)
## Test 37: CTCAEv4 Lipase increased ----
test_that("derive_var_atoxgr Test 37: CTCAEv4 Lipase increased", {
actual_lip <- derive_var_atoxgr_dir(
input_lip,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lip,
compare = actual_lip,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 38: CTCAEv5 Lipase increased ----
test_that("derive_var_atoxgr Test 38: CTCAEv5 Lipase increased", {
actual_lip <- derive_var_atoxgr_dir(
input_lip,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lip,
compare = actual_lip,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Lymphocyte count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.2 x 10e9 /L
### Grade 3: <0.5 - 0.2 x 10e9 /L
### Grade 2: <0.8 - 0.5 x 10e9 /L
### Grade 1: <LLN - 0.8 x 10e9/L
expected_lymd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 80, 120, 200, "10^9/L", NA, 1,
NA_character_, 60, 50, 100, "10^9/L", NA, 2,
# ANRLO not missing
"Lymphocyte count decreased", 0.19, 140, NA, "10^9/L", "4", 3,
"Lymphocyte count decreased", 0.2, 140, NA, "10^9/L", "3", 4,
"Lymphocyte count decreased", 0.49, 140, NA, "10^9/L", "3", 5,
"Lymphocyte count decreased", 0.5, 140, NA, "10^9/L", "2", 6,
"Lymphocyte count decreased", 0.79, 140, NA, "10^9/L", "2", 7,
"Lymphocyte count decreased", 0.8, 140, NA, "10^9/L", "1", 8,
"Lymphocyte count decreased", 1.09, 1.1, NA, "10^9/L", "1", 9,
"Lymphocyte count decreased", 1.1, 1.1, NA, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4
"Lymphocyte count decreased", 0.19, NA, NA, "10^9/L", "4", 11,
"Lymphocyte count decreased", 0.2, NA, NA, "10^9/L", "3", 12,
"Lymphocyte count decreased", 0.49, NA, NA, "10^9/L", "3", 13,
"Lymphocyte count decreased", 0.5, NA, NA, "10^9/L", "2", 14,
"Lymphocyte count decreased", 0.79, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Lymphocyte count decreased", 0.8, NA, NA, "10^9/L", NA, 16,
"Lymphocyte count decreased", 1.09, NA, NA, "10^9/L", NA, 17,
"Lymphocyte count decreased", 1.1, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"Lymphocyte count decreased", 1.1, 1.1, NA, NA, NA, 19,
# AVAL missing cannot grade
"Lymphocyte count decreased", 1.1, 1.1, NA, "10^9/L", "0", 20,
)
input_lymd <- expected_lymd %>%
select(-ATOXGRL)
## Test 39: CTCAEv4 Lymphocyte count decreased ----
test_that("derive_var_atoxgr Test 39: CTCAEv4 Lymphocyte count decreased", {
actual_lymd <- derive_var_atoxgr_dir(
input_lymd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymd,
compare = actual_lymd,
keys = c("TESTNUM")
)
})
## Test 40: CTCAEv5 Lymphocyte count decreased ----
test_that("derive_var_atoxgr Test 40: CTCAEv5 Lymphocyte count decreased", {
actual_lymd <- derive_var_atoxgr_dir(
input_lymd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymd,
compare = actual_lymd,
keys = c("TESTNUM")
)
})
### Lymphocyte count increased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: >20,000/mm3
### Grade 2: >4000/mm3 - 20,000/mm3
expected_lymi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, "10^9/L", NA,
NA_character_, 60, 50, 100, "10^9/L", NA,
"Lymphocyte count increased", 21, NA, NA, "10^9/L", "3",
"Lymphocyte count increased", 20, NA, NA, "10^9/L", "2",
"Lymphocyte count increased", 4.1, NA, NA, "10^9/L", "2",
"Lymphocyte count increased", 4, NA, NA, "10^9/L", "0",
# Unit missing cannot grade
"Lymphocyte count increased", 4, NA, NA, NA, NA,
# AVAL missing cannot grade
"Lymphocyte count increased", NA, NA, NA, "10^9/L", NA,
)
input_lymi <- expected_lymi %>%
select(-ATOXGRH)
## Test 41: CTCAEv4 Lymphocyte count increased ----
test_that("derive_var_atoxgr Test 41: CTCAEv4 Lymphocyte count increased", {
actual_lymi <- derive_var_atoxgr_dir(
input_lymi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymi,
compare = actual_lymi,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 42: CTCAEv5 Lymphocyte count increased ----
test_that("derive_var_atoxgr Test 42: CTCAEv5 Lymphocyte count increased", {
actual_lymi <- derive_var_atoxgr_dir(
input_lymi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymi,
compare = actual_lymi,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Neutrophil count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <25.0 x 10e9 /L
### Grade 3: <1.0 - 0.5 x 10e9 /L
### Grade 2: <1.5 - 1.0 x 10e9 /L
### Grade 1: <LLN - 1.5 x 10e9 /L
expected_neut <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 80, 120, 200, "10^9/L", NA,
NA_character_, 60, 50, 100, "10^9/L", NA,
# ANRLO not missing
"Neutrophil count decreased", 0.49, 2, NA, "10^9/L", "4",
"Neutrophil count decreased", 0.5, 2, NA, "10^9/L", "3",
"Neutrophil count decreased", 0.99, 2, NA, "10^9/L", "3",
"Neutrophil count decreased", 1, 2, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.49, 2, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.5, 2, NA, "10^9/L", "1",
"Neutrophil count decreased", 1.9, 2, NA, "10^9/L", "1",
"Neutrophil count decreased", 2, 2, NA, "10^9/L", "0",
# ANRLO missing - can grade 2-4
"Neutrophil count decreased", 0.49, NA, NA, "10^9/L", "4",
"Neutrophil count decreased", 0.5, NA, NA, "10^9/L", "3",
"Neutrophil count decreased", 0.99, NA, NA, "10^9/L", "3",
"Neutrophil count decreased", 1, NA, NA, "10^9/L", "2",
"Neutrophil count decreased", 1.49, NA, NA, "10^9/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Neutrophil count decreased", 1.5, NA, NA, "10^9/L", NA,
"Neutrophil count decreased", 1.9, NA, NA, "10^9/L", NA,
"Neutrophil count decreased", 2, NA, NA, "10^9/L", NA,
# Unit missing cannot grade
"Neutrophil count decreased", 2, 2, NA, NA, NA,
# AVAL missing cannot grade
"Neutrophil count decreased", NA, 2, NA, "10^9/L", NA,
)
input_neut <- expected_neut %>%
select(-ATOXGRL)
## Test 43: CTCAEv4 Neutrophil count decreased ----
test_that("derive_var_atoxgr Test 43: CTCAEv4 Neutrophil count decreased", {
actual_neut <- derive_var_atoxgr_dir(
input_neut,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_neut,
compare = actual_neut,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 44: CTCAEv5 Neutrophil count decreased ----
test_that("derive_var_atoxgr Test 44: CTCAEv5 Neutrophil count decreased", {
actual_neut <- derive_var_atoxgr_dir(
input_neut,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_neut,
compare = actual_neut,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Platelet count decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <25.0 x 10e9 /L
### Grade 3: <50.0 - 25.0 x 10e9 /L
### Grade 2: <75.0 - 50.0 x 10e9 /L
### Grade 1: <LLN - 75.0 x 10e9 /L
expected_plate <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 80, 120, 200, "10^9/L", NA, 1,
NA_character_, 60, 50, 100, "10^9/L", NA, 2,
# ANRLO not missing
"Platelet count decreased", 24, 100, 150, "10^9/L", "4", 3,
"Platelet count decreased", 25, 100, 150, "10^9/L", "3", 4,
"Platelet count decreased", 49, 100, 150, "10^9/L", "3", 5,
"Platelet count decreased", 50, 100, 150, "10^9/L", "2", 6,
"Platelet count decreased", 74, 100, 150, "10^9/L", "2", 7,
"Platelet count decreased", 75, 100, 150, "10^9/L", "1", 8,
"Platelet count decreased", 99, 100, NA, "10^9/L", "1", 9,
"Platelet count decreased", 100, 100, NA, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4 1,
"Platelet count decreased", 24, NA, NA, "10^9/L", "4", 11,
"Platelet count decreased", 25, NA, NA, "10^9/L", "3", 12,
"Platelet count decreased", 49, NA, NA, "10^9/L", "3", 13,
"Platelet count decreased", 50, NA, NA, "10^9/L", "2", 14,
"Platelet count decreased", 74, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Platelet count decreased", 75, NA, NA, "10^9/L", NA, 16,
"Platelet count decreased", 99, NA, NA, "10^9/L", NA, 17,
"Platelet count decreased", 100, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"Platelet count decreased", 100, 100, NA, NA, NA, 19,
# AVAL missing cannot grade
"Platelet count decreased", NA, 100, NA, "10^9/L", NA, 20,
)
input_plate <- expected_plate %>%
select(-ATOXGRL)
## Test 45: CTCAEv4 Platelet count decreased ----
test_that("derive_var_atoxgr Test 45: CTCAEv4 Platelet count decreased", {
actual_plate <- derive_var_atoxgr_dir(
input_plate,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plate,
compare = actual_plate,
keys = c("TESTNUM")
)
})
## Test 46: CTCAEv5 Platelet count decreased ----
test_that("derive_var_atoxgr Test 46: CTCAEv5 Platelet count decreased", {
actual_plate <- derive_var_atoxgr_dir(
input_plate,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plate,
compare = actual_plate,
keys = c("TESTNUM")
)
})
### Serum amylase increased
### NCICTCAEv4 and NCICTCAEv5 criteria essentially the same
### Grade 4: >5.0 x ULN
### Grade 3: >2.0 - 5.0 x ULN
### Grade 2: >1.5 - 2.0 x ULN
### Grade 1: >ULN - 1.5 x ULN
expected_seri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 120, 200, NA_character_, NA,
NA_character_, 60, 50, 100, NA_character_, NA,
"Serum amylase increased", 501, 0, 100, NA_character_, "4",
"Serum amylase increased", 500, 0, 100, NA_character_, "3",
"Serum amylase increased", 201, 0, 100, NA_character_, "3",
"Serum amylase increased", 200, 0, 100, NA_character_, "2",
"Serum amylase increased", 151, 0, 100, NA_character_, "2",
"Serum amylase increased", 150, 0, 100, NA_character_, "1",
"Serum amylase increased", 101, 0, 100, NA_character_, "1",
"Serum amylase increased", 100, 0, 100, NA_character_, "0",
# ANRHI missing cannot grade
"Serum amylase increased", 200, 0, NA, NA_character_, NA,
# AVAL missing cannot grade
"Serum amylase increased", NA, 0, 100, NA_character_, NA,
)
input_seri <- expected_seri %>%
select(-ATOXGRH)
## Test 47: CTCAEv4 Serum amylase increased ----
test_that("derive_var_atoxgr Test 47: CTCAEv4 Serum amylase increased", {
actual_seri <- derive_var_atoxgr_dir(
input_seri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_seri,
compare = actual_seri,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 48: CTCAEv5 Serum amylase increased ----
test_that("derive_var_atoxgr Test 48: CTCAEv5 Serum amylase increased", {
actual_seri <- derive_var_atoxgr_dir(
input_seri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_seri,
compare = actual_seri,
keys = c("AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### White blood cell decreased
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.0 x 10e9 /L
### Grade 3: <2.0 - 1.0 x 10e9 /L
### Grade 2: <3.0 - 2.0 x 10e9 /L
### Grade 1: <LLN - 3.0 x 10e9 /L
expected_wbcd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 1, 5, 15, "10^9/L", NA, 1,
NA_character_, 2, 5, 15, "10^9/L", NA, 2,
# ANRLO not missing
"White blood cell decreased", 0.9, 5, 15, "10^9/L", "4", 3,
"White blood cell decreased", 1, 5, 15, "10^9/L", "3", 4,
"White blood cell decreased", 1.9, 5, 15, "10^9/L", "3", 5,
"White blood cell decreased", 2, 5, 15, "10^9/L", "2", 6,
"White blood cell decreased", 2.9, 5, 15, "10^9/L", "2", 7,
"White blood cell decreased", 3, 5, 15, "10^9/L", "1", 8,
"White blood cell decreased", 4.9, 5, 15, "10^9/L", "1", 9,
"White blood cell decreased", 5, 5, 15, "10^9/L", "0", 10,
# ANRLO missing - can grade 2-4
"White blood cell decreased", 0.9, NA, NA, "10^9/L", "4", 11,
"White blood cell decreased", 1, NA, NA, "10^9/L", "3", 12,
"White blood cell decreased", 1.9, NA, NA, "10^9/L", "3", 13,
"White blood cell decreased", 2, NA, NA, "10^9/L", "2", 14,
"White blood cell decreased", 2.9, NA, NA, "10^9/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 16,
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 17,
"White blood cell decreased", 3, NA, NA, "10^9/L", NA, 18,
# Unit missing cannot grade
"White blood cell decreased", 3, 100, NA, NA, NA, 19,
# AVAL missing cannot grade
"White blood cell decreased", NA, 100, NA, "10^9/L", NA, 20,
)
input_wbcd <- expected_wbcd %>%
select(-ATOXGRL)
## Test 49: CTCAEv4 White blood cell decreased ----
test_that("derive_var_atoxgr Test 49: CTCAEv4 White blood cell decreased", {
actual_wbcd <- derive_var_atoxgr_dir(
input_wbcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd,
compare = actual_wbcd,
keys = c("TESTNUM")
)
})
## Test 50: CTCAEv5 White blood cell decreased ----
test_that("derive_var_atoxgr Test 50: CTCAEv5 White blood cell decreased", {
actual_wbcd <- derive_var_atoxgr_dir(
input_wbcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd,
compare = actual_wbcd,
keys = c("TESTNUM")
)
})
## Metabolism and nutrition disorders
### Hypercalcemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >3.4 mmol/L
### Grade 3: >3.1 - 3.4 mmol/L
### Grade 2: >2.9 - 3.1 mmol/L
### Grade 1: >ULN - 2.9 mmol/L
expected_calci <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, 0, 2.5, "mmol/L", NA, 1,
NA_character_, 3.5, 0, 2.5, "mmol/L", NA, 2,
# ANRHI not missing
"Hypercalcemia", 3.5, 0, 2.5, "mmol/L", "4", 3,
"Hypercalcemia", 3.4, 0, 2.5, "mmol/L", "3", 4,
"Hypercalcemia", 3.2, 0, 2.5, "mmol/L", "3", 5,
"Hypercalcemia", 3.1, 0, 2.5, "mmol/L", "2", 6,
"Hypercalcemia", 3, 0, 2.5, "mmol/L", "2", 7,
"Hypercalcemia", 2.9, 0, 2.5, "mmol/L", "1", 8,
"Hypercalcemia", 2.6, 0, 2.5, "mmol/L", "1", 9,
"Hypercalcemia", 2.5, 0, 2.5, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hypercalcemia", 3.5, 0, NA, "mmol/L", "4", 11,
"Hypercalcemia", 3.4, 0, NA, "mmol/L", "3", 12,
"Hypercalcemia", 3.2, 0, NA, "mmol/L", "3", 13,
"Hypercalcemia", 3.1, 0, NA, "mmol/L", "2", 14,
"Hypercalcemia", 3, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypercalcemia", 2.9, 0, NA, "mmol/L", NA, 16,
"Hypercalcemia", 2.6, 0, NA, "mmol/L", NA, 17,
"Hypercalcemia", 2.5, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hypercalcemia", 2.5, 0, 2.5, NA, NA, 19,
# AVAL missing cannot grade
"Hypercalcemia", NA, 0, 2.5, "mmol/L", NA, 20,
)
input_calci <- expected_calci %>%
select(-ATOXGRH)
## Test 51: CTCAEv4 Hypercalcemia ----
test_that("derive_var_atoxgr Test 51: CTCAEv4 Hypercalcemia", {
actual_calci <- derive_var_atoxgr_dir(
input_calci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci,
compare = actual_calci,
keys = c("TESTNUM")
)
})
## Test 52: CTCAEv5 Hypercalcemia ----
test_that("derive_var_atoxgr Test 52: CTCAEv5 Hypercalcemia", {
actual_calci <- derive_var_atoxgr_dir(
input_calci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci,
compare = actual_calci,
keys = c("TESTNUM")
)
})
### Hypercalcemia (Ionized)
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >1.8 mmol/L
### Grade 3: >1.6 - 1.8 mmol/L
### Grade 2: >1.5 - 1.6 mmol/L
### Grade 1: >ULN - 1.5 mmol/L
expected_calioni <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.9, 0, 1.3, "mmol/L", NA, 1,
NA_character_, 1.9, 0, 1.3, "mmol/L", NA, 2,
# ANRHI not missing
"Hypercalcemia (Ionized)", 1.9, 0, 1.3, "mmol/L", "4", 3,
"Hypercalcemia (Ionized)", 1.8, 0, 1.3, "mmol/L", "3", 4,
"Hypercalcemia (Ionized)", 1.7, 0, 1.3, "mmol/L", "3", 5,
"Hypercalcemia (Ionized)", 1.6, 0, 1.3, "mmol/L", "2", 6,
"Hypercalcemia (Ionized)", 1.51, 0, 1.3, "mmol/L", "2", 7,
"Hypercalcemia (Ionized)", 1.5, 0, 1.3, "mmol/L", "1", 8,
"Hypercalcemia (Ionized)", 1.4, 0, 1.3, "mmol/L", "1", 9,
"Hypercalcemia (Ionized)", 1.3, 0, 1.3, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hypercalcemia (Ionized)", 1.9, 0, NA, "mmol/L", "4", 11,
"Hypercalcemia (Ionized)", 1.8, 0, NA, "mmol/L", "3", 12,
"Hypercalcemia (Ionized)", 1.7, 0, NA, "mmol/L", "3", 13,
"Hypercalcemia (Ionized)", 1.6, 0, NA, "mmol/L", "2", 14,
"Hypercalcemia (Ionized)", 1.51, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypercalcemia (Ionized)", 1.5, 0, NA, "mmol/L", NA, 16,
"Hypercalcemia (Ionized)", 1.4, 0, NA, "mmol/L", NA, 17,
"Hypercalcemia (Ionized)", 1.3, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade 1,
"Hypercalcemia (Ionized)", 1.3, 0, 1.3, NA, NA, 19,
# AVAL missing cannot grade
"Hypercalcemia (Ionized)", NA, 0, 1.3, "mmol/L", NA, 20,
)
input_calioni <- expected_calioni %>%
select(-ATOXGRH)
## Test 53: CTCAEv4 Hypercalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 53: CTCAEv4 Hypercalcemia (Ionized)", {
actual_calioni <- derive_var_atoxgr_dir(
input_calioni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni,
compare = actual_calioni,
keys = c("TESTNUM")
)
})
## Test 54: CTCAEv5 Hypercalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 54: CTCAEv5 Hypercalcemia (Ionized)", {
actual_calioni <- derive_var_atoxgr_dir(
input_calioni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni,
compare = actual_calioni,
keys = c("TESTNUM")
)
})
### Hyperglycemia (Fasting) (NCICTCAEv4)
### not included in NCICTCAEv5
### Grade 4: >27.8 mmol/L
### Grade 3: >13.9 - 27.8 mmol/L
### Grade 2: >8.9 - 13.9 mmol/L
### Grade 1: >ULN - 8.9 mmol/L
## Test 55: CTCAEv4 Hyperglycemia (Fasting) ----
test_that("derive_var_atoxgr Test 55: CTCAEv4 Hyperglycemia (Fasting)", {
expected_glycfi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 27.9, 0, 5.3, "mmol/L", NA, 1,
NA_character_, 27.9, 0, 5.3, "mmol/L", NA, 2,
# ANRHI not missing
"Hyperglycemia (Fasting)", 27.9, 0, 5.3, "mmol/L", "4", 3,
"Hyperglycemia (Fasting)", 27.8, 0, 5.3, "mmol/L", "3", 4,
"Hyperglycemia (Fasting)", 14, 0, 5.3, "mmol/L", "3", 5,
"Hyperglycemia (Fasting)", 13.9, 0, 5.3, "mmol/L", "2", 6,
"Hyperglycemia (Fasting)", 9, 0, 5.3, "mmol/L", "2", 7,
"Hyperglycemia (Fasting)", 8.9, 0, 5.3, "mmol/L", "1", 8,
"Hyperglycemia (Fasting)", 5.4, 0, 5.3, "mmol/L", "1", 9,
"Hyperglycemia (Fasting)", 5.3, 0, 5.3, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hyperglycemia (Fasting)", 27.9, 0, NA, "mmol/L", "4", 11,
"Hyperglycemia (Fasting)", 27.8, 0, NA, "mmol/L", "3", 12,
"Hyperglycemia (Fasting)", 14, 0, NA, "mmol/L", "3", 13,
"Hyperglycemia (Fasting)", 13.9, 0, NA, "mmol/L", "2", 14,
"Hyperglycemia (Fasting)", 9, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hyperglycemia (Fasting)", 8.9, 0, NA, "mmol/L", NA, 16,
"Hyperglycemia (Fasting)", 5.4, 0, NA, "mmol/L", NA, 17,
"Hyperglycemia (Fasting)", 5.3, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hyperglycemia (Fasting)", 5.3, 0, 5.3, NA, NA, 19,
# AVAL missing cannot grade
"Hyperglycemia (Fasting)", NA, 0, 5.3, "mmol/L", NA, 20,
)
input_glycfi <- expected_glycfi %>%
select(-ATOXGRH)
actual_glycfi <- derive_var_atoxgr_dir(
input_glycfi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycfi,
compare = actual_glycfi,
keys = c("TESTNUM")
)
})
### Hyperglycemia (NCICTCAEv4)
### not included in NCICTCAEv5
### Grade 4: >27.8 mmol/L
### Grade 3: >13.9 - 27.8 mmol/L
## Test 56: CTCAEv4 Hyperglycemia ----
test_that("derive_var_atoxgr Test 56: CTCAEv4 Hyperglycemia", {
expected_glyci <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 27.9, 0, 5.3, "mmol/L", NA, 1,
NA_character_, 27.9, 0, 5.3, "mmol/L", NA, 2,
"Hyperglycemia", 27.9, 0, 5.3, "mmol/L", "4", 3,
"Hyperglycemia", 27.8, 0, 5.3, "mmol/L", "3", 4,
"Hyperglycemia", 14, 0, 5.3, "mmol/L", "3", 5,
"Hyperglycemia", 13.9, 0, 5.3, "mmol/L", "0", 6,
"Hyperglycemia", 5.3, 0, NA, "mmol/L", "0", 7,
# Unit missing cannot grade
"Hyperglycemia", 5.3, 0, 5.3, NA, NA, 8,
# AVAL missing cannot grade
"Hyperglycemia", NA, 0, 5.3, "mmol/L", NA, 9,
)
input_glyci <- expected_glyci %>%
select(-ATOXGRH)
actual_glyci <- derive_var_atoxgr_dir(
input_glyci,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glyci,
compare = actual_glyci,
keys = c("TESTNUM")
)
})
### Hyperkalemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >7.0 mmol/L
### Grade 3: >6.0 - 7.0 mmol/L
### Grade 2: >5.5 - 6.0 mmol/L
### Grade 1: >ULN - 5.5 mmol/L
expected_kalei <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7.1, 0, 5.1, "mmol/L", NA, 1,
NA_character_, 7.1, 0, 5.1, "mmol/L", NA, 2,
# ANRHI not missing
"Hyperkalemia", 7.1, 0, 5.1, "mmol/L", "4", 3,
"Hyperkalemia", 7, 0, 5.1, "mmol/L", "3", 4,
"Hyperkalemia", 6.1, 0, 5.1, "mmol/L", "3", 5,
"Hyperkalemia", 6, 0, 5.1, "mmol/L", "2", 6,
"Hyperkalemia", 5.6, 0, 5.1, "mmol/L", "2", 7,
"Hyperkalemia", 5.5, 0, 5.1, "mmol/L", "1", 8,
"Hyperkalemia", 5.2, 0, 5.1, "mmol/L", "1", 9,
"Hyperkalemia", 5.1, 0, 5.1, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Hyperkalemia", 7.1, 0, NA, "mmol/L", "4", 11,
"Hyperkalemia", 7, 0, NA, "mmol/L", "3", 12,
"Hyperkalemia", 6.1, 0, NA, "mmol/L", "3", 13,
"Hyperkalemia", 6, 0, NA, "mmol/L", "2", 14,
"Hyperkalemia", 5.6, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hyperkalemia", 5.5, 0, NA, "mmol/L", NA, 16,
"Hyperkalemia", 5.2, 0, NA, "mmol/L", NA, 17,
"Hyperkalemia", 5.1, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hyperkalemia", 5.1, 0, 5.1, NA, NA, 19,
# AVAL missing cannot grade
"Hyperkalemia", NA, 0, 5.1, "mmol/L", NA, 20,
)
input_kalei <- expected_kalei %>%
select(-ATOXGRH)
## Test 57: CTCAEv4 Hyperkalemia ----
test_that("derive_var_atoxgr Test 57: CTCAEv4 Hyperkalemia", {
actual_kalei <- derive_var_atoxgr_dir(
input_kalei,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kalei,
compare = actual_kalei,
keys = c("TESTNUM")
)
})
## Test 58: CTCAEv5 Hyperkalemia ----
test_that("derive_var_atoxgr Test 58: CTCAEv5 Hyperkalemia", {
actual_kalei <- derive_var_atoxgr_dir(
input_kalei,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kalei,
compare = actual_kalei,
keys = c("TESTNUM")
)
})
### Hypermagnesemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >3.30 mmol/L
### Grade 3: >1.23 - 3.30 mmol/L
### Grade 1: >ULN - 1.23 mmol/L
expected_magni <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.4, 0, 0.8, "mmol/L", NA, 1,
NA_character_, 3.4, 0, 0.8, "mmol/L", NA, 2,
# ANRHI not missing
"Hypermagnesemia", 3.4, 0, 0.8, "mmol/L", "4", 3,
"Hypermagnesemia", 3.3, 0, 0.8, "mmol/L", "3", 4,
"Hypermagnesemia", 1.24, 0, 0.8, "mmol/L", "3", 5,
"Hypermagnesemia", 1.23, 0, 0.8, "mmol/L", "1", 6,
"Hypermagnesemia", 0.81, 0, 0.8, "mmol/L", "1", 7,
"Hypermagnesemia", 0.8, 0, 0.8, "mmol/L", "0", 8,
# ANRHI missing - can grade 3-4
"Hypermagnesemia", 3.4, 0, NA, "mmol/L", "4", 9,
"Hypermagnesemia", 3.3, 0, NA, "mmol/L", "3", 10,
"Hypermagnesemia", 1.24, 0, NA, "mmol/L", "3", 11,
# ANRHI missing - can NOT grade 0 or 1
"Hypermagnesemia", 1.23, 0, NA, "mmol/L", NA, 12,
"Hypermagnesemia", 0.81, 0, NA, "mmol/L", NA, 13,
"Hypermagnesemia", 0.8, 0, NA, "mmol/L", NA, 14,
# Unit missing cannot grade
"Hypermagnesemia", 0.8, 0, 0.8, NA, NA, 15,
# AVAL missing cannot grade
"Hypermagnesemia", NA, 0, 0.8, "mmol/L", NA, 16,
)
input_magni <- expected_magni %>%
select(-ATOXGRH)
## Test 59: CTCAEv4 Hypermagnesemia ----
test_that("derive_var_atoxgr Test 59: CTCAEv4 Hypermagnesemia", {
actual_magni <- derive_var_atoxgr_dir(
input_magni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magni,
compare = actual_magni,
keys = c("TESTNUM")
)
})
## Test 60: CTCAEv5 Hypermagnesemia ----
test_that("derive_var_atoxgr Test 60: CTCAEv5 Hypermagnesemia", {
actual_magni <- derive_var_atoxgr_dir(
input_magni,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magni,
compare = actual_magni,
keys = c("TESTNUM")
)
})
### Hypernatremia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >160 mmol/L
### Grade 3: >155 - 160 mmol/L
### Grade 2: >150 - 155 mmol/L
### Grade 1: >ULN - 150 mmol/L
expected_natri <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 161, 0, 140, "mmol/L", NA, 1,
NA_character_, 161, 0, 140, "mmol/L", NA, 2,
# ANRHI not missing
"Hypernatremia", 161, 0, 140, "mmol/L", "4", 3,
"Hypernatremia", 160, 0, 140, "mmol/L", "3", 4,
"Hypernatremia", 156, 0, 140, "mmol/L", "3", 5,
"Hypernatremia", 155, 0, 140, "mmol/L", "2", 6,
"Hypernatremia", 151, 0, 140, "mmol/L", "2", 7,
"Hypernatremia", 150, 0, 140, "mmol/L", "1", 8,
"Hypernatremia", 141, 0, 140, "mmol/L", "1", 9,
"Hypernatremia", 140, 0, 140, "mmol/L", "0", 10,
# ANRHI missing - can grade 3-4
"Hypernatremia", 161, 0, NA, "mmol/L", "4", 11,
"Hypernatremia", 160, 0, NA, "mmol/L", "3", 12,
"Hypernatremia", 156, 0, NA, "mmol/L", "3", 13,
"Hypernatremia", 155, 0, NA, "mmol/L", "2", 14,
"Hypernatremia", 151, 0, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Hypernatremia", 150, 0, NA, "mmol/L", NA, 16,
"Hypernatremia", 141, 0, NA, "mmol/L", NA, 17,
"Hypernatremia", 140, 0, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Hypernatremia", 140, 0, 140, NA, NA, 19,
# AVAL missing cannot grade
"Hypernatremia", NA, 0, 140, "mmol/L", NA, 20,
)
input_natri <- expected_natri %>%
select(-ATOXGRH)
## Test 61: CTCAEv4 Hypernatremia ----
test_that("derive_var_atoxgr Test 61: CTCAEv4 Hypernatremia", {
actual_natri <- derive_var_atoxgr_dir(
input_natri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natri,
compare = actual_natri,
keys = c("TESTNUM")
)
})
## Test 62: CTCAEv5 Hypernatremia ----
test_that("derive_var_atoxgr Test 62: CTCAEv5 Hypernatremia", {
actual_natri <- derive_var_atoxgr_dir(
input_natri,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natri,
compare = actual_natri,
keys = c("TESTNUM")
)
})
### Hypertriglyceridemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: >11.4 mmol/L
### Grade 3: >5.7 mmol/L - 11.4 mmol/L
### Grade 2: >3.42 mmol/L - 5.7 mmol/L
### Grade 1: 1.71 mmol/L - 3.42 mmol/L
expected_trigi <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 11.5, 0, 2.1, "mmol/L", NA,
NA_character_, 11.5, 0, 2.1, "mmol/L", NA,
"Hypertriglyceridemia", 11.5, 0, 2.1, "mmol/L", "4",
"Hypertriglyceridemia", 11.4, 0, 2.1, "mmol/L", "3",
"Hypertriglyceridemia", 5.8, 0, 2.1, "mmol/L", "3",
"Hypertriglyceridemia", 5.7, 0, 2.1, "mmol/L", "2",
"Hypertriglyceridemia", 3.43, 0, 2.1, "mmol/L", "2",
"Hypertriglyceridemia", 3.42, 0, 2.1, "mmol/L", "1",
"Hypertriglyceridemia", 1.72, 0, 2.1, "mmol/L", "1",
"Hypertriglyceridemia", 1.71, 0, 2.1, "mmol/L", "0",
# Unit missing cannot grade
"Hypertriglyceridemia", 1.71, 0, 2.1, NA, NA,
# AVAL missing cannot grade
"Hypertriglyceridemia", NA, 0, 2.1, "mmol/L", NA,
)
input_trigi <- expected_trigi %>%
select(-ATOXGRH)
## Test 63: CTCAEv4 Hypertriglyceridemia ----
test_that("derive_var_atoxgr Test 63: CTCAEv4 Hypertriglyceridemia", {
actual_trigi <- derive_var_atoxgr_dir(
input_trigi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigi,
compare = actual_trigi,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
## Test 64: CTCAEv5 Hypertriglyceridemia ----
test_that("derive_var_atoxgr Test 64: CTCAEv5 Hypertriglyceridemia", {
actual_trigi <- derive_var_atoxgr_dir(
input_trigi,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigi,
compare = actual_trigi,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
### Hyperuricemia (NCICTCAEv4)
### NCICTCAEv5 only has grade 3
### Grade 4: >0.59 mmol/L;
### Grade 3: >ULN - 10 mg/dL (0.59 mmol/L)
expected_urici <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 591, 0, 200, "umol/L", NA,
NA_character_, 591, 0, 200, "umol/L", NA,
# ANRHI not missing
"Hyperuricemia", 591, 0, 200, "umol/L", "4",
"Hyperuricemia", 590, 0, 200, "umol/L", "3",
"Hyperuricemia", 201, 0, 200, "umol/L", "3",
"Hyperuricemia", 200, 0, 200, "umol/L", "0",
# ANRHI missing - can grade 4
"Hyperuricemia", 591, 0, NA, "umol/L", "4",
# ANRHI missing - can NOT grade 0 or 3
"Hyperuricemia", 590, 0, NA, "umol/L", NA,
"Hyperuricemia", 201, 0, NA, "umol/L", NA,
"Hyperuricemia", 200, 0, NA, "umol/L", NA,
# Unit missing cannot grade
"Hyperuricemia", 200, 0, 200, NA, "0",
# AVAL missing cannot grade
"Hyperuricemia", NA, 0, 200, "umol/L", NA,
)
input_urici <- expected_urici %>%
select(-ATOXGRH)
### Hyperuricemia (NCICTCAEv5)
### NCICTCAEv5 only has grade 3
### Grade 3: >ULN
## Test 65: CTCAEv5 Hyperuricemia ----
test_that("derive_var_atoxgr Test 65: CTCAEv5 Hyperuricemia", {
expected_urici <- expected_urici %>%
filter(is.na(ATOXGRH) | ATOXGRH != "4")
input_urici <- expected_urici %>%
select(-ATOXGRH)
actual_urici <- derive_var_atoxgr_dir(
input_urici,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici,
compare = actual_urici,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
# If unit missing then grade CANNOT be calculated as needed for grade 4
## Test 66: CTCAEv4 Hyperuricemia ----
test_that("derive_var_atoxgr Test 66: CTCAEv4 Hyperuricemia", {
expected_urici <- expected_urici %>%
mutate(ATOXGRH = if_else(is.na(AVALU), NA_character_, ATOXGRH))
input_urici <- expected_urici %>%
select(-ATOXGRH)
actual_urici <- derive_var_atoxgr_dir(
input_urici,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici,
compare = actual_urici,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Hypoalbuminemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 3: <20 g/L
### Grade 2: <30 - 20 g/L
### Grade 1: <LLN - 30 g/L
expected_albd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 19, 40, 100, "G/L", NA,
NA_character_, 19, 40, 100, "G/L", NA,
# ANRLO not missing
"Hypoalbuminemia", 19, 40, 100, "G/L", "3",
"Hypoalbuminemia", 20, 40, 100, "G/L", "2",
"Hypoalbuminemia", 29, 40, 100, "G/L", "2",
"Hypoalbuminemia", 30, 40, 100, "G/L", "1",
"Hypoalbuminemia", 39, 40, 100, "G/L", "1",
"Hypoalbuminemia", 40, 40, 100, "G/L", "0",
"Hypoalbuminemia", 40, 40, NA, "G/L", "0",
# ANRLO missing - can grade 2-3
"Hypoalbuminemia", 19, NA, 100, "G/L", "3",
"Hypoalbuminemia", 20, NA, 100, "G/L", "2",
"Hypoalbuminemia", 29, NA, 100, "G/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypoalbuminemia", 30, NA, 100, "G/L", NA,
"Hypoalbuminemia", 39, NA, 100, "G/L", NA,
"Hypoalbuminemia", 40, NA, 100, "G/L", NA,
# Unit missing cannot grade
"Hypoalbuminemia", 40, 40, 100, NA, NA,
# AVAL missing cannot grade
"Hypoalbuminemia", NA, 40, 100, "G/L", NA,
)
input_albd <- expected_albd %>%
select(-ATOXGRL)
## Test 67: CTCAEv4 Hypoalbuminemia ----
test_that("derive_var_atoxgr Test 67: CTCAEv4 Hypoalbuminemia", {
actual_albd <- derive_var_atoxgr_dir(
input_albd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albd,
compare = actual_albd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 68: CTCAEv5 Hypoalbuminemia ----
test_that("derive_var_atoxgr Test 68: CTCAEv5 Hypoalbuminemia", {
actual_albd <- derive_var_atoxgr_dir(
input_albd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albd,
compare = actual_albd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypocalcemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.5 mmol/L
### Grade 3: <1.75 - 1.5 mmol/L
### Grade 2: <2.0 - 1.75 mmol/L
### Grade 1: <LLN - 2.0 mmol/L
expected_calcd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 1.4, 4, 100, "mmol/L", NA,
NA_character_, 1.4, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypocalcemia", 1.4, 4, 100, "mmol/L", "4",
"Hypocalcemia", 1.5, 4, 100, "mmol/L", "3",
"Hypocalcemia", 1.74, 4, 100, "mmol/L", "3",
"Hypocalcemia", 1.75, 4, 100, "mmol/L", "2",
"Hypocalcemia", 1.9, 4, 100, "mmol/L", "2",
"Hypocalcemia", 2, 4, 100, "mmol/L", "1",
"Hypocalcemia", 3, 4, 100, "mmol/L", "1",
"Hypocalcemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypocalcemia", 1.4, 4, NA, "mmol/L", "4",
"Hypocalcemia", 1.5, 4, NA, "mmol/L", "3",
"Hypocalcemia", 1.74, 4, NA, "mmol/L", "3",
"Hypocalcemia", 1.75, 4, NA, "mmol/L", "2",
"Hypocalcemia", 1.9, 4, NA, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypocalcemia", 2, 4, NA, "mmol/L", "1",
"Hypocalcemia", 3, 4, NA, "mmol/L", "1",
"Hypocalcemia", 4, 4, NA, "mmol/L", "0",
# Unit missing cannot grade
"Hypocalcemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypocalcemia", NA, 4, 100, "mmol/L", NA,
)
input_calcd <- expected_calcd %>%
select(-ATOXGRL)
## Test 69: CTCAEv4 Hypocalcemia ----
test_that("derive_var_atoxgr Test 69: CTCAEv4 Hypocalcemia", {
actual_calcd <- derive_var_atoxgr_dir(
input_calcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd,
compare = actual_calcd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 70: CTCAEv5 Hypocalcemia ----
test_that("derive_var_atoxgr Test 70: CTCAEv5 Hypocalcemia", {
actual_calcd <- derive_var_atoxgr_dir(
input_calcd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd,
compare = actual_calcd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypocalcemia (Ionized)
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.8 mmol/L
### Grade 3: <0.9 - 0.8 mmol/L
### Grade 2: <1.0 - 0.9 mmol/L
### Grade 1: <LLN - 1.0 mmol/L
expected_caliond <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.79, 1.3, 100, "mmol/L", NA,
NA_character_, 0.79, 1.3, 100, "mmol/L", NA,
# ANRLO not missing
"Hypocalcemia (Ionized)", 0.79, 1.3, 100, "mmol/L", "4",
"Hypocalcemia (Ionized)", 0.8, 1.3, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.89, 1.3, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.9, 1.3, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 0.99, 1.3, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 1, 1.3, 100, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.29, 1.3, 100, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.3, 1.3, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypocalcemia (Ionized)", 0.79, NA, 100, "mmol/L", "4",
"Hypocalcemia (Ionized)", 0.8, NA, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.89, NA, 100, "mmol/L", "3",
"Hypocalcemia (Ionized)", 0.9, NA, 100, "mmol/L", "2",
"Hypocalcemia (Ionized)", 0.99, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypocalcemia (Ionized)", 1, 1.3, NA, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.29, 1.3, NA, "mmol/L", "1",
"Hypocalcemia (Ionized)", 1.3, 1.3, NA, "mmol/L", "0",
# Unit missing cannot grade
"Hypocalcemia (Ionized)", 1.3, 1.3, 100, NA, NA,
# AVAL missing cannot grade
"Hypocalcemia (Ionized)", NA, 1.3, 100, "mmol/L", NA,
)
input_caliond <- expected_caliond %>%
select(-ATOXGRL)
## Test 71: CTCAEv4 Hypocalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 71: CTCAEv4 Hypocalcemia (Ionized)", {
actual_caliond <- derive_var_atoxgr_dir(
input_caliond,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond,
compare = actual_caliond,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 72: CTCAEv5 Hypocalcemia (Ionized) ----
test_that("derive_var_atoxgr Test 72: CTCAEv5 Hypocalcemia (Ionized)", {
actual_caliond <- derive_var_atoxgr_dir(
input_caliond,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond,
compare = actual_caliond,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypoglycemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <1.7 mmol/L
### Grade 3: <2.2 - 1.7 mmol/L
### Grade 2: <3.0 - 2.2 mmol/L
### Grade 1: <LLN - 3.0 mmol/L
expected_glycd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 1.69, 4, 100, "mmol/L", NA,
NA_character_, 1.69, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypoglycemia", 1.69, 4, 100, "mmol/L", "4",
"Hypoglycemia", 1.7, 4, 100, "mmol/L", "3",
"Hypoglycemia", 2.19, 4, 100, "mmol/L", "3",
"Hypoglycemia", 2.2, 4, 100, "mmol/L", "2",
"Hypoglycemia", 2.9, 4, 100, "mmol/L", "2",
"Hypoglycemia", 3, 4, 100, "mmol/L", "1",
"Hypoglycemia", 3.9, 4, 100, "mmol/L", "1",
"Hypoglycemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypoglycemia", 1.69, NA, 100, "mmol/L", "4",
"Hypoglycemia", 1.7, NA, 100, "mmol/L", "3",
"Hypoglycemia", 2.19, NA, 100, "mmol/L", "3",
"Hypoglycemia", 2.2, NA, 100, "mmol/L", "2",
"Hypoglycemia", 2.9, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypoglycemia", 3, NA, 100, "mmol/L", NA,
"Hypoglycemia", 3.9, NA, 100, "mmol/L", NA,
"Hypoglycemia", 4, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypoglycemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypoglycemia", NA, 4, 100, "mmol/L", NA,
)
input_glycd <- expected_glycd %>%
select(-ATOXGRL)
## Test 73: CTCAEv4 Hypoglycemia ----
test_that("derive_var_atoxgr Test 73: CTCAEv4 Hypoglycemia", {
actual_glycd <- derive_var_atoxgr_dir(
input_glycd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycd,
compare = actual_glycd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 74: CTCAEv5 Hypoglycemia ----
test_that("derive_var_atoxgr Test 74: CTCAEv5 Hypoglycemia", {
actual_glycd <- derive_var_atoxgr_dir(
input_glycd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glycd,
compare = actual_glycd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypokalemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <2.5 mmol/L
### Grade 3: <3.0 - 2.5 mmol/L
### Grade 2: <LLN - 3.0 mmol/L
expected_kaled <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 2.49, 4, 100, "mmol/L", NA,
NA_character_, 2.49, 4, 100, "mmol/L", NA,
# ANRLO not missing
"Hypokalemia", 2.49, 4, 100, "mmol/L", "4",
"Hypokalemia", 2.5, 4, 100, "mmol/L", "3",
"Hypokalemia", 2.9, 4, 100, "mmol/L", "3",
"Hypokalemia", 3, 4, 100, "mmol/L", "2",
"Hypokalemia", 3.9, 4, 100, "mmol/L", "2",
"Hypokalemia", 4, 4, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hypokalemia", 2.49, NA, 100, "mmol/L", "4",
"Hypokalemia", 2.5, NA, 100, "mmol/L", "3",
"Hypokalemia", 2.9, NA, 100, "mmol/L", "3",
# ANRLO missing - can NOT grade 0 or 2
"Hypokalemia", 3, NA, 100, "mmol/L", NA,
"Hypokalemia", 3.9, NA, 100, "mmol/L", NA,
"Hypokalemia", 4, NA, NA, "mmol/L", NA,
# Unit missing cannot grade
"Hypokalemia", 4, 4, 100, NA, NA,
# AVAL missing cannot grade
"Hypokalemia", NA, 4, 100, "mmol/L", NA,
)
input_kaled <- expected_kaled %>%
select(-ATOXGRL)
## Test 75: CTCAEv4 Hypokalemia ----
test_that("derive_var_atoxgr Test 75: CTCAEv4 Hypokalemia", {
actual_kaled <- derive_var_atoxgr_dir(
input_kaled,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kaled,
compare = actual_kaled,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 76: CTCAEv5 Hypokalemia ----
test_that("derive_var_atoxgr Test 76: CTCAEv5 Hypokalemia", {
actual_kaled <- derive_var_atoxgr_dir(
input_kaled,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_kaled,
compare = actual_kaled,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypomagnesemia
### NCICTCAEv4 and NCICTCAEv5 criteria is the same
### Grade 4: <0.3 mmol/L
### Grade 3: <0.4 - 0.3 mmol/L
### Grade 2: <0.5 - 0.4 mmol/L
### Grade 1: <LLN - 0.5 mmol/L
expected_magnd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.29, 1, 100, "mmol/L", NA,
NA_character_, 0.29, 1, 100, "mmol/L", NA,
# ANRLO not missing
"Hypomagnesemia", 0.29, 1, 100, "mmol/L", "4",
"Hypomagnesemia", 0.3, 1, 100, "mmol/L", "3",
"Hypomagnesemia", 0.39, 1, 100, "mmol/L", "3",
"Hypomagnesemia", 0.4, 1, 100, "mmol/L", "2",
"Hypomagnesemia", 0.49, 1, 100, "mmol/L", "2",
"Hypomagnesemia", 0.5, 1, 100, "mmol/L", "1",
"Hypomagnesemia", 0.9, 1, 100, "mmol/L", "1",
"Hypomagnesemia", 1, 1, 100, "mmol/L", "0",
# ANRLO missing - can grade 2-4
"Hypomagnesemia", 0.29, NA, 100, "mmol/L", "4",
"Hypomagnesemia", 0.3, NA, 100, "mmol/L", "3",
"Hypomagnesemia", 0.39, NA, 100, "mmol/L", "3",
"Hypomagnesemia", 0.4, NA, 100, "mmol/L", "2",
"Hypomagnesemia", 0.49, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypomagnesemia", 0.5, NA, 100, "mmol/L", NA,
"Hypomagnesemia", 0.9, NA, 100, "mmol/L", NA,
"Hypomagnesemia", 1, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypomagnesemia", 1, 1, 100, NA, NA,
# AVAL missing cannot grade
"Hypomagnesemia", NA, 1, 100, "mmol/L", NA,
)
input_magnd <- expected_magnd %>%
select(-ATOXGRL)
## Test 77: CTCAEv4 Hypomagnesemia ----
test_that("derive_var_atoxgr Test 77: CTCAEv4 Hypomagnesemia", {
actual_magnd <- derive_var_atoxgr_dir(
input_magnd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magnd,
compare = actual_magnd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 78: CTCAEv5 Hypomagnesemia ----
test_that("derive_var_atoxgr Test 78: CTCAEv5 Hypomagnesemia", {
actual_magnd <- derive_var_atoxgr_dir(
input_magnd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magnd,
compare = actual_magnd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hyponatremia (NCICTCAEv4)
### NCICTCAEv4 and NCICTCAEv5 essentially the same (slightly different text)
### Grade 4: <120 mmol/L
### Grade 3: <130 - 120 mmol/L
### Grade 1: <LLN - 130 mmol/L
expected_natrd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 119, 140, 100, "mmol/L", NA,
NA_character_, 119, 140, 100, "mmol/L", NA,
# ANRLO not missing
"Hyponatremia", 119, 140, 100, "mmol/L", "4",
"Hyponatremia", 120, 140, 100, "mmol/L", "3",
"Hyponatremia", 129, 140, 100, "mmol/L", "3",
"Hyponatremia", 130, 140, 100, "mmol/L", "1",
"Hyponatremia", 139, 140, 100, "mmol/L", "1",
"Hyponatremia", 140, 140, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hyponatremia", 119, NA, 100, "mmol/L", "4",
"Hyponatremia", 120, NA, 100, "mmol/L", "3",
"Hyponatremia", 129, NA, 100, "mmol/L", "3",
# ANRLO missing - can NOT grade 0 or 1
"Hyponatremia", 130, NA, 100, "mmol/L", NA,
"Hyponatremia", 139, NA, 100, "mmol/L", NA,
"Hyponatremia", 140, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hyponatremia", 140, 140, 100, NA, NA,
# AVAL missing cannot grade
"Hyponatremia", NA, 140, 100, "mmol/L", NA,
)
input_natrd <- expected_natrd %>%
select(-ATOXGRL)
## Test 79: CTCAEv4 Hyponatremia ----
test_that("derive_var_atoxgr Test 79: CTCAEv4 Hyponatremia", {
actual_natrd <- derive_var_atoxgr_dir(
input_natrd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natrd,
compare = actual_natrd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
## Test 80: CTCAEv5 Hyponatremia ----
test_that("derive_var_atoxgr Test 80: CTCAEv5 Hyponatremia", {
actual_natrd <- derive_var_atoxgr_dir(
input_natrd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv5,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_natrd,
compare = actual_natrd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
### Hypophosphatemia
### Only in NCICTCAEv4 (not NCICTCAEv5)
### Grade 4: <0.3 mmol/L
### Grade 3: <0.6 - 0.3 mmol/L
### Grade 2: <0.8 - 0.6 mmol/L
### Grade 1: <LLN - 0.8 mmol/L
## Test 81: CTCAEv4 Hypophosphatemia ----
test_that("derive_var_atoxgr Test 81: CTCAEv4 Hypophosphatemia", {
expected_phosd <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL,
"Not a term", 0.29, 1, 100, "mmol/L", NA,
NA_character_, 0.29, 1, 100, "mmol/L", NA,
# ANRLO not missing
"Hypophosphatemia", 0.29, 1, 100, "mmol/L", "4",
"Hypophosphatemia", 0.3, 1, 100, "mmol/L", "3",
"Hypophosphatemia", 0.59, 1, 100, "mmol/L", "3",
"Hypophosphatemia", 0.6, 1, 100, "mmol/L", "2",
"Hypophosphatemia", 0.79, 1, 100, "mmol/L", "2",
"Hypophosphatemia", 0.8, 1, 100, "mmol/L", "1",
"Hypophosphatemia", 0.9, 1, 100, "mmol/L", "1",
"Hypophosphatemia", 1, 1, 100, "mmol/L", "0",
# ANRLO missing - can grade 3-4
"Hypophosphatemia", 0.29, NA, 100, "mmol/L", "4",
"Hypophosphatemia", 0.3, NA, 100, "mmol/L", "3",
"Hypophosphatemia", 0.59, NA, 100, "mmol/L", "3",
"Hypophosphatemia", 0.6, NA, 100, "mmol/L", "2",
"Hypophosphatemia", 0.79, NA, 100, "mmol/L", "2",
# ANRLO missing - can NOT grade 0 or 1
"Hypophosphatemia", 0.8, NA, 100, "mmol/L", NA,
"Hypophosphatemia", 0.9, NA, 100, "mmol/L", NA,
"Hypophosphatemia", 1, NA, 100, "mmol/L", NA,
# Unit missing cannot grade
"Hypophosphatemia", 1, 1, 100, NA, NA,
# AVAL missing cannot grade
"Hypophosphatemia", NA, 1, 100, "mmol/L", NA,
)
input_phosd <- expected_phosd %>%
select(-ATOXGRL)
actual_phosd <- derive_var_atoxgr_dir(
input_phosd,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_ctcv4,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_phosd,
compare = actual_phosd,
keys = c("ATOXDSCL", "AVAL", "ANRLO", "ANRHI", "AVALU")
)
})
# DAIDS grading----
### Acidosis
### Grade 4: pH < 7.3 with lifethreatening consequences
### Grade 3: pH < 7.3 without lifethreatening consequences
### Grade 2: pH ≥ 7.3 to < LLN
## Test 82: DAIDS Acidosis ----
test_that("derive_var_atoxgr Test 82: DAIDS Acidosis", {
expected_acido_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~ATOXGRL, ~TESTNUM,
"Not a term", 7.3, 7.35, 7.4, NA, 1,
NA_character_, 7.3, 7.35, 7.4, NA, 2,
# ANRLO not missing
"Acidosis", 7.29, 7.35, 7.4, "4", 3,
"Acidosis", 7.3, 7.35, 7.4, "2", 4,
"Acidosis", 7.34, 7.35, 7.4, "2", 5,
"Acidosis", 7.35, 7.35, 7.4, "0", 6,
"Acidosis", 7.36, 7.35, 7.4, "0", 7,
# ANRLO missing - can grade 4
"Acidosis", 7.29, NA, 7.4, "4", 8,
# ANRLO missing - can NOT grade 0 or 2
"Acidosis", 7.3, NA, 7.4, NA, 9,
"Acidosis", 7.34, NA, 7.4, NA, 10,
"Acidosis", 7.35, NA, 7.4, NA, 11,
"Acidosis", 7.36, NA, 7.4, NA, 12,
# AVAL missing cannot grade
"Acidosis", NA, 1.1, 1.4, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_acido_daids <- expected_acido_daids %>%
select(-ATOXGRL)
actual_acido_daids <- derive_var_atoxgr_dir(
input_acido_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_acido_daids,
compare = actual_acido_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Albumin, Low
### Grade 3: < 20
### Grade 2: >= 20 to < 30
### Grade 1: 30 to < LLN
## Test 83: DAIDS Albumin, Low ----
test_that("derive_var_atoxgr Test 83: DAIDS Albumin, Low", {
expected_albl_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 35, 40, "g/L", NA, 1,
NA_character_, 35, 40, "g/L", NA, 2,
# ANRLO not missing
"Albumin, Low", 19, 40, "g/L", "3", 3,
"Albumin, Low", 20, 40, "g/L", "2", 4,
"Albumin, Low", 29, 40, "g/L", "2", 5,
"Albumin, Low", 30, 40, "g/L", "1", 6,
"Albumin, Low", 39, 40, "g/L", "1", 7,
"Albumin, Low", 40, 40, "g/L", "0", 8,
# ANRLO missing - can grade 2 and 3
"Albumin, Low", 19, NA, "g/L", "3", 9,
"Albumin, Low", 20, NA, "g/L", "2", 10,
"Albumin, Low", 29, NA, "g/L", "2", 11,
# ANRLO missing - can NOT grade 0 or 1
"Albumin, Low", 30, NA, "g/L", NA, 12,
"Albumin, Low", 39, NA, "g/L", NA, 13,
"Albumin, Low", 40, NA, "g/L", NA, 14,
# AVALU missing cannot grade
"Albumin, Low", 40, 40, NA, NA, 15,
# AVAL missing cannot grade
"Albumin, Low", NA, 40, "g/L", NA, 16,
)
input_albl_daids <- expected_albl_daids %>%
select(-ATOXGRL)
actual_albl_daids <- derive_var_atoxgr_dir(
input_albl_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_albl_daids,
compare = actual_albl_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Alkaline Phosphatase, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 84: DAIDS Alkaline Phosphatase, High ----
test_that("derive_var_atoxgr Test 84: DAIDS Alkaline Phosphatase, High", {
expected_alkphi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 40, NA, 1,
NA_character_, 30, 40, NA, 2,
# ANRHI not missing
"Alkaline Phosphatase, High", 401, 40, "4", 3,
"Alkaline Phosphatase, High", 400, 40, "4", 4,
"Alkaline Phosphatase, High", 399, 40, "3", 5,
"Alkaline Phosphatase, High", 200, 40, "3", 6,
"Alkaline Phosphatase, High", 199, 40, "2", 7,
"Alkaline Phosphatase, High", 100, 40, "2", 8,
"Alkaline Phosphatase, High", 99, 40, "1", 9,
"Alkaline Phosphatase, High", 51, 40, "1", 10,
"Alkaline Phosphatase, High", 50, 40, "1", 11,
"Alkaline Phosphatase, High", 49, 40, "0", 12,
# ANRHI missing cannot grade
"Alkaline Phosphatase, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"Alkaline Phosphatase, High", NA, 40, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_alkphi_daids <- expected_alkphi_daids %>%
select(-ATOXGRH)
actual_alkphi_daids <- derive_var_atoxgr_dir(
input_alkphi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkphi_daids,
compare = actual_alkphi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Alkalosis
### Grade 4: pH > 7.5 with lifethreatening consequences
### Grade 3: pH > 7.5 without lifethreatening consequences
### Grade 2: pH > ULN to ≤ 7.5
## Test 85: DAIDS Alkalosis ----
test_that("derive_var_atoxgr Test 85: DAIDS Alkalosis", {
expected_alkalo_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 7.3, 7.35, 7.4, NA, 1,
NA_character_, 7.3, 7.35, 7.4, NA, 2,
# ANRHI not missing
"Alkalosis", 7.51, 7.35, 7.4, "4", 3,
"Alkalosis", 7.5, 7.35, 7.4, "2", 4,
"Alkalosis", 7.41, 7.35, 7.4, "2", 5,
"Alkalosis", 7.4, 7.35, 7.4, "0", 6,
"Alkalosis", 7.39, 7.35, 7.4, "0", 7,
# ANRHI missing - can grade 4
"Alkalosis", 7.51, 7.35, NA, "4", 8,
# ANRHI missing - can NOT grade 0 or 2
"Alkalosis", 7.5, 7.35, NA, NA, 9,
"Alkalosis", 7.41, 7.35, NA, NA, 10,
"Alkalosis", 7.4, 7.35, NA, NA, 11,
"Alkalosis", 7.39, 7.35, NA, NA, 12,
# AVAL missing cannot grade
"Alkalosis", NA, 1.1, NA, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_alkalo_daids <- expected_alkalo_daids %>%
select(-ATOXGRH)
actual_alkalo_daids <- derive_var_atoxgr_dir(
input_alkalo_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alkalo_daids,
compare = actual_alkalo_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### ALT, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 86: DAIDS ALT, High ----
test_that("derive_var_atoxgr Test 86: DAIDS ALT, High", {
expected_alti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"ALT, High", 601, 60, "4", 3,
"ALT, High", 600, 60, "4", 4,
"ALT, High", 599, 60, "3", 5,
"ALT, High", 300, 60, "3", 6,
"ALT, High", 299, 60, "2", 7,
"ALT, High", 150, 60, "2", 8,
"ALT, High", 149, 60, "1", 9,
"ALT, High", 76, 60, "1", 10,
"ALT, High", 75, 60, "1", 11,
"ALT, High", 74, 60, "0", 12,
# ANRHI missing cannot grade
"ALT, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"ALT, High", NA, 60, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_alti_daids <- expected_alti_daids %>%
select(-ATOXGRH)
actual_alti_daids <- derive_var_atoxgr_dir(
input_alti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_alti_daids,
compare = actual_alti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Amylase, High
### Grade 4: >= 5.0 x ULN
### Grade 3: 3.0 to < 5.0 x ULN
### Grade 2: 1.5 to < 3.0 x ULN
### Grade 1: 1.1 to < 1.5 x ULN
## Test 87: DAIDS Amylase, High ----
test_that("derive_var_atoxgr Test 87: DAIDS Amylase, High", {
expected_amyli_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"Amylase, High", 301, 60, "4", 3,
"Amylase, High", 300, 60, "4", 4,
"Amylase, High", 299, 60, "3", 5,
"Amylase, High", 180, 60, "3", 6,
"Amylase, High", 179, 60, "2", 7,
"Amylase, High", 90, 60, "2", 8,
"Amylase, High", 89, 60, "1", 9,
"Amylase, High", 66, 60, "1", 10,
"Amylase, High", 65, 60, "0", 11,
# ANRHI missing cannot grade
"Amylase, High", 65, NA, NA, 12,
# AVAL missing cannot grade
"Amylase, High", NA, 60, NA, 13,
) %>%
mutate(AVALU = NA_character_)
input_amyli_daids <- expected_amyli_daids %>%
select(-ATOXGRH)
actual_amyli_daids <- derive_var_atoxgr_dir(
input_amyli_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_amyli_daids,
compare = actual_amyli_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### AST, High
### Grade 4: >= 10.0 x ULN
### Grade 3: 5.0 to < 10.0 x ULN
### Grade 2: 2.5 to < 5.0 x ULN
### Grade 1: 1.25 to < 2.5 x ULN
## Test 88: DAIDS AST, High ----
test_that("derive_var_atoxgr Test 88: DAIDS AST, High", {
expected_asti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 30, 60, NA, 1,
NA_character_, 30, 60, NA, 2,
# ANRHI not missing
"AST, High", 601, 60, "4", 3,
"AST, High", 600, 60, "4", 4,
"AST, High", 599, 60, "3", 5,
"AST, High", 300, 60, "3", 6,
"AST, High", 299, 60, "2", 7,
"AST, High", 150, 60, "2", 8,
"AST, High", 149, 60, "1", 9,
"AST, High", 76, 60, "1", 10,
"AST, High", 75, 60, "1", 11,
"AST, High", 74, 60, "0", 12,
# ANRHI missing cannot grade
"AST, High", 49, NA, NA, 13,
# AVAL missing cannot grade
"AST, High", NA, 60, NA, 14,
) %>%
mutate(AVALU = NA_character_)
input_asti_daids <- expected_asti_daids %>%
select(-ATOXGRH)
actual_asti_daids <- derive_var_atoxgr_dir(
input_asti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_asti_daids,
compare = actual_asti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Bicarbonate, Low
### Grade 4: < 8.0 mmol/L
### Grade 3: 8.0 -< 11.0 mmol/L
### Grade 2: 11.0 -< 16.0 mmol/L
### Grade 1: 16.0 mmol/L -< LLN
## Test 89: DAIDS Bicarbonate, Low ----
test_that("derive_var_atoxgr Test 89: DAIDS Bicarbonate, Low", {
expected_bicarbd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 22, 20, "mmol/L", NA, 1,
NA_character_, 22, 20, "mmol/L", NA, 2,
# ANRLO not missing
"Bicarbonate, Low", 7.9, 20, "mmol/L", "4", 3,
"Bicarbonate, Low", 8, 20, "mmol/L", "3", 4,
"Bicarbonate, Low", 10.9, 20, "mmol/L", "3", 5,
"Bicarbonate, Low", 11, 20, "mmol/L", "2", 6,
"Bicarbonate, Low", 15.9, 20, "mmol/L", "2", 7,
"Bicarbonate, Low", 16, 20, "mmol/L", "1", 8,
"Bicarbonate, Low", 19, 20, "mmol/L", "1", 9,
"Bicarbonate, Low", 20, 20, "mmol/L", "0", 10,
# ANRLO missing - can grade 2-4
"Bicarbonate, Low", 7.9, NA, "mmol/L", "4", 11,
"Bicarbonate, Low", 8, NA, "mmol/L", "3", 12,
"Bicarbonate, Low", 10.9, NA, "mmol/L", "3", 13,
"Bicarbonate, Low", 11, NA, "mmol/L", "2", 14,
"Bicarbonate, Low", 15.9, NA, "mmol/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Bicarbonate, Low", 16, NA, "mmol/L", NA, 16,
"Bicarbonate, Low", 19, NA, "mmol/L", NA, 17,
"Bicarbonate, Low", 20, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Bicarbonate, Low", 20, 20, NA, NA, 19,
# AVAL missing cannot grade
"Bicarbonate, Low", NA, 20, "mmol/L", NA, 20,
)
input_bicarbd_daids <- expected_bicarbd_daids %>%
select(-ATOXGRL)
actual_bicarbd_daids <- derive_var_atoxgr_dir(
input_bicarbd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_bicarbd_daids,
compare = actual_bicarbd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Direct Bilirubin, High
### 17.1 used as conversion from "mg/dL" to "umol/L"
### > 28 days of age
### Grade 4: > ULN
expected_dbiligt28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7, 8, "umol/L", NA, 1,
NA_character_, 7, 8, "umol/L", NA, 2,
# ANRHI not missing
"Direct Bilirubin, High", 8.1, 8, "umol/L", "4", 3,
"Direct Bilirubin, High", 8, 8, "umol/L", "0", 4,
"Direct Bilirubin, High", 7.9, 8, "umol/L", "0", 5,
# ANRHI missing cannot still grade 0 or 4
"Direct Bilirubin, High", 8.1, NA, "umol/L", NA, 6,
"Direct Bilirubin, High", 8, NA, "umol/L", NA, 7,
"Direct Bilirubin, High", 7.9, NA, "umol/L", NA, 8,
# AVAL missing cannot grade
"Direct Bilirubin, High", NA, 8, "umol/L", NA, 9,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-30")
)
### <= 28 days of age
### Grade 4: > 2 mg/dL (> 34.2 umol/L)
### Grade 3: > 1.5 to <= 2 mg/dL (> 25.65 to <= 34.2 umol/L)
### Grade 2: > 1 to <= 1.5 mg/dL (> 17.1 to <= 25.65 umol/L)
### Grade 1: ULN to <= 1 mg/dL (ULN to <= 17.1 umol/L)
expected_dbilile28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 7, 8, "umol/L", NA, 10,
NA_character_, 7, 8, "umol/L", NA, 11,
# ANRHI not missing
"Direct Bilirubin, High", 34.3, 8, "umol/L", "4", 12,
"Direct Bilirubin, High", 34.2, 8, "umol/L", "3", 13,
"Direct Bilirubin, High", 25.66, 8, "umol/L", "3", 14,
"Direct Bilirubin, High", 25.65, 8, "umol/L", "2", 15,
"Direct Bilirubin, High", 17.19, 8, "umol/L", "2", 16,
"Direct Bilirubin, High", 17.1, 8, "umol/L", "1", 17,
"Direct Bilirubin, High", 8, 8, "umol/L", "1", 18,
"Direct Bilirubin, High", 7.9, 8, "umol/L", "0", 19,
# ANRHI missing can still grade 2 - 4
"Direct Bilirubin, High", 34.3, NA, "umol/L", "4", 20,
"Direct Bilirubin, High", 34.2, NA, "umol/L", "3", 21,
"Direct Bilirubin, High", 25.66, NA, "umol/L", "3", 22,
"Direct Bilirubin, High", 25.65, NA, "umol/L", "2", 23,
"Direct Bilirubin, High", 17.19, NA, "umol/L", "2", 24,
# ANRHI missing cannot still grade 0 - 1
"Direct Bilirubin, High", 17.1, NA, "umol/L", NA, 25,
"Direct Bilirubin, High", 8, NA, "umol/L", NA, 26,
"Direct Bilirubin, High", 7.9, NA, "umol/L", NA, 27,
# AVAL missing cannot grade
"Direct Bilirubin, High", NA, 8, "umol/L", NA, 28,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-29")
)
### add subjects with missing LBDT or BRTHDT
expected_dbilinoage_daids <- expected_dbilile28d_daids %>%
filter(TESTNUM %in% c(18, 19)) %>%
mutate(
LBDT = if_else(TESTNUM == 18, NA, LBDT),
BRTHDT = if_else(TESTNUM == 19, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 18, 29, 30)
)
### put all data together
expected_dbili_daids <- expected_dbilinoage_daids %>%
bind_rows(
expected_dbilile28d_daids,
expected_dbiligt28d_daids
)
## Test 90: DAIDS Direct Bilirubin, High ----
test_that("derive_var_atoxgr Test 90: DAIDS Direct Bilirubin, High", {
input_dbili_daids <- expected_dbili_daids %>%
select(-ATOXGRH)
actual_dbili_daids <- derive_var_atoxgr_dir(
input_dbili_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_dbili_daids,
compare = actual_dbili_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Total Bilirubin, High
### > 28 days of age
### Grade 4: >= 5.0 x ULN
### Grade 3: 2.6 to < 5.0 x ULN
### Grade 2: 1.6 to < 2.6 x ULN
### Grade 1: 1.1 to < 1.6 x ULN
expected_tbiligt28d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9, 10, "umol/L", NA, 1,
NA_character_, 9, 10, "umol/L", NA, 2,
# ANRHI not missing
"Total Bilirubin, High", 50, 10, "umol/L", "4", 3,
"Total Bilirubin, High", 49, 10, "umol/L", "3", 4,
"Total Bilirubin, High", 26, 10, "umol/L", "3", 5,
"Total Bilirubin, High", 25.9, 10, "umol/L", "2", 6,
"Total Bilirubin, High", 16, 10, "umol/L", "2", 7,
"Total Bilirubin, High", 15.9, 10, "umol/L", "1", 8,
"Total Bilirubin, High", 11, 10, "umol/L", "1", 9,
"Total Bilirubin, High", 10.9, 10, "umol/L", "0", 10,
# Unit missing can grade - grade based on comparison of AVAL with ANRHI
"Total Bilirubin, High", 10.9, 10, NA, "0", 11,
# ANRHI missing - cannot grade
"Total Bilirubin, High", 10.9, NA, "umol/L", NA, 12,
# AVAL missing cannot grade
"Total Bilirubin, High", NA, 10, "umol/L", NA, 13,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-30")
)
### make Age <= 28 all results NA for ATOXGRH
expected_tbilile28d_daids <- expected_tbiligt28d_daids %>%
mutate(
LBDT = lubridate::ymd("2023-01-29"),
ATOXGRH = NA_character_,
TESTNUM = TESTNUM + 13
)
### make Age missing results NA for ATOXGRH
expected_tbilinoage_daids <- expected_tbiligt28d_daids %>%
filter(TESTNUM %in% c(10, 11)) %>%
mutate(
LBDT = if_else(TESTNUM == 10, NA, LBDT),
BRTHDT = if_else(TESTNUM == 11, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 10, 27, 28)
)
expected_tbili_daids <- expected_tbilinoage_daids %>%
bind_rows(
expected_tbiligt28d_daids,
expected_tbilile28d_daids
)
## Test 91: DAIDS Total Bilirubin, High ----
test_that("derive_var_atoxgr Test 91: DAIDS Total Bilirubin, High", {
input_tbili_daids <- expected_tbili_daids %>%
select(-ATOXGRH)
actual_tbili_daids <- derive_var_atoxgr_dir(
input_tbili_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_tbili_daids,
compare = actual_tbili_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Calcium, High
### >= 7 days of age
### Grade 4: >= 3.38 mmol/L
### Grade 3: 3.13 -< 3.38 mmol/L
### Grade 2: 2.88 -< 3.13 mmol/L
### Grade 1: 2.65 -< 2.88 mmol/L
expected_calcige7d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 1,
NA_character_, 3.5, "mmol/L", NA, 2,
# ANRHI not missing
"Calcium, High", 3.38, "mmol/L", "4", 3,
"Calcium, High", 3.37, "mmol/L", "3", 4,
"Calcium, High", 3.13, "mmol/L", "3", 5,
"Calcium, High", 3.12, "mmol/L", "2", 6,
"Calcium, High", 2.88, "mmol/L", "2", 7,
"Calcium, High", 2.87, "mmol/L", "1", 8,
"Calcium, High", 2.65, "mmol/L", "1", 9,
"Calcium, High", 2.64, "mmol/L", "0", 10,
# Unit missing cannot grade
"Calcium, High", 2.5, NA, NA, 11,
# AVAL missing cannot grade
"Calcium, High", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 7 days of age
### Grade 4: >= 3.38 mmol/L
### Grade 3: 3.23 -< 3.38 mmol/L
### Grade 2: 3.1 -< 3.23 mmol/L
### Grade 1: 2.88 -< 3.1 mmol/L
expected_calcilt7d_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 13,
NA_character_, 3.5, "mmol/L", NA, 14,
# ANRHI not missing
"Calcium, High", 3.38, "mmol/L", "4", 15,
"Calcium, High", 3.37, "mmol/L", "3", 16,
"Calcium, High", 3.23, "mmol/L", "3", 17,
"Calcium, High", 3.22, "mmol/L", "2", 18,
"Calcium, High", 3.1, "mmol/L", "2", 19,
"Calcium, High", 3.09, "mmol/L", "1", 20,
"Calcium, High", 2.88, "mmol/L", "1", 21,
"Calcium, High", 2.87, "mmol/L", "0", 22,
# Unit missing cannot grade
"Calcium, High", 3.5, NA, NA, 23,
# AVAL missing cannot grade
"Calcium, High", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_calcinoage_daids <- expected_calcige7d_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_calci_daids <- expected_calcinoage_daids %>%
bind_rows(
expected_calcige7d_daids,
expected_calcilt7d_daids
)
## Test 92: DAIDS Calcium, High ----
test_that("derive_var_atoxgr Test 92: DAIDS Calcium, High", {
input_calci_daids <- expected_calci_daids %>%
select(-ATOXGRH)
actual_calci_daids <- derive_var_atoxgr_dir(
input_calci_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calci_daids,
compare = actual_calci_daids,
keys = c("TESTNUM")
)
})
### Calcium (Ionized), High
### Grade 4: >= 1.8 mmol/L
### Grade 3: 1.6 -< 1.8 mmol/L
### Grade 2: 1.5 -< 1.6 mmol/L
### Grade 1: >ULN -< 1.5 mmol/L
## Test 93: DAIDS Calcium (Ionized), High ----
test_that("derive_var_atoxgr Test 93: DAIDS Calcium (Ionized), High", {
expected_calioni_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.8, 1.1, 1.4, "mmol/L", NA, 1,
NA_character_, 1.79, 1.1, 1.4, "mmol/L", NA, 2,
# ANRHI not missing
"Calcium (Ionized), High", 1.8, 1.1, 1.4, "mmol/L", "4", 3,
"Calcium (Ionized), High", 1.79, 1.1, 1.4, "mmol/L", "3", 4,
"Calcium (Ionized), High", 1.6, 1.1, 1.4, "mmol/L", "3", 5,
"Calcium (Ionized), High", 1.59, 1.1, 1.4, "mmol/L", "2", 6,
"Calcium (Ionized), High", 1.5, 1.1, 1.4, "mmol/L", "2", 7,
"Calcium (Ionized), High", 1.49, 1.1, 1.4, "mmol/L", "1", 8,
"Calcium (Ionized), High", 1.41, 1.1, 1.4, "mmol/L", "1", 9,
"Calcium (Ionized), High", 1.4, 1.1, 1.4, "mmol/L", "0", 10,
# ANRHI missing - can grade 2-4
"Calcium (Ionized), High", 1.8, 1.1, NA, "mmol/L", "4", 11,
"Calcium (Ionized), High", 1.79, 1.1, NA, "mmol/L", "3", 12,
"Calcium (Ionized), High", 1.6, 1.1, NA, "mmol/L", "3", 13,
"Calcium (Ionized), High", 1.59, 1.1, NA, "mmol/L", "2", 14,
"Calcium (Ionized), High", 1.5, 1.1, NA, "mmol/L", "2", 15,
# ANRHI missing - can NOT grade 0 or 1
"Calcium (Ionized), High", 1.49, 1.1, NA, "mmol/L", NA, 16,
"Calcium (Ionized), High", 1.41, 1.1, NA, "mmol/L", NA, 17,
"Calcium (Ionized), High", 1.4, 1.1, NA, "mmol/L", NA, 18,
# Unit missing cannot grade
"Calcium (Ionized), High", 1.3, 1.1, 1.4, NA, NA, 19,
# AVAL missing cannot grade
"Calcium (Ionized), High", NA, 1.1, 1.4, "mmol/L", NA, 20,
)
input_calioni_daids <- expected_calioni_daids %>%
select(-ATOXGRH)
actual_calioni_daids <- derive_var_atoxgr_dir(
input_calioni_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calioni_daids,
compare = actual_calioni_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Calcium, Low
### >= 7 days of age
### Grade 4: < 1.53 mmol/L
### Grade 3: 1.53 -< 1.75 mmol/L
### Grade 2: 1.75 -< 1.95 mmol/L
### Grade 1: 1.95 -< 2.10 mmol/L
expected_calcdge7d_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2.2, "mmol/L", NA, 1,
NA_character_, 2.2, "mmol/L", NA, 2,
# ANRLO not missing
"Calcium, Low", 1.52, "mmol/L", "4", 3,
"Calcium, Low", 1.53, "mmol/L", "3", 4,
"Calcium, Low", 1.74, "mmol/L", "3", 5,
"Calcium, Low", 1.75, "mmol/L", "2", 6,
"Calcium, Low", 1.94, "mmol/L", "2", 7,
"Calcium, Low", 1.95, "mmol/L", "1", 8,
"Calcium, Low", 2.09, "mmol/L", "1", 9,
"Calcium, Low", 2.1, "mmol/L", "0", 10,
# Unit missing cannot grade
"Calcium, Low", 2.5, NA, NA, 11,
# AVAL missing cannot grade
"Calcium, Low", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 7 days of age
### Grade 4: < 1.38 mmol/L
### Grade 3: 1.38 -< 1.5 mmol/L
### Grade 2: 1.5 -< 1.63 mmol/L
### Grade 1: 1.63 -< 1.88 mmol/L
expected_calcdlt7d_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2.2, "mmol/L", NA, 13,
NA_character_, 2.2, "mmol/L", NA, 14,
# ANRLO not missing
"Calcium, Low", 1.37, "mmol/L", "4", 15,
"Calcium, Low", 1.38, "mmol/L", "3", 16,
"Calcium, Low", 1.49, "mmol/L", "3", 17,
"Calcium, Low", 1.5, "mmol/L", "2", 18,
"Calcium, Low", 1.62, "mmol/L", "2", 19,
"Calcium, Low", 1.63, "mmol/L", "1", 20,
"Calcium, Low", 1.87, "mmol/L", "1", 21,
"Calcium, Low", 1.88, "mmol/L", "0", 22,
# Unit missing cannot grade
"Calcium, Low", 2.2, NA, NA, 23,
# AVAL missing cannot grade
"Calcium, Low", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-01-01"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_calcdnoage_daids <- expected_calcdge7d_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_calcd_daids <- expected_calcdnoage_daids %>%
bind_rows(
expected_calcdge7d_daids,
expected_calcdlt7d_daids
)
## Test 94: DAIDS Calcium, Low ----
test_that("derive_var_atoxgr Test 94: DAIDS Calcium, Low", {
input_calcd_daids <- expected_calcd_daids %>%
select(-ATOXGRL)
actual_calcd_daids <- derive_var_atoxgr_dir(
input_calcd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_calcd_daids,
compare = actual_calcd_daids,
keys = c("TESTNUM")
)
})
### Calcium (Ionized), Low
### Grade 4: <0.8 mmol/L
### Grade 3: 0.8 -< 0.9 mmol/L
### Grade 2: 0.9 -< 1.0 mmol/L
### Grade 1: 1.0 mmol/L -< LLN
## Test 95: DAIDS Calcium (Ionized), Low ----
test_that("derive_var_atoxgr Test 95: DAIDS Calcium (Ionized), Low", {
expected_caliond_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~ANRHI, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 0.79, 1.1, 100, "mmol/L", NA, 1,
NA_character_, 0.79, 1.1, 100, "mmol/L", NA, 2,
# ANRLO not missing
"Calcium (Ionized), Low", 0.79, 1.1, 100, "mmol/L", "4", 3,
"Calcium (Ionized), Low", 0.8, 1.1, 100, "mmol/L", "3", 4,
"Calcium (Ionized), Low", 0.89, 1.1, 100, "mmol/L", "3", 5,
"Calcium (Ionized), Low", 0.9, 1.1, 100, "mmol/L", "2", 6,
"Calcium (Ionized), Low", 0.99, 1.1, 100, "mmol/L", "2", 7,
"Calcium (Ionized), Low", 1, 1.1, 100, "mmol/L", "1", 8,
"Calcium (Ionized), Low", 1.09, 1.1, 100, "mmol/L", "1", 9,
"Calcium (Ionized), Low", 1.1, 1.1, 100, "mmol/L", "0", 10,
# ANRLO missing - can grade 2-4
"Calcium (Ionized), Low", 0.79, NA, 100, "mmol/L", "4", 11,
"Calcium (Ionized), Low", 0.8, NA, 100, "mmol/L", "3", 12,
"Calcium (Ionized), Low", 0.89, NA, 100, "mmol/L", "3", 13,
"Calcium (Ionized), Low", 0.9, NA, 100, "mmol/L", "2", 14,
"Calcium (Ionized), Low", 0.99, NA, 100, "mmol/L", "2", 15,
# ANRLO missing - can NOT grade 0 or 1
"Calcium (Ionized), Low", 1, NA, 100, "mmol/L", NA, 16,
"Calcium (Ionized), Low", 1.09, NA, 100, "mmol/L", NA, 17,
"Calcium (Ionized), Low", 1.1, NA, 100, "mmol/L", NA, 18,
# Unit missing cannot grade
"Calcium (Ionized), Low", 1.1, 1.1, 100, NA, NA, 19,
# AVAL missing cannot grade
"Calcium (Ionized), Low", NA, 1.1, 100, "mmol/L", NA, 20,
)
input_caliond_daids <- expected_caliond_daids %>%
select(-ATOXGRL)
actual_caliond_daids <- derive_var_atoxgr_dir(
input_caliond_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_caliond_daids,
compare = actual_caliond_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Creatine Kinase, High
### Grade 4: >= 20.0 x ULN
### Grade 3: 10.0 -< 20.0 x ULN
### Grade 2: 6 -< 10.0 x ULN
### Grade 1: 3 -< 6 x ULN
## Test 96: DAIDS Creatine Kinase, High ----
test_that("derive_var_atoxgr Test 96: DAIDS Creatine Kinase, High", {
expected_cki_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 10, 5, NA_character_, NA, 1,
NA_character_, 10, 5, NA_character_, NA, 2,
"Creatine Kinase, High", 100, 5, NA_character_, "4", 3,
"Creatine Kinase, High", 99, 5, NA_character_, "3", 4,
"Creatine Kinase, High", 50, 5, NA_character_, "3", 5,
"Creatine Kinase, High", 49, 5, NA_character_, "2", 6,
"Creatine Kinase, High", 30, 5, NA_character_, "2", 7,
"Creatine Kinase, High", 29, 5, NA_character_, "1", 8,
"Creatine Kinase, High", 15, 5, NA_character_, "1", 9,
"Creatine Kinase, High", 14, 5, NA_character_, "0", 10,
# ANRHI missing - cannot grade
"Creatine Kinase, High", 4, NA, NA_character_, NA, 11,
# AVAL missing cannot grade
"Creatine Kinase, High", NA, NA, NA_character_, NA, 12,
)
input_cki_daids <- expected_cki_daids %>%
select(-ATOXGRH)
actual_cki_daids <- derive_var_atoxgr_dir(
input_cki_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cki_daids,
compare = actual_cki_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Creatinine, High
### Grade 4: >= 3.5 x ULN or >= 2 X BASE
### Grade 3: >1.8 -< 3.5 x ULN or 1.5 -< 2 x BASE
### Grade 2: >1.3 - 1.8 x ULN or 1.3 - < 1.5 x BASE
### Grade 1: 1.1 - 1.3 x ULN
## Test 97: DAIDS Creatinine, High ----
test_that("derive_var_atoxgr Test 97: DAIDS Creatinine, High", {
expected_creati_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~BASE, ~ATOXGRH, ~TESTNUM,
"Not a term", 10, 10, 34, NA, 1,
NA_character_, 10, 10, 34, NA, 2,
"Creatinine, High", 35, 10, 34, "4", 3,
"Creatinine, High", 10, 10, 5, "4", 4,
"Creatinine, High", 34, 10, 34, "3", 5,
"Creatinine, High", 19, 10, 20, "3", 6,
"Creatinine, High", 9, 10, 5, "3", 7,
"Creatinine, High", 7.5, 10, 5, "3", 8,
"Creatinine, High", 18, 10, 34, "2", 9,
"Creatinine, High", 14, 10, 20, "2", 10,
"Creatinine, High", 7.4, 10, 5, "2", 11,
"Creatinine, High", 6.5, 10, 5, "2", 12,
"Creatinine, High", 13, 10, 34, "1", 13,
"Creatinine, High", 11, 10, 20, "1", 14,
"Creatinine, High", 10, 10, 20, "0", 15,
# ANRHI missing - cannot grade
"Creatinine, High", 10, NA, 20, NA, 16,
# AVAL missing cannot grade
"Creatinine, High", NA, 10, 20, NA, 18,
) %>%
mutate(AVALU = NA_character_)
input_creati_daids <- expected_creati_daids %>%
select(-ATOXGRH)
actual_creati_daids <- derive_var_atoxgr_dir(
input_creati_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_creati_daids,
compare = actual_creati_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose Fasting, High
### Grade 4: >= 27.75 mmol/L
### Grade 3: 13.89 -< 27.75 mmol/L
### Grade 2: 6.95 -< 13.89 mmol/L
### Grade 1: 6.11 -< 6.95 mmol/L
## Test 98: DAIDS Glucose Fasting, High ----
test_that("derive_var_atoxgr Test 98: DAIDS Glucose Fasting, High", {
expected_glucfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 9.5, "mmol/L", NA, 2,
"Glucose Fasting, High", 27.75, "mmol/L", "4", 3,
"Glucose Fasting, High", 27.74, "mmol/L", "3", 4,
"Glucose Fasting, High", 13.89, "mmol/L", "3", 5,
"Glucose Fasting, High", 13.88, "mmol/L", "2", 6,
"Glucose Fasting, High", 6.95, "mmol/L", "2", 7,
"Glucose Fasting, High", 6.94, "mmol/L", "1", 8,
"Glucose Fasting, High", 6.11, "mmol/L", "1", 9,
"Glucose Fasting, High", 6.1, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose Fasting, High", 7, NA, NA, 11,
# AVAL missing cannot grade
"Glucose Fasting, High", NA, "mmol/L", NA, 12,
)
input_glucfi_daids <- expected_glucfi_daids %>%
select(-ATOXGRH)
actual_glucfi_daids <- derive_var_atoxgr_dir(
input_glucfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucfi_daids,
compare = actual_glucfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose Nonfasting, High
### Grade 4: >= 27.75 mmol/L
### Grade 3: 13.89 -< 27.75 mmol/L
### Grade 2: 8.89 -< 13.89 mmol/L
### Grade 1: 6.44 -< 8.89 mmol/L
## Test 99: DAIDS Glucose Nonfasting, High ----
test_that("derive_var_atoxgr Test 99: DAIDS Glucose Nonfasting, High", {
expected_glucnfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 9.5, "mmol/L", NA, 2,
"Glucose Nonfasting, High", 27.75, "mmol/L", "4", 3,
"Glucose Nonfasting, High", 27.74, "mmol/L", "3", 4,
"Glucose Nonfasting, High", 13.89, "mmol/L", "3", 5,
"Glucose Nonfasting, High", 13.88, "mmol/L", "2", 6,
"Glucose Nonfasting, High", 8.89, "mmol/L", "2", 7,
"Glucose Nonfasting, High", 8.88, "mmol/L", "1", 8,
"Glucose Nonfasting, High", 6.44, "mmol/L", "1", 9,
"Glucose Nonfasting, High", 6.43, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose Nonfasting, High", 7, NA, NA, 11,
# AVAL missing cannot grade
"Glucose Nonfasting, High", NA, "mmol/L", NA, 12,
)
input_glucnfi_daids <- expected_glucnfi_daids %>%
select(-ATOXGRH)
actual_glucnfi_daids <- derive_var_atoxgr_dir(
input_glucnfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucnfi_daids,
compare = actual_glucnfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Glucose, Low
### >= 1 month of age
### Grade 4: < 1.67 mmol/L
### Grade 3: 1.67 -< 2.22 mmol/L
### Grade 2: 2.22 -< 3.05 mmol/L
### Grade 1: 3.05 -< 3.55 mmol/L
expected_glucdge1m_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 1,
NA_character_, 4.1, "mmol/L", NA, 2,
"Glucose, Low", 1.66, "mmol/L", "4", 3,
"Glucose, Low", 1.67, "mmol/L", "3", 4,
"Glucose, Low", 2.21, "mmol/L", "3", 5,
"Glucose, Low", 2.22, "mmol/L", "2", 6,
"Glucose, Low", 3.04, "mmol/L", "2", 7,
"Glucose, Low", 3.05, "mmol/L", "1", 8,
"Glucose, Low", 3.54, "mmol/L", "1", 9,
"Glucose, Low", 3.55, "mmol/L", "0", 10,
# AVALU missing cannot grade
"Glucose, Low", 4, NA, NA, 11,
# AVAL missing cannot grade
"Glucose, Low", NA, "mmol/L", NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2022-11-30"),
LBDT = lubridate::ymd("2022-12-30"),
)
### < 1 month of age
### Grade 4: < 1.67 mmol/L
### Grade 3: 1.67 -< 2.22 mmol/L
### Grade 2: 2.22 -< 2.78 mmol/L
### Grade 1: 2.78 -< 3.00 mmol/L
expected_glucdlt1m_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 9.5, "mg/L", NA, 13,
NA_character_, 4.1, "mmol/L", NA, 14,
"Glucose, Low", 1.66, "mmol/L", "4", 15,
"Glucose, Low", 1.67, "mmol/L", "3", 16,
"Glucose, Low", 2.21, "mmol/L", "3", 17,
"Glucose, Low", 2.22, "mmol/L", "2", 18,
"Glucose, Low", 2.77, "mmol/L", "2", 19,
"Glucose, Low", 2.78, "mmol/L", "1", 20,
"Glucose, Low", 2.99, "mmol/L", "1", 21,
"Glucose, Low", 3, "mmol/L", "0", 22,
# AVALU missing cannot grade
"Glucose, Low", 4, NA, NA, 23,
# AVAL missing cannot grade
"Glucose, Low", NA, "mmol/L", NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2022-11-30"),
LBDT = lubridate::ymd("2022-12-29"),
)
expected_glucdnoage_daids <- expected_glucdge1m_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
ATOXGRL = NA_character_,
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_glucd_daids <- expected_glucdnoage_daids %>%
bind_rows(
expected_glucdge1m_daids,
expected_glucdlt1m_daids
)
## Test 100: DAIDS Glucose, Low ----
test_that("derive_var_atoxgr Test 100: DAIDS Glucose, Low", {
input_glucd_daids <- expected_glucd_daids %>%
select(-ATOXGRL)
actual_glucd_daids <- derive_var_atoxgr_dir(
input_glucd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_glucd_daids,
compare = actual_glucd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Lactate, High
### Grade 2: >= 2.0 x ULN
### Grade 1: ULN -< 2.0 x ULN
## Test 101: DAIDS Lactate, High ----
test_that("derive_var_atoxgr Test 101: DAIDS Lactate, High", {
expected_lacti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 105, 100, NA, 1,
NA_character_, 105, 100, NA, 2,
"Lactate, High", 200, 100, "2", 3,
"Lactate, High", 199, 100, "1", 4,
"Lactate, High", 100, 100, "1", 5,
"Lactate, High", 99, 100, "0", 6,
# ANRHI missing cannot grade
"Lactate, High", 200, NA, NA, 7,
# AVAL missing cannot grade
"Lactate, High", NA, 100, NA, 8,
) %>%
mutate(AVALU = NA_character_)
input_lacti_daids <- expected_lacti_daids %>%
select(-ATOXGRH)
actual_lacti_daids <- derive_var_atoxgr_dir(
input_lacti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lacti_daids,
compare = actual_lacti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Lipase, High
### Grade 4: >= 5.0 x ULN
### Grade 3: 3.0 -< 5.0 x ULN
### Grade 2: 1.5 -< 3.0 x ULN
### Grade 1: 1.1 -< 1.5 x ULN
## Test 102: DAIDS Lipase, High ----
test_that("derive_var_atoxgr Test 102: DAIDS Lipase, High", {
expected_lipi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~ATOXGRH, ~TESTNUM,
"Not a term", 80, 100, NA, 1,
NA_character_, 60, 100, NA, 2,
"Lipase, High", 500, 100, "4", 3,
"Lipase, High", 499, 100, "3", 4,
"Lipase, High", 300, 100, "3", 5,
"Lipase, High", 299, 100, "2", 6,
"Lipase, High", 150, 100, "2", 7,
"Lipase, High", 149, 100, "1", 8,
"Lipase, High", 110, 100, "1", 9,
"Lipase, High", 109, 100, "0", 10,
# ANRHI missing cannot grade
"Lipase, High", 200, NA, NA, 11,
# AVAL missing cannot grade
"Lipase, High", NA, 100, NA, 12,
) %>%
mutate(AVALU = NA_character_)
input_lipi_daids <- expected_lipi_daids %>%
select(-ATOXGRH)
actual_lipi_daids <- derive_var_atoxgr_dir(
input_lipi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lipi_daids,
compare = actual_lipi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Cholesterol, Fasting, High
### >= 18 years of age
### Grade 3: >= 7.77 mmol/L
### Grade 2: 6.19 -< 7.77 mmol/L
### Grade 1: 5.18 -< 6.19 mmol/L
expected_cholfige18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 1,
NA_character_, 3.5, "mmol/L", NA, 2,
"Cholesterol, Fasting, High", 7.77, "mmol/L", "3", 3,
"Cholesterol, Fasting, High", 7.76, "mmol/L", "2", 4,
"Cholesterol, Fasting, High", 6.19, "mmol/L", "2", 5,
"Cholesterol, Fasting, High", 6.18, "mmol/L", "1", 6,
"Cholesterol, Fasting, High", 5.18, "mmol/L", "1", 7,
"Cholesterol, Fasting, High", 5.17, "mmol/L", "0", 8,
# Unit missing cannot grade
"Cholesterol, Fasting, High", 3.5, NA, NA, 9,
# AVAL missing cannot grade
"Cholesterol, Fasting, High", NA, "mmol/L", NA, 10,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-08")
)
### < 18 years of age
### Grade 3: >= 7.77 mmol/L
### Grade 2: 5.15 -< 7.77 mmol/L
### Grade 1: 4.4 -< 5.15 mmol/L
expected_cholfilt18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.5, "mmol/L", NA, 13,
NA_character_, 3.5, "mmol/L", NA, 14,
"Cholesterol, Fasting, High", 7.77, "mmol/L", "3", 15,
"Cholesterol, Fasting, High", 7.76, "mmol/L", "2", 16,
"Cholesterol, Fasting, High", 5.15, "mmol/L", "2", 17,
"Cholesterol, Fasting, High", 5.14, "mmol/L", "1", 18,
"Cholesterol, Fasting, High", 4.4, "mmol/L", "1", 19,
"Cholesterol, Fasting, High", 4.39, "mmol/L", "0", 20,
# Unit missing cannot grade
"Cholesterol, Fasting, High", 3.5, NA, NA, 21,
# AVAL missing cannot grade
"Cholesterol, Fasting, High", NA, "mmol/L", NA, 22,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_cholfinoage_daids <- expected_cholfige18y_daids %>%
filter(TESTNUM %in% c(9, 10)) %>%
mutate(
LBDT = if_else(TESTNUM == 9, NA, LBDT),
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 9, 25, 26)
)
expected_cholfi_daids <- expected_cholfinoage_daids %>%
bind_rows(
expected_cholfige18y_daids,
expected_cholfilt18y_daids
)
## Test 103: DAIDS Cholesterol, Fasting, High ----
test_that("derive_var_atoxgr Test 103: DAIDS Cholesterol, Fasting, High", {
input_cholfi_daids <- expected_cholfi_daids %>%
select(-ATOXGRH)
actual_cholfi_daids <- derive_var_atoxgr_dir(
input_cholfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cholfi_daids,
compare = actual_cholfi_daids,
keys = c("TESTNUM")
)
})
### LDL, Fasting, High
### >= 18 years of age
### Grade 3: >= 4.90 mmol/L
### Grade 2: 4.12 -< 4.90 mmol/L
### Grade 1: 3.17 -< 4.12 mmol/L
expected_ldlfige18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 3.1, "mmol/L", NA, 1,
NA_character_, 3.1, "mmol/L", NA, 2,
"LDL, Fasting, High", 4.9, "mmol/L", "3", 3,
"LDL, Fasting, High", 4.89, "mmol/L", "2", 4,
"LDL, Fasting, High", 4.12, "mmol/L", "2", 5,
"LDL, Fasting, High", 4.11, "mmol/L", "1", 6,
"LDL, Fasting, High", 3.37, "mmol/L", "1", 7,
"LDL, Fasting, High", 3.36, "mmol/L", "0", 8,
# Unit missing cannot grade
"LDL, Fasting, High", 3.1, NA, NA, 9,
# AVAL missing cannot grade
"LDL, Fasting, High", NA, "mmol/L", NA, 10,
) %>%
mutate(
BRTHDT = lubridate::ymd("2005-01-08"),
LBDT = lubridate::ymd("2023-01-08")
)
### > 2 to < 18 years of age
### Grade 3: >= 4.90 mmol/L
### Grade 2: 3.34 -< 4.90 mmol/L
### Grade 1: 2.85 -< 3.34 mmol/L
expected_ldlfilt18y_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 2.8, "mmol/L", NA, 11,
NA_character_, 2.8, "mmol/L", NA, 12,
"LDL, Fasting, High", 4.9, "mmol/L", "3", 13,
"LDL, Fasting, High", 4.89, "mmol/L", "2", 14,
"LDL, Fasting, High", 3.34, "mmol/L", "2", 15,
"LDL, Fasting, High", 3.33, "mmol/L", "1", 16,
"LDL, Fasting, High", 2.85, "mmol/L", "1", 17,
"LDL, Fasting, High", 2.84, "mmol/L", "0", 18,
# Unit missing cannot grade
"LDL, Fasting, High", 3.5, NA, NA, 19,
# AVAL missing cannot grade
"LDL, Fasting, High", NA, "mmol/L", NA, 20,
) %>%
mutate(
BRTHDT = lubridate::ymd("2020-01-07"),
LBDT = lubridate::ymd("2023-01-07")
)
expected_ldlfinoage_daids <- expected_ldlfige18y_daids %>%
filter(TESTNUM %in% c(7, 8)) %>%
mutate(
LBDT = if_else(TESTNUM == 7, NA, LBDT),
BRTHDT = if_else(TESTNUM == 8, NA, BRTHDT),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 7, 25, 26)
)
expected_ldlfile2y_daids <- expected_ldlfige18y_daids %>%
filter(TESTNUM %in% c(7, 8)) %>%
mutate(
BRTHDT = if_else(TESTNUM == 7, lubridate::ymd("2021-01-07"), lubridate::ymd("2022-01-07")),
ATOXGRH = NA_character_,
TESTNUM = if_else(TESTNUM == 7, 27, 28)
)
expected_ldlfi_daids <- expected_ldlfile2y_daids %>%
bind_rows(
expected_ldlfinoage_daids,
expected_ldlfige18y_daids,
expected_ldlfilt18y_daids
)
## Test 104: DAIDS LDL, Fasting, High ----
test_that("derive_var_atoxgr Test 104: DAIDS LDL, Fasting, High", {
input_ldlfi_daids <- expected_ldlfi_daids %>%
select(-ATOXGRH)
actual_ldlfi_daids <- derive_var_atoxgr_dir(
input_ldlfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ldlfi_daids,
compare = actual_ldlfi_daids,
keys = c("TESTNUM")
)
})
### Triglycerides, Fasting, High
### Grade 4: > 11.4 mmol/L
### Grade 3: >5.7 - 11.4 mmol/L
### Grade 2: >3.42 - 5.7 mmol/L
### Grade 1: 1.71 - 3.42 mmol/L
## Test 105: DAIDS Triglycerides, Fasting, High ----
test_that("derive_var_atoxgr Test 105: DAIDS Triglycerides, Fasting, High", {
expected_trigfi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 1.5, "mmol/L", NA, 1,
NA_character_, 1.5, "mmol/L", NA, 2,
"Triglycerides, Fasting, High", 11.5, "mmol/L", "4", 3,
"Triglycerides, Fasting, High", 11.4, "mmol/L", "3", 4,
"Triglycerides, Fasting, High", 5.8, "mmol/L", "3", 5,
"Triglycerides, Fasting, High", 5.7, "mmol/L", "2", 6,
"Triglycerides, Fasting, High", 3.43, "mmol/L", "2", 7,
"Triglycerides, Fasting, High", 3.42, "mmol/L", "1", 8,
"Triglycerides, Fasting, High", 1.71, "mmol/L", "1", 9,
"Triglycerides, Fasting, High", 1.7, "mmol/L", "0", 10,
# Unit missing cannot grade
"Triglycerides, Fasting, High", 1.5, NA, NA, 11,
# AVAL missing cannot grade
"Triglycerides, Fasting, High", NA, "mmol/L", NA, 12,
)
input_trigfi_daids <- expected_trigfi_daids %>%
select(-ATOXGRH)
actual_trigfi_daids <- derive_var_atoxgr_dir(
input_trigfi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_trigfi_daids,
compare = actual_trigfi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Magnesium, Low
### Grade 4: <0.3 mmol/L
### Grade 3: 0.3 -< 0.45 mmol/L
### Grade 2: 0.45 -< 0.6 mmol/L
### Grade 1: 0.6 -< 0.7 mmol/L
## Test 106: DAIDS Magnesium, Low ----
test_that("derive_var_atoxgr Test 106: DAIDS Magnesium, Low", {
expected_magd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 0.5, "mmol/L", NA, 1,
NA_character_, 0.5, "mmol/L", NA, 2,
"Magnesium, Low", 0.29, "mmol/L", "4", 3,
"Magnesium, Low", 0.3, "mmol/L", "3", 4,
"Magnesium, Low", 0.44, "mmol/L", "3", 5,
"Magnesium, Low", 0.45, "mmol/L", "2", 6,
"Magnesium, Low", 0.59, "mmol/L", "2", 7,
"Magnesium, Low", 0.6, "mmol/L", "1", 8,
"Magnesium, Low", 0.69, "mmol/L", "1", 9,
"Magnesium, Low", 0.7, "mmol/L", "0", 10,
# Unit missing cannot grade
"Magnesium, Low", 0.5, NA, NA, 11,
# AVAL missing cannot grade
"Magnesium, Low", NA, "mmol/L", NA, 12,
)
input_magd_daids <- expected_magd_daids %>%
select(-ATOXGRL)
actual_magd_daids <- derive_var_atoxgr_dir(
input_magd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_magd_daids,
compare = actual_magd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Phosphate, Low
### > 14 years of age
### Grade 4: < 0.32 mmol/L
### Grade 3: 0.32 to < 0.45 mmol/L
### Grade 2: 0.45 to < 0.65 mmol/L
### Grade 1: 0.65 mmol/L to < LLN mmol/L
expected_phosd_daids_gt14y <- tibble::tribble(
~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.9, 0.8, "MM3", NA, 1,
0.31, 0.8, "mmol/L", "4", 2,
0.32, 0.8, "mmol/L", "3", 3,
0.44, 0.8, "mmol/L", "3", 4,
0.45, 0.8, "mmol/L", "2", 5,
0.64, 0.8, "mmol/L", "2", 6,
0.65, 0.8, "mmol/L", "1", 7,
0.79, 0.8, "mmol/L", "1", 8,
0.8, 0.8, "mmol/L", "0", 9,
# missing ANRLO - can grade 2 - 4
0.31, 0.8, "mmol/L", "4", 10,
0.32, 0.8, "mmol/L", "3", 11,
0.44, 0.8, "mmol/L", "3", 12,
0.45, 0.8, "mmol/L", "2", 13,
0.64, 0.8, "mmol/L", "2", 14,
# missing ANRLO - can grade 0 - 1
0.65, 0.8, "mmol/L", "1", 15,
0.79, 0.8, "mmol/L", "1", 16,
0.8, 0.8, "mmol/L", "0", 17,
# missing AVAL
NA, 0.8, "mmol/L", NA, 18,
# missing UNIT
1, 0.8, NA, NA, 19,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2008-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### 1 to 14 years of age
### Grade 4: < 0.48 mmol/L
### Grade 3: 0.48 to < 0.81 mmol/L
### Grade 2: 0.81 to < 0.97 mmol/L
### Grade 1: 0.97 to <1.13 mmol/L
expected_phosd_daids_le14y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.2, "MM3", NA, 20,
0.47, "mmol/L", "4", 21,
0.48, "mmol/L", "3", 22,
0.8, "mmol/L", "3", 23,
0.81, "mmol/L", "2", 24,
0.96, "mmol/L", "2", 25,
0.97, "mmol/L", "1", 26,
1.12, "mmol/L", "1", 27,
1.13, "mmol/L", "0", 28,
NA, "mmol/L", NA, 29,
1, NA, NA, 30,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2022-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### < 1 year of age
### Grade 4: < 0.48 mmol/L
### Grade 3: 0.48 to < 0.81 mmol/L
### Grade 2: 0.81 to < 1.13 mmol/L
### Grade 1: 1.13 to < 1.45 mmol/L
expected_phosd_daids_lt1y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.5, "MM3", NA, 31,
0.47, "mmol/L", "4", 32,
0.48, "mmol/L", "3", 33,
0.8, "mmol/L", "3", 34,
0.81, "mmol/L", "2", 35,
1.12, "mmol/L", "2", 36,
1.13, "mmol/L", "1", 37,
1.44, "mmol/L", "1", 38,
1.45, "mmol/L", "0", 39,
NA, "mmol/L", NA, 40,
1.5, NA, NA, 41,
) %>%
mutate(
ATOXDSCL = "Phosphate, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-02")
)
# Set lab date or birth date to missing
expected_phosd_daids_noage <- expected_phosd_daids_gt14y %>%
filter(TESTNUM %in% c(8, 9)) %>%
mutate(
LBDT = if_else(TESTNUM == 8, NA, LBDT),
BRTHDT = if_else(TESTNUM == 9, NA, BRTHDT),
ATOXGRL = NA,
TESTNUM = if_else(TESTNUM == 8, 42, 43)
)
expected_phosd_daids <- expected_phosd_daids_gt14y %>%
bind_rows(
expected_phosd_daids_le14y,
expected_phosd_daids_lt1y,
expected_phosd_daids_noage
)
## Test 107: DAIDS Phosphate, Low ----
test_that("derive_var_atoxgr Test 107: DAIDS Phosphate, Low", {
input_phosd_daids <- expected_phosd_daids %>%
select(-ATOXGRL)
actual_phosd_daids <- derive_var_atoxgr_dir(
input_phosd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_phosd_daids,
compare = actual_phosd_daids,
keys = c("TESTNUM")
)
})
### Potassium, High
### Grade 4: >= 7 mmol/L
### Grade 3: 6.5 -< 7 mmol/L
### Grade 2: 6 -< 6.5 mmol/L
### Grade 1: 5.6 -< 6 mmol/L
## Test 108: DAIDS Potassium, High ----
test_that("derive_var_atoxgr Test 108: DAIDS Potassium, High", {
expected_poti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 5, "mmol/L", NA, 1,
NA_character_, 5, "mmol/L", NA, 2,
"Potassium, High", 7, "mmol/L", "4", 3,
"Potassium, High", 6.9, "mmol/L", "3", 4,
"Potassium, High", 6.5, "mmol/L", "3", 5,
"Potassium, High", 6.4, "mmol/L", "2", 6,
"Potassium, High", 6, "mmol/L", "2", 7,
"Potassium, High", 5.9, "mmol/L", "1", 8,
"Potassium, High", 5.6, "mmol/L", "1", 9,
"Potassium, High", 5.5, "mmol/L", "0", 10,
# Unit missing cannot grade
"Potassium, High", 5, NA, NA, 11,
# AVAL missing cannot grade
"Potassium, High", NA, "mmol/L", NA, 12,
)
input_poti_daids <- expected_poti_daids %>%
select(-ATOXGRH)
actual_poti_daids <- derive_var_atoxgr_dir(
input_poti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_poti_daids,
compare = actual_poti_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Potassium, Low
### Grade 4: <2 mmol/L
### Grade 3: 2 -< 2.5 mmol/L
### Grade 2: 2.5 -< 3 mmol/L
### Grade 1: 3 -< 3.4 mmol/L
## Test 109: DAIDS Potassium, Low ----
test_that("derive_var_atoxgr Test 109: DAIDS Potassium, Low", {
expected_potd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 3, "mmol/L", NA, 1,
NA_character_, 3, "mmol/L", NA, 2,
"Potassium, Low", 1.9, "mmol/L", "4", 3,
"Potassium, Low", 2, "mmol/L", "3", 4,
"Potassium, Low", 2.4, "mmol/L", "3", 5,
"Potassium, Low", 2.5, "mmol/L", "2", 6,
"Potassium, Low", 2.9, "mmol/L", "2", 7,
"Potassium, Low", 3, "mmol/L", "1", 8,
"Potassium, Low", 3.3, "mmol/L", "1", 9,
"Potassium, Low", 3.4, "mmol/L", "0", 10,
# Unit missing cannot grade
"Potassium, Low", 3, NA, NA, 11,
# AVAL missing cannot grade
"Potassium, Low", NA, "mmol/L", NA, 12,
)
input_potd_daids <- expected_potd_daids %>%
select(-ATOXGRL)
actual_potd_daids <- derive_var_atoxgr_dir(
input_potd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_potd_daids,
compare = actual_potd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Sodium, High
### Grade 4: >= 160 mmol/L
### Grade 3: 154 -< 160 mmol/L
### Grade 2: 150 -< 154 mmol/L
### Grade 1: 146 -< 150 mmol/L
## Test 110: DAIDS Sodium, High ----
test_that("derive_var_atoxgr Test 110: DAIDS Sodium, High", {
expected_sodi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 146, "mmol/L", NA, 1,
NA_character_, 146, "mmol/L", NA, 2,
"Sodium, High", 160, "mmol/L", "4", 3,
"Sodium, High", 159, "mmol/L", "3", 4,
"Sodium, High", 154, "mmol/L", "3", 5,
"Sodium, High", 153, "mmol/L", "2", 6,
"Sodium, High", 150, "mmol/L", "2", 7,
"Sodium, High", 149, "mmol/L", "1", 8,
"Sodium, High", 146, "mmol/L", "1", 9,
"Sodium, High", 145, "mmol/L", "0", 10,
# Unit missing cannot grade
"Sodium, High", 140, NA, NA, 11,
# AVAL missing cannot grade
"Sodium, High", NA, "mmol/L", NA, 12,
)
input_sodi_daids <- expected_sodi_daids %>%
select(-ATOXGRH)
actual_sodi_daids <- derive_var_atoxgr_dir(
input_sodi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_sodi_daids,
compare = actual_sodi_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Sodium, Low
### Grade 4: <= 120 mmol/L
### Grade 3: >120 -< 125 mmol/L
### Grade 2: 125 -< 130 mmol/L
### Grade 1: 130 -< 135 mmol/L
## Test 111: DAIDS Sodium, Low ----
test_that("derive_var_atoxgr Test 111: DAIDS Sodium, Low", {
expected_sodd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 119, "mmol/L", NA, 1,
NA_character_, 119, "mmol/L", NA, 2,
"Sodium, Low", 120, "mmol/L", "4", 3,
"Sodium, Low", 121, "mmol/L", "3", 4,
"Sodium, Low", 124, "mmol/L", "3", 5,
"Sodium, Low", 125, "mmol/L", "2", 6,
"Sodium, Low", 129, "mmol/L", "2", 7,
"Sodium, Low", 130, "mmol/L", "1", 8,
"Sodium, Low", 134, "mmol/L", "1", 9,
"Sodium, Low", 135, "mmol/L", "0", 10,
# Unit missing cannot grade
"Sodium, Low", 140, NA, NA, 11,
# AVAL missing cannot grade
"Sodium, Low", NA, "mmol/L", NA, 12,
)
input_sodd_daids <- expected_sodd_daids %>%
select(-ATOXGRL)
actual_sodd_daids <- derive_var_atoxgr_dir(
input_sodd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_sodd_daids,
compare = actual_sodd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### Uric Acid, High
### Grade 4: >= 890 umol/L (0.89 mmol/L)
### Grade 3: 710 -< 890 umol/L (0.71 - <0.89 mmol/L)
### Grade 2: 590 -< 710 umol/L (0.59 - <0.71 mmol/L)
### Grade 1: 450 -< 590 umol/L (0.45 - <0.59 mmol/L)
## Test 112: DAIDS Uric Acid, High ----
test_that("derive_var_atoxgr Test 112: DAIDS Uric Acid, High", {
expected_urici_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH, ~TESTNUM,
"Not a term", 591, "umol/L", NA, 1,
NA_character_, 591, "umol/L", NA, 2,
"Uric Acid, High", 890, "umol/L", "4", 3,
"Uric Acid, High", 889, "umol/L", "3", 4,
"Uric Acid, High", 710, "umol/L", "3", 5,
"Uric Acid, High", 709, "umol/L", "2", 6,
"Uric Acid, High", 590, "umol/L", "2", 7,
"Uric Acid, High", 589, "umol/L", "1", 8,
"Uric Acid, High", 450, "umol/L", "1", 9,
"Uric Acid, High", 449, "umol/L", "0", 10,
# Unit missing cannot grade
"Uric Acid, High", 200, NA, NA, 11,
# AVAL missing cannot grade
"Uric Acid, High", NA, "umol/L", NA, 12,
)
input_urici_daids <- expected_urici_daids %>%
select(-ATOXGRH)
actual_urici_daids <- derive_var_atoxgr_dir(
input_urici_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_urici_daids,
compare = actual_urici_daids,
keys = c("ATOXDSCH", "TESTNUM")
)
})
### Absolute CD4+ Count, Low
### > 5 years of age
### Grade 4: < 0.1 10^9/L
### Grade 3: 0.1 to < 0.2 10^9/L
### Grade 2: 0.2 to < 0.3 10^9/L
### Grade 1: 0.3 to < 0.4 10^9/L
## Test 113: DAIDS Absolute Lymphocyte Count, Low ----
test_that("derive_var_atoxgr Test 113: DAIDS Absolute Lymphocyte Count, Low", {
expected_cd4d_daids_gt5y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.1, "MM3", NA, 1,
0.09, "10^9/L", "4", 2,
0.1, "10^9/L", "3", 3,
0.19, "10^9/L", "3", 4,
0.2, "10^9/L", "2", 5,
0.29, "10^9/L", "2", 6,
0.3, "10^9/L", "1", 7,
0.39, "10^9/L", "1", 8,
0.4, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute CD4+ Count, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2029-07-01")
)
# no criteria for age <= 5 years set grade to missing
expected_cd4d_daids_le5y <- expected_cd4d_daids_gt5y %>%
mutate(
LBDT = lubridate::ymd("2028-07-01"),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
# add missing LBDT and BRTHDT
expected_cd4d_daids_noage <- expected_cd4d_daids_gt5y %>%
filter(TESTNUM %in% c(5, 6)) %>%
mutate(
LBDT = if_else(TESTNUM == 5, NA, LBDT),
BRTHDT = if_else(TESTNUM == 6, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 5, 23, 24)
)
expected_cd4d_daids <- expected_cd4d_daids_gt5y %>%
bind_rows(
expected_cd4d_daids_le5y,
expected_cd4d_daids_noage
)
input_cd4d_daids <- expected_cd4d_daids %>%
select(-ATOXGRL)
actual_cd4d_daids <- derive_var_atoxgr_dir(
input_cd4d_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_cd4d_daids,
compare = actual_cd4d_daids,
keys = c("TESTNUM")
)
})
### Absolute Lymphocyte Count, Low
### > 5 years of age
### Grade 4: < 0.35 10^9/L
### Grade 3: 0.35 to < 0.5 10^9/L
### Grade 2: 0.5 to < 0.6 10^9/L
### Grade 1: 0.6 to < 0.65 10^9/L
## Test 114: DAIDS Absolute Lymphocyte Count, Low ----
test_that("derive_var_atoxgr Test 114: DAIDS Absolute Lymphocyte Count, Low", {
expected_lymphd_daids_gt5y <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.35, "MM3", NA, 1,
0.34, "10^9/L", "4", 2,
0.35, "10^9/L", "3", 3,
0.49, "10^9/L", "3", 4,
0.5, "10^9/L", "2", 5,
0.59, "10^9/L", "2", 6,
0.6, "10^9/L", "1", 7,
0.64, "10^9/L", "1", 8,
0.65, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute Lymphocyte Count, Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2029-07-01")
)
# no criteria for age <= 5 years set grade to missing
expected_lymphd_daids_le5y <- expected_lymphd_daids_gt5y %>%
mutate(
LBDT = lubridate::ymd("2028-07-01"),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
# add missing LBDT and BRTHDT
expected_lymphd_daids_noage <- expected_lymphd_daids_gt5y %>%
filter(TESTNUM %in% c(5, 6)) %>%
mutate(
LBDT = if_else(TESTNUM == 5, NA, LBDT),
BRTHDT = if_else(TESTNUM == 6, NA, BRTHDT),
ATOXGRL = NA_character_,
TESTNUM = if_else(TESTNUM == 5, 23, 24)
)
expected_lymphd_daids <- expected_lymphd_daids_gt5y %>%
bind_rows(
expected_lymphd_daids_le5y,
expected_lymphd_daids_noage
)
input_lymphd_daids <- expected_lymphd_daids %>%
select(-ATOXGRL)
actual_lymphd_daids <- derive_var_atoxgr_dir(
input_lymphd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_lymphd_daids,
compare = actual_lymphd_daids,
keys = c("TESTNUM")
)
})
### Absolute Neutrophil Count (ANC), Low
### > 7 days of age
### Grade 4: < 0.4 10^9/L
### Grade 3: 0.4 to < 0.6 10^9/L
### Grade 2: 0.6 to < 0.8 10^9/L
### Grade 1: 0.8 to 1 10^9/L
expected_ancd_daids_gt7d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.3, "MM3", NA, 1,
0.399, "10^9/L", "4", 2,
0.4, "10^9/L", "3", 3,
0.599, "10^9/L", "3", 4,
0.6, "10^9/L", "2", 5,
0.799, "10^9/L", "2", 6,
0.8, "10^9/L", "1", 7,
1, "10^9/L", "1", 8,
1.01, "10^9/L", "0", 9,
NA, "10^9/L", NA, 10,
1, NA, NA, 11,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-09")
)
### 2 to 7 days of age
### Grade 4: < 0.75 10^9/L
### Grade 3: 0.75 to < 1.0 10^9/L
### Grade 2: 1.0 to < 1.25 10^9/L
### Grade 1: 1.25 to 1.5 10^9/L
expected_ancd_daids_ge2d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
0.7, "MM3", NA, 12,
0.749, "10^9/L", "4", 13,
0.75, "10^9/L", "3", 14,
0.999, "10^9/L", "3", 15,
1, "10^9/L", "2", 16,
1.249, "10^9/L", "2", 17,
1.25, "10^9/L", "1", 18,
1.5, "10^9/L", "1", 19,
1.51, "10^9/L", "0", 20,
NA, "10^9/L", NA, 21,
1, NA, NA, 22,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-03")
)
### <= 1 day of age
### Grade 4: < 1.50 10^9/L
### Grade 3: 1.50 to < 3.0 10^9/L
### Grade 2: 3.0 to < 4.0 10^9/L
### Grade 1: 4.0 to 5.0 10^9/L
expected_ancd_daids_le1d <- tibble::tribble(
~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
1.5, "MM3", NA, 23,
1.499, "10^9/L", "4", 24,
1.5, "10^9/L", "3", 25,
2.999, "10^9/L", "3", 26,
3, "10^9/L", "2", 27,
3.999, "10^9/L", "2", 28,
4, "10^9/L", "1", 29,
5, "10^9/L", "1", 30,
5.01, "10^9/L", "0", 31,
NA, "10^9/L", NA, 32,
5, NA, NA, 33,
) %>%
mutate(
ATOXDSCL = "Absolute Neutrophil Count (ANC), Low",
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-02")
)
expected_ancd_daids <- expected_ancd_daids_gt7d %>%
bind_rows(
expected_ancd_daids_ge2d,
expected_ancd_daids_le1d
)
# Set lab date/birth date to missing
expected_ancd_daids_noage <- expected_ancd_daids %>%
filter(TESTNUM %in% c(20, 31)) %>%
mutate(
LBDT = if_else(TESTNUM == 20, NA, LBDT),
BRTHDT = if_else(TESTNUM == 31, NA, BRTHDT),
ATOXGRL = NA,
TESTNUM = case_when(
TESTNUM == 20 ~ 34,
TESTNUM == 31 ~ 35
)
)
expected_ancd_daids <- expected_ancd_daids %>%
bind_rows(expected_ancd_daids_noage)
input_ancd_daids <- expected_ancd_daids %>%
select(-ATOXGRL)
## Test 115: DAIDS ANC Low ----
test_that("derive_var_atoxgr Test 115: DAIDS ANC Low", {
actual_ancd_daids <- derive_var_atoxgr_dir(
input_ancd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ancd_daids,
compare = actual_ancd_daids,
keys = c("TESTNUM")
)
})
### Fibrinogen Decreased
### Grade 4: <0.5 g/L OR < 0.25 x LLN
### Grade 3: 0.5 to <0.75 g/L OR 0.25 to < 0.50 x LLN
### Grade 2: 0.75 to <1 g/L OR ≥ 0.50 to < 0.75 x LLN
### Grade 1: 1 to < 2 g/L OR 0.75 to < 1.00 x LLN
## Test 116: DAIDS Fibrinogen Decreased ----
test_that("derive_var_atoxgr Test 116: DAIDS Fibrinogen Decreased", {
expected_fibd_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~ANRLO, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 2, 1, "g/L", NA, 1,
NA_character_, 2, 1, "g/L", NA, 2,
"Fibrinogen Decreased", 2, 1, "g/dL", NA, 3,
# test first half of criteria
"Fibrinogen Decreased", 0.49, 1, "g/L", "4", 4,
"Fibrinogen Decreased", 0.5, 1, "g/L", "3", 5,
"Fibrinogen Decreased", 0.74, 1, "g/L", "3", 6,
"Fibrinogen Decreased", 0.75, 1, "g/L", "2", 7,
"Fibrinogen Decreased", 0.99, 1, "g/L", "2", 8,
"Fibrinogen Decreased", 1, 1, "g/L", "1", 9,
"Fibrinogen Decreased", 1.99, 1, "g/L", "1", 10,
"Fibrinogen Decreased", 2, 1, "g/L", "0", 11,
# test second half of criteria
"Fibrinogen Decreased", 0.74, 3, "g/L", "4", 12,
"Fibrinogen Decreased", 0.75, 3, "g/L", "3", 13,
"Fibrinogen Decreased", 1.49, 3, "g/L", "3", 14,
"Fibrinogen Decreased", 1.5, 3, "g/L", "2", 15,
"Fibrinogen Decreased", 2.24, 3, "g/L", "2", 16,
"Fibrinogen Decreased", 2.25, 3, "g/L", "1", 17,
"Fibrinogen Decreased", 2.99, 3, "g/L", "1", 18,
"Fibrinogen Decreased", 3, 3, "g/L", "0", 19,
# TEST for missing values
"Fibrinogen Decreased", 0.49, NA, "g/L", "4", 20,
"Fibrinogen Decreased", 0.5, NA, "g/L", NA, 21,
"Fibrinogen Decreased", 2, 1, NA, NA, 22,
"Fibrinogen Decreased", NA, 1, "g/L", NA, 23,
)
input_fibd_daids <- expected_fibd_daids %>%
select(-ATOXGRL)
actual_fibd_daids <- derive_var_atoxgr_dir(
input_fibd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_fibd_daids,
compare = actual_fibd_daids,
keys = c("TESTNUM")
)
})
### Hemoglobin, Low
### >= 13 years of age (male only)
### Grade 4: < 70 g/L
### Grade 3: 70 to < 90 g/L
### Grade 2: 90 to < 100 g/L
### Grade 1: 100 to 109 g/L
expected_hgbd_daids_ge13ym <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~SEX, ~TESTNUM,
"Hemoglobin, Low", 69, "MM3", NA, "M", 1,
"Hemoglobin, Low", 69, "g/L", "4", "M", 2,
"Hemoglobin, Low", 70, "g/L", "3", "M", 3,
"Hemoglobin, Low", 89, "g/L", "3", "M", 4,
"Hemoglobin, Low", 90, "g/L", "2", "M", 5,
"Hemoglobin, Low", 99, "g/L", "2", "M", 6,
"Hemoglobin, Low", 100, "g/L", "1", "M", 7,
"Hemoglobin, Low", 109, "g/L", "1", "M", 8,
"Hemoglobin, Low", 110, "g/L", "0", "M", 9,
"Hemoglobin, Low", NA, "g/L", NA, "M", 10,
"Hemoglobin, Low", 110, NA, NA, "M", 11,
"Hemoglobin, Low", 110, "g/L", NA, NA, 12,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### >= 13 years of age (female only)
### Grade 4: < 65 g/L
### Grade 3: 65 to < 85 g/L
### Grade 2: 85 to < 95 g/L
### Grade 1: 95 to 104 g/L
expected_hgbd_daids_ge13yf <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~SEX, ~TESTNUM,
"Hemoglobin, Low", 64, "MM3", NA, "F", 13,
"Hemoglobin, Low", 64, "g/L", "4", "F", 14,
"Hemoglobin, Low", 65, "g/L", "3", "F", 15,
"Hemoglobin, Low", 84, "g/L", "3", "F", 16,
"Hemoglobin, Low", 85, "g/L", "2", "F", 17,
"Hemoglobin, Low", 94, "g/L", "2", "F", 18,
"Hemoglobin, Low", 95, "g/L", "1", "F", 19,
"Hemoglobin, Low", 104, "g/L", "1", "F", 20,
"Hemoglobin, Low", 105, "g/L", "0", "F", 21,
"Hemoglobin, Low", NA, "g/L", NA, "F", 22,
"Hemoglobin, Low", 110, NA, NA, "F", 23,
"Hemoglobin, Low", 110, "g/L", NA, NA, 24,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-07-01")
)
### 57 days to < 13 years of age (male and female)
### Grade 4: < 65 g/L
### Grade 3: 65 to < 85 g/L
### Grade 2: 85 to < 95 g/L
### Grade 1: 95 to 104 g/L
expected_hgbd_daids_lt13y <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 64, "MM3", NA, 25,
"Hemoglobin, Low", 64, "g/L", "4", 26,
"Hemoglobin, Low", 65, "g/L", "3", 27,
"Hemoglobin, Low", 84, "g/L", "3", 28,
"Hemoglobin, Low", 85, "g/L", "2", 29,
"Hemoglobin, Low", 94, "g/L", "2", 30,
"Hemoglobin, Low", 95, "g/L", "1", 31,
"Hemoglobin, Low", 104, "g/L", "1", 32,
"Hemoglobin, Low", 105, "g/L", "0", 33,
"Hemoglobin, Low", NA, "g/L", NA, 34,
"Hemoglobin, Low", 110, NA, NA, 35,
) %>%
mutate(
BRTHDT = lubridate::ymd("2010-07-01"),
LBDT = lubridate::ymd("2023-06-30")
)
### 36 to ≤ 56 days of age (male and female)
### Grade 4: < 60 g/L
### Grade 3: 60 to < 70 g/L
### Grade 2: 70 to < 85 g/L
### Grade 1: 85 to 96 g/L
expected_hgbd_daids_le56d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 59, "MM3", NA, 36,
"Hemoglobin, Low", 59, "g/L", "4", 37,
"Hemoglobin, Low", 60, "g/L", "3", 38,
"Hemoglobin, Low", 69, "g/L", "3", 39,
"Hemoglobin, Low", 70, "g/L", "2", 40,
"Hemoglobin, Low", 84, "g/L", "2", 41,
"Hemoglobin, Low", 85, "g/L", "1", 42,
"Hemoglobin, Low", 96, "g/L", "1", 43,
"Hemoglobin, Low", 97, "g/L", "0", 44,
"Hemoglobin, Low", NA, "g/L", NA, 45,
"Hemoglobin, Low", 110, NA, NA, 46,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-08-26")
)
### 22 to ≤ 35 days of age (male and female)
### Grade 4: < 67 g/L
### Grade 3: 67 to < 80 g/L
### Grade 2: 80 to < 95 g/L
### Grade 1: 95 to 110 g/L
expected_hgbd_daids_le35d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 66, "MM3", NA, 47,
"Hemoglobin, Low", 66, "g/L", "4", 48,
"Hemoglobin, Low", 67, "g/L", "3", 49,
"Hemoglobin, Low", 79, "g/L", "3", 50,
"Hemoglobin, Low", 80, "g/L", "2", 51,
"Hemoglobin, Low", 94, "g/L", "2", 52,
"Hemoglobin, Low", 95, "g/L", "1", 53,
"Hemoglobin, Low", 110, "g/L", "1", 54,
"Hemoglobin, Low", 111, "g/L", "0", 55,
"Hemoglobin, Low", NA, "g/L", NA, 56,
"Hemoglobin, Low", 110, NA, NA, 57,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-08-05")
)
### 8 to ≤ 21 days of age (male and female)
### Grade 4: < 80 g/L
### Grade 3: 80 to < 90 g/L
### Grade 2: 90 to < 110 g/L
### Grade 1: 110 to 130 g/L
expected_hgbd_daids_le21d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 79, "MM3", NA, 58,
"Hemoglobin, Low", 79, "g/L", "4", 59,
"Hemoglobin, Low", 80, "g/L", "3", 60,
"Hemoglobin, Low", 89, "g/L", "3", 61,
"Hemoglobin, Low", 90, "g/L", "2", 62,
"Hemoglobin, Low", 109, "g/L", "2", 63,
"Hemoglobin, Low", 110, "g/L", "1", 64,
"Hemoglobin, Low", 130, "g/L", "1", 65,
"Hemoglobin, Low", 131, "g/L", "0", 66,
"Hemoglobin, Low", NA, "g/L", NA, 67,
"Hemoglobin, Low", 110, NA, NA, 68,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-22")
)
### ≤ 7 days of age (male and female)
### Grade 4: < 90 g/L
### Grade 3: 90 to < 100 g/L
### Grade 2: 100 to < 130 g/L
### Grade 1: 130 to 140 g/L
expected_hgbd_daids_le7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Hemoglobin, Low", 89, "MM3", NA, 69,
"Hemoglobin, Low", 89, "g/L", "4", 70,
"Hemoglobin, Low", 90, "g/L", "3", 71,
"Hemoglobin, Low", 99, "g/L", "3", 72,
"Hemoglobin, Low", 100, "g/L", "2", 73,
"Hemoglobin, Low", 129, "g/L", "2", 74,
"Hemoglobin, Low", 130, "g/L", "1", 75,
"Hemoglobin, Low", 140, "g/L", "1", 76,
"Hemoglobin, Low", 141, "g/L", "0", 77,
"Hemoglobin, Low", NA, "g/L", NA, 78,
"Hemoglobin, Low", 110, NA, NA, 79,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-08")
)
expected_hgbd_daids <- expected_hgbd_daids_ge13ym %>%
bind_rows(
expected_hgbd_daids_ge13yf,
expected_hgbd_daids_lt13y,
expected_hgbd_daids_le56d,
expected_hgbd_daids_le35d,
expected_hgbd_daids_le21d,
expected_hgbd_daids_le7d
)
# Set lab date to missing fo each type, ie SEX is M, F or missing
expected_hgbd_daids_noage <- expected_hgbd_daids %>%
filter(TESTNUM %in% c(5, 17, 29)) %>%
mutate(
LBDT = NA,
ATOXGRL = NA,
TESTNUM = case_when(
TESTNUM == 5 ~ 80,
TESTNUM == 17 ~ 81,
TESTNUM == 29 ~ 82
)
)
expected_hgbd_daids <- expected_hgbd_daids %>%
bind_rows(expected_hgbd_daids_noage)
input_hgbd_daids <- expected_hgbd_daids %>%
select(-ATOXGRL)
## Test 117: DAIDS HGB Low ----
test_that("derive_var_atoxgr Test 117: DAIDS HGB Low", {
actual_hgbd_daids <- derive_var_atoxgr_dir(
input_hgbd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_hgbd_daids,
compare = actual_hgbd_daids,
keys = c("ATOXDSCL", "TESTNUM")
)
})
### INR, high
### Grade 4: >=3 x ULN
### Grade 3: 2 to <3 x ULN
### Grade 2: 1.5 to < 2 x ULN
### Grade 1: 1.1 to < 1.5 x ULN
## Test 118: DAIDS INR High ----
test_that("derive_var_atoxgr Test 118: DAIDS INR High", {
expected_inri_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 80, NA_character_, NA,
NA_character_, 60, 80, NA_character_, NA,
"INR, High", 240, 80, NA_character_, "4",
"INR, High", 239, 80, NA_character_, "3",
"INR, High", 160, 80, NA_character_, "3",
"INR, High", 159, 80, NA_character_, "2",
"INR, High", 120, 80, NA_character_, "2",
"INR, High", 119, 80, NA_character_, "1",
"INR, High", 88, 80, NA_character_, "1",
"INR, High", 87, 80, NA_character_, "0",
# ANRHI missing - cannot grade
"INR, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"INR, High", NA, 80, NA_character_, NA,
)
input_inri_daids <- expected_inri_daids %>%
select(-ATOXGRH)
actual_inri_daids <- derive_var_atoxgr_dir(
input_inri_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_inri_daids,
compare = actual_inri_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Methemoglobin
### Grade 4: >=20.0%
### Grade 3: 15 to < 20%
### Grade 2: 10 to < 15%
### Grade 1: 5 to <10%
## Test 119: DAIDS Methemoglobin ----
test_that("derive_var_atoxgr Test 119: DAIDS Methemoglobin", {
expected_methi_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~AVALU, ~ATOXGRH,
"Not a term", 20, "%", NA,
NA_character_, 20, "%", NA,
"Methemoglobin", 20, "%", "4",
"Methemoglobin", 19, "%", "3",
"Methemoglobin", 15, "%", "3",
"Methemoglobin", 14, "%", "2",
"Methemoglobin", 10, "%", "2",
"Methemoglobin", 9, "%", "1",
"Methemoglobin", 5, "%", "1",
"Methemoglobin", 4, "%", "0",
# Unit wrong - cannot grade
"Methemoglobin", 100, NA, NA,
# AVAL missing cannot grade
"Methemoglobin", NA, "%", NA,
)
input_methi_daids <- expected_methi_daids %>%
select(-ATOXGRH)
actual_methi_daids <- derive_var_atoxgr_dir(
input_methi_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_methi_daids,
compare = actual_methi_daids,
keys = c("ATOXDSCH", "AVAL", "AVALU")
)
})
### PTT, high
### Grade 4: >=3 x ULN
### Grade 3: 2.33 to <3 x ULN
### Grade 2: 1.66 to < 2.33 x ULN
### Grade 1: 1.1 to < 1.66 x ULN
## Test 120: DAIDS PTT High ----
test_that("derive_var_atoxgr Test 120: DAIDS PTT High", {
expected_ptti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 80, NA_character_, NA,
NA_character_, 60, 80, NA_character_, NA,
"PTT, High", 240, 80, NA_character_, "4",
"PTT, High", 239, 80, NA_character_, "3",
"PTT, High", 186.4, 80, NA_character_, "3",
"PTT, High", 186.3, 80, NA_character_, "2",
"PTT, High", 132.8, 80, NA_character_, "2",
"PTT, High", 132.7, 80, NA_character_, "1",
"PTT, High", 88, 80, NA_character_, "1",
"PTT, High", 87, 80, NA_character_, "0",
# ANRHI missing - cannot grade
"PTT, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"PTT, High", NA, 80, NA_character_, NA,
)
input_ptti_daids <- expected_ptti_daids %>%
select(-ATOXGRH)
actual_ptti_daids <- derive_var_atoxgr_dir(
input_ptti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_ptti_daids,
compare = actual_ptti_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### Platelets, Decreased
### Grade 4: <25 x 10e9 /L
### Grade 3: 25 to <50 x 10e9 /L
### Grade 2: 50 to <100 - x 10e9
### Grade 1: 100 - 125 x 10e9 /L
## Test 121: DAIDS Platelets decreased ----
test_that("derive_var_atoxgr Test 121: DAIDS Platelets decreased", {
expected_plated_daids <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 126, "10^9/L", NA, 1,
NA_character_, 120, "10^9/L", NA, 2,
"Platelets, Decreased", 115, "MM3", NA, 3,
"Platelets, Decreased", 24.9, "10^9/L", "4", 4,
"Platelets, Decreased", 25, "10^9/L", "3", 5,
"Platelets, Decreased", 49.9, "10^9/L", "3", 6,
"Platelets, Decreased", 50, "10^9/L", "2", 7,
"Platelets, Decreased", 99.9, "10^9/L", "2", 8,
"Platelets, Decreased", 100, "10^9/L", "1", 9,
"Platelets, Decreased", 124.9, "10^9/L", "1", 10,
"Platelets, Decreased", 125, "10^9/L", "0", 11,
)
input_plated_daids <- expected_plated_daids %>%
select(-ATOXGRL)
actual_plated_daids <- derive_var_atoxgr_dir(
input_plated_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_plated_daids,
compare = actual_plated_daids,
keys = c("TESTNUM")
)
})
### PT, high
### Grade 4: >=3 x ULN
### Grade 3: 1.5 - <3 x ULN
### Grade 2: 1.25 - <1.5 x ULN
### Grade 1: 1.1 - <1.25 x ULN
## Test 122: DAIDS PT High ----
test_that("derive_var_atoxgr Test 122: DAIDS PT High", {
expected_pti_daids <- tibble::tribble(
~ATOXDSCH, ~AVAL, ~ANRHI, ~AVALU, ~ATOXGRH,
"Not a term", 80, 100, NA_character_, NA,
NA_character_, 60, 100, NA_character_, NA,
"PT, High", 300, 100, NA_character_, "4",
"PT, High", 299, 100, NA_character_, "3",
"PT, High", 150, 100, NA_character_, "3",
"PT, High", 149, 100, NA_character_, "2",
"PT, High", 125, 100, NA_character_, "2",
"PT, High", 124, 100, NA_character_, "1",
"PT, High", 110, 100, NA_character_, "1",
"PT, High", 109, 100, NA_character_, "0",
# ANRHI missing - cannot grade
"PT, High", 100, NA, NA_character_, NA,
# AVAL missing cannot grade
"PT, High", NA, 100, NA_character_, NA,
)
input_pti_daids <- expected_pti_daids %>%
select(-ATOXGRH)
actual_pti_daids <- derive_var_atoxgr_dir(
input_pti_daids,
new_var = ATOXGRH,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCH,
criteria_direction = "H",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_pti_daids,
compare = actual_pti_daids,
keys = c("ATOXDSCH", "AVAL", "ANRHI", "AVALU")
)
})
### White blood cell decreased (> 7 days of age)
### Grade 4: <1 x 10e9/L
### Grade 3: 1 to 1.499 x 10e9/L
### Grade 2: 1.5 to 1.999 x 10e9/L
### Grade 1: 2 to 2.499 x 10e9/L
expected_wbcd_daids_gt7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"Not a term", 1, "10^9/L", NA, 1,
NA_character_, 2, "10^9/L", NA, 2,
"WBC, Decreased", 0.9, "MM3", NA, 3,
"WBC, Decreased", 0.9, "10^9/L", "4", 4,
"WBC, Decreased", 1, "10^9/L", "3", 5,
"WBC, Decreased", 1.49, "10^9/L", "3", 6,
"WBC, Decreased", 1.5, "10^9/L", "2", 7,
"WBC, Decreased", 1.99, "10^9/L", "2", 8,
"WBC, Decreased", 2, "10^9/L", "1", 9,
"WBC, Decreased", 2.49, "10^9/L", "1", 10,
"WBC, Decreased", 2.5, "10^9/L", "0", 11,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-09")
)
### White blood cell decreased (<= 7 days of age)
### Grade 4: <2.500 x 10e9/L
### Grade 3: 2.5 to 3.999 x 10e9/L
### Grade 2: 4 to 5.499 x 10e9/L
### Grade 1: 5.5 to 6.999 x 10e9/L
expected_wbcd_daids_le7d <- tibble::tribble(
~ATOXDSCL, ~AVAL, ~AVALU, ~ATOXGRL, ~TESTNUM,
"WBC, Decreased", 2.49, "MM3", NA, 12,
"WBC, Decreased", 2.49, "10^9/L", "4", 13,
"WBC, Decreased", 2.5, "10^9/L", "3", 14,
"WBC, Decreased", 3.99, "10^9/L", "3", 15,
"WBC, Decreased", 4, "10^9/L", "2", 16,
"WBC, Decreased", 5.49, "10^9/L", "2", 17,
"WBC, Decreased", 5.5, "10^9/L", "1", 18,
"WBC, Decreased", 6.99, "10^9/L", "1", 19,
"WBC, Decreased", 7, "10^9/L", "0", 20,
) %>%
mutate(
BRTHDT = lubridate::ymd("2023-07-01"),
LBDT = lubridate::ymd("2023-07-08")
)
expected_wbcd_daids_noage <- expected_wbcd_daids_gt7d %>%
filter(TESTNUM %in% c(10, 11)) %>%
mutate(
BRTHDT = if_else(TESTNUM == 10, NA, BRTHDT),
LBDT = if_else(TESTNUM == 11, NA, LBDT),
ATOXGRL = NA_character_,
TESTNUM = TESTNUM + 11
)
expected_wbcd_daids <- expected_wbcd_daids_gt7d %>%
bind_rows(
expected_wbcd_daids_le7d,
expected_wbcd_daids_noage
)
input_wbcd_daids <- expected_wbcd_daids %>%
select(-ATOXGRL)
## Test 123: DAIDS White blood cell decreased ----
test_that("derive_var_atoxgr Test 123: DAIDS White blood cell decreased", {
actual_wbcd_daids <- derive_var_atoxgr_dir(
input_wbcd_daids,
new_var = ATOXGRL,
meta_criteria = atoxgr_criteria_daids,
tox_description_var = ATOXDSCL,
criteria_direction = "L",
get_unit_expr = AVALU
)
expect_dfs_equal(
base = expected_wbcd_daids,
compare = actual_wbcd_daids,
keys = c("TESTNUM")
)
})
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