tests/testthat/test-derive_vars_cat.R
In Roche-GSK/admiral: ADaM in R Asset Library
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "<160", 2,
"01-701-1023", "Height", 162.56, ">=160", 1,
"01-701-1028", "Height", 177.8, ">=160", 1,
"01-701-1033", "Height", 175.26, ">=160", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, ">=160", 1,
"01-701-1111", "Height", 158.24, "<160", 2,
"01-701-1115", "Height", 181.61, ">=160", 1,
"01-701-1118", "Height", 180.34, ">=160", 1,
"01-701-1015", "Weight", 53.98, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA
)
advs <- expected_result %>% select(
USUBJID, VSTEST, AVAL
)
## Test 1: Basic functionality without by_vars ----
test_that("derive_vars_cat Test 1: Basic functionality without by_vars", {
# Define the condition and categories
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL >= 160, ">=160", 1,
VSTEST == "Height" & AVAL < 160, "<160", 2
)
expect_dfs_equal(
base =
derive_vars_cat(
advs,
definition
),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 2: Basic functionality with by_vars ----
test_that("derive_vars_cat Test 2: Basic functionality with by_vars", {
# Define the condition and categories
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_dfs_equal(
base =
derive_vars_cat(
advs,
definition,
by_vars = exprs(VSTEST)
),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 3: Forgot to specify by_vars ----
test_that("derive_vars_cat Test 3: Forgot to specify by_vars", {
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_snapshot_warning(derive_vars_cat(advs, definition))
})
## Test 4: Error when dataset is not a dataframe ----
test_that("derive_vars_cat Test 4: Error when dataset is not a dataframe", {
# Define the condition and categories
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL >= 160, ">=160", 1,
VSTEST == "Height" & AVAL < 160, "<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(list(1, 2, 3), definition),
class = "assert_data_frame"
)
})
## Test 5: Error when definition is not an exprs object ----
test_that("derive_vars_cat Test 5: Error when definition is not an exprs object", {
definition <- tribble(
~condition, ~AVALCAT1, ~AVALCA1N,
"AVAL >= 160", ">=160", 1,
"AVAL < 160", "<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(advs, definition),
class = "assert_expr_list"
)
})
## Test 6: Error when required columns are missing from dataset ----
test_that("derive_vars_cat Test 6: Error when required columns are missing from dataset", {
# Define the condition and categories (without VSTEST in the dataset)
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
# Remove VSTEST column from dataset
advs_missing_col <- advs %>% select(-VSTEST)
# Snapshot the error message
expect_error(
derive_vars_cat(advs_missing_col, definition, by_vars = exprs(VSTEST)),
class = "assert_data_frame"
)
})
## Test 7: Correct behavior when no conditions are met ----
test_that("derive_vars_cat Test 7: Correct behavior when no conditions are met", {
# Define conditions that do not match any rows
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL < 0, "<0", 1
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, NA_character_, NA_real_,
"01-701-1023", "Height", 162.56, NA_character_, NA_real_,
"01-701-1028", "Height", 177.8, NA_character_, NA_real_,
"01-701-1033", "Height", 175.26, NA_character_, NA_real_,
"01-701-1034", "Height", NA, NA_character_, NA_real_,
"01-701-1047", "Height", NA, NA_character_, NA_real_,
"01-701-1097", "Height", 168.91, NA_character_, NA_real_,
"01-701-1111", "Height", 158.24, NA_character_, NA_real_,
"01-701-1115", "Height", 181.61, NA_character_, NA_real_,
"01-701-1118", "Height", 180.34, NA_character_, NA_real_,
"01-701-1015", "Weight", 53.98, NA_character_, NA_real_,
"01-701-1023", "Weight", 78.47, NA_character_, NA_real_,
"01-701-1028", "Weight", 98.88, NA_character_, NA_real_,
"01-701-1033", "Weight", 88.45, NA_character_, NA_real_,
"01-701-1034", "Weight", NA, NA_character_, NA_real_,
"01-701-1047", "Weight", NA, NA_character_, NA_real_,
"01-701-1097", "Weight", 78.02, NA_character_, NA_real_,
"01-701-1111", "Weight", 60.33, NA_character_, NA_real_,
"01-701-1115", "Weight", 78.7, NA_character_, NA_real_,
"01-701-1118", "Weight", 71.67, NA_character_, NA_real_
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 8: Overlapping conditions handled correctly ----
test_that("derive_vars_cat Test 8: Overlapping conditions handled correctly", {
# Define overlapping conditions
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL < 160, "<160", 3,
"Height", AVAL < 170, "<170", 2,
"Height", AVAL >= 170, ">=170", 1
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "<160", 3,
"01-701-1023", "Height", 162.56, "<170", 2,
"01-701-1028", "Height", 177.8, ">=170", 1,
"01-701-1033", "Height", 175.26, ">=170", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, "<170", 2,
"01-701-1111", "Height", 158.24, "<160", 3,
"01-701-1115", "Height", 181.61, ">=170", 1,
"01-701-1118", "Height", 180.34, ">=170", 1,
"01-701-1015", "Weight", 53.98, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 9: Error when condition is missing from `definition` ----
test_that("derive_vars_cat Test 9: Error when condition is missing from `definition`", {
# Define the condition but omit the 'condition' column from the definition
definition <- exprs(
~AVALCAT1, ~AVALCA1N,
">=160", 1,
"<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(advs, definition),
class = "assert_data_frame"
)
})
## Test 10: Conditions for multiple VSTESTs (Height and Weight) ----
test_that("derive_vars_cat Test 10: Conditions for multiple VSTESTs (Height and Weight)", {
# Define conditions for two different VSTEST values: Height and BILI
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, "Height >= 160", 1,
"Height", AVAL < 160, "Height < 160", 2,
"Weight", AVAL >= 66.68, "Weight >= 66.68", 1,
"Weight", AVAL < 66.68, "Weight < 66.68", 2
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "Height < 160", 2,
"01-701-1023", "Height", 162.56, "Height >= 160", 1,
"01-701-1028", "Height", 177.8, "Height >= 160", 1,
"01-701-1033", "Height", 175.26, "Height >= 160", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, "Height >= 160", 1,
"01-701-1111", "Height", 158.24, "Height < 160", 2,
"01-701-1115", "Height", 181.61, "Height >= 160", 1,
"01-701-1118", "Height", 180.34, "Height >= 160", 1,
"01-701-1015", "Weight", 53.98, "Weight < 66.68", 2,
"01-701-1023", "Weight", 78.47, "Weight >= 66.68", 1,
"01-701-1028", "Weight", 98.88, "Weight >= 66.68", 1,
"01-701-1033", "Weight", 88.45, "Weight >= 66.68", 1,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, "Weight >= 66.68", 1,
"01-701-1111", "Weight", 60.33, "Weight < 66.68", 2,
"01-701-1115", "Weight", 78.7, "Weight >= 66.68", 1,
"01-701-1118", "Weight", 71.67, "Weight >= 66.68", 1
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 11: Adding an extra variable (flag) to the dataset ----
test_that("derive_vars_cat Test 11: Adding an extra variable (flag) to the dataset", {
# Define conditions and add a third variable (flag) that is TRUE or FALSE
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, ~extra_var,
"Height", AVAL >= 160, ">=160", 1, TRUE,
"Height", AVAL < 160, "<160", 2, FALSE
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N, ~extra_var,
"01-701-1015", "Height", 147.32, "<160", 2, FALSE,
"01-701-1023", "Height", 162.56, ">=160", 1, TRUE,
"01-701-1028", "Height", 177.8, ">=160", 1, TRUE,
"01-701-1033", "Height", 175.26, ">=160", 1, TRUE,
"01-701-1034", "Height", NA, NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA, NA,
"01-701-1097", "Height", 168.91, ">=160", 1, TRUE,
"01-701-1111", "Height", 158.24, "<160", 2, FALSE,
"01-701-1115", "Height", 181.61, ">=160", 1, TRUE,
"01-701-1118", "Height", 180.34, ">=160", 1, TRUE,
"01-701-1015", "Weight", 53.98, NA, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA, NA,
"01-701-1034", "Weight", NA, NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA, NA
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 12: Wrong input for by_vars ----
test_that("derive_vars_cat Test 12: Wrong input for by_vars", {
# Define conditions
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_error(derive_vars_cat(advs, definition, by_vars = exprs(VSTEST == "Height")),
class = "assert_vars"
)
})
## Test 13: definition has wrong shape ----
test_that("derive_vars_cat Test 13: definition has wrong shape", {
# Define conditions
definition_wrong_shape <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160"
)
expect_snapshot_error(derive_vars_cat(advs, definition_wrong_shape, by_vars = exprs(VSTEST)))
})
## Test 14: two by_vars variables ----
test_that("derive_vars_cat Test 14: two by_vars variables", {
# Define conditions
definition <- exprs(
~VISIT, ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Week 24", "Height", AVAL >= 160, ">=160", 1,
"Week 24", "Height", AVAL < 160, "<160", 2,
)
advs_visit <- advs %>% mutate(
VISIT = "Week 24"
)
expect_snapshot_error(derive_vars_cat(advs_visit, definition, by_vars = exprs(VSTEST, VISIT)))
})
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expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "<160", 2,
"01-701-1023", "Height", 162.56, ">=160", 1,
"01-701-1028", "Height", 177.8, ">=160", 1,
"01-701-1033", "Height", 175.26, ">=160", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, ">=160", 1,
"01-701-1111", "Height", 158.24, "<160", 2,
"01-701-1115", "Height", 181.61, ">=160", 1,
"01-701-1118", "Height", 180.34, ">=160", 1,
"01-701-1015", "Weight", 53.98, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA
)
advs <- expected_result %>% select(
USUBJID, VSTEST, AVAL
)
## Test 1: Basic functionality without by_vars ----
test_that("derive_vars_cat Test 1: Basic functionality without by_vars", {
# Define the condition and categories
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL >= 160, ">=160", 1,
VSTEST == "Height" & AVAL < 160, "<160", 2
)
expect_dfs_equal(
base =
derive_vars_cat(
advs,
definition
),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 2: Basic functionality with by_vars ----
test_that("derive_vars_cat Test 2: Basic functionality with by_vars", {
# Define the condition and categories
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_dfs_equal(
base =
derive_vars_cat(
advs,
definition,
by_vars = exprs(VSTEST)
),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 3: Forgot to specify by_vars ----
test_that("derive_vars_cat Test 3: Forgot to specify by_vars", {
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_snapshot_warning(derive_vars_cat(advs, definition))
})
## Test 4: Error when dataset is not a dataframe ----
test_that("derive_vars_cat Test 4: Error when dataset is not a dataframe", {
# Define the condition and categories
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL >= 160, ">=160", 1,
VSTEST == "Height" & AVAL < 160, "<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(list(1, 2, 3), definition),
class = "assert_data_frame"
)
})
## Test 5: Error when definition is not an exprs object ----
test_that("derive_vars_cat Test 5: Error when definition is not an exprs object", {
definition <- tribble(
~condition, ~AVALCAT1, ~AVALCA1N,
"AVAL >= 160", ">=160", 1,
"AVAL < 160", "<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(advs, definition),
class = "assert_expr_list"
)
})
## Test 6: Error when required columns are missing from dataset ----
test_that("derive_vars_cat Test 6: Error when required columns are missing from dataset", {
# Define the condition and categories (without VSTEST in the dataset)
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
# Remove VSTEST column from dataset
advs_missing_col <- advs %>% select(-VSTEST)
# Snapshot the error message
expect_error(
derive_vars_cat(advs_missing_col, definition, by_vars = exprs(VSTEST)),
class = "assert_data_frame"
)
})
## Test 7: Correct behavior when no conditions are met ----
test_that("derive_vars_cat Test 7: Correct behavior when no conditions are met", {
# Define conditions that do not match any rows
definition <- exprs(
~condition, ~AVALCAT1, ~AVALCA1N,
VSTEST == "Height" & AVAL < 0, "<0", 1
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, NA_character_, NA_real_,
"01-701-1023", "Height", 162.56, NA_character_, NA_real_,
"01-701-1028", "Height", 177.8, NA_character_, NA_real_,
"01-701-1033", "Height", 175.26, NA_character_, NA_real_,
"01-701-1034", "Height", NA, NA_character_, NA_real_,
"01-701-1047", "Height", NA, NA_character_, NA_real_,
"01-701-1097", "Height", 168.91, NA_character_, NA_real_,
"01-701-1111", "Height", 158.24, NA_character_, NA_real_,
"01-701-1115", "Height", 181.61, NA_character_, NA_real_,
"01-701-1118", "Height", 180.34, NA_character_, NA_real_,
"01-701-1015", "Weight", 53.98, NA_character_, NA_real_,
"01-701-1023", "Weight", 78.47, NA_character_, NA_real_,
"01-701-1028", "Weight", 98.88, NA_character_, NA_real_,
"01-701-1033", "Weight", 88.45, NA_character_, NA_real_,
"01-701-1034", "Weight", NA, NA_character_, NA_real_,
"01-701-1047", "Weight", NA, NA_character_, NA_real_,
"01-701-1097", "Weight", 78.02, NA_character_, NA_real_,
"01-701-1111", "Weight", 60.33, NA_character_, NA_real_,
"01-701-1115", "Weight", 78.7, NA_character_, NA_real_,
"01-701-1118", "Weight", 71.67, NA_character_, NA_real_
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 8: Overlapping conditions handled correctly ----
test_that("derive_vars_cat Test 8: Overlapping conditions handled correctly", {
# Define overlapping conditions
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL < 160, "<160", 3,
"Height", AVAL < 170, "<170", 2,
"Height", AVAL >= 170, ">=170", 1
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "<160", 3,
"01-701-1023", "Height", 162.56, "<170", 2,
"01-701-1028", "Height", 177.8, ">=170", 1,
"01-701-1033", "Height", 175.26, ">=170", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, "<170", 2,
"01-701-1111", "Height", 158.24, "<160", 3,
"01-701-1115", "Height", 181.61, ">=170", 1,
"01-701-1118", "Height", 180.34, ">=170", 1,
"01-701-1015", "Weight", 53.98, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 9: Error when condition is missing from `definition` ----
test_that("derive_vars_cat Test 9: Error when condition is missing from `definition`", {
# Define the condition but omit the 'condition' column from the definition
definition <- exprs(
~AVALCAT1, ~AVALCA1N,
">=160", 1,
"<160", 2
)
# Snapshot the error message
expect_error(
derive_vars_cat(advs, definition),
class = "assert_data_frame"
)
})
## Test 10: Conditions for multiple VSTESTs (Height and Weight) ----
test_that("derive_vars_cat Test 10: Conditions for multiple VSTESTs (Height and Weight)", {
# Define conditions for two different VSTEST values: Height and BILI
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, "Height >= 160", 1,
"Height", AVAL < 160, "Height < 160", 2,
"Weight", AVAL >= 66.68, "Weight >= 66.68", 1,
"Weight", AVAL < 66.68, "Weight < 66.68", 2
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N,
"01-701-1015", "Height", 147.32, "Height < 160", 2,
"01-701-1023", "Height", 162.56, "Height >= 160", 1,
"01-701-1028", "Height", 177.8, "Height >= 160", 1,
"01-701-1033", "Height", 175.26, "Height >= 160", 1,
"01-701-1034", "Height", NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA,
"01-701-1097", "Height", 168.91, "Height >= 160", 1,
"01-701-1111", "Height", 158.24, "Height < 160", 2,
"01-701-1115", "Height", 181.61, "Height >= 160", 1,
"01-701-1118", "Height", 180.34, "Height >= 160", 1,
"01-701-1015", "Weight", 53.98, "Weight < 66.68", 2,
"01-701-1023", "Weight", 78.47, "Weight >= 66.68", 1,
"01-701-1028", "Weight", 98.88, "Weight >= 66.68", 1,
"01-701-1033", "Weight", 88.45, "Weight >= 66.68", 1,
"01-701-1034", "Weight", NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA,
"01-701-1097", "Weight", 78.02, "Weight >= 66.68", 1,
"01-701-1111", "Weight", 60.33, "Weight < 66.68", 2,
"01-701-1115", "Weight", 78.7, "Weight >= 66.68", 1,
"01-701-1118", "Weight", 71.67, "Weight >= 66.68", 1
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 11: Adding an extra variable (flag) to the dataset ----
test_that("derive_vars_cat Test 11: Adding an extra variable (flag) to the dataset", {
# Define conditions and add a third variable (flag) that is TRUE or FALSE
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N, ~extra_var,
"Height", AVAL >= 160, ">=160", 1, TRUE,
"Height", AVAL < 160, "<160", 2, FALSE
)
expected_result <- tibble::tribble(
~USUBJID, ~VSTEST, ~AVAL, ~AVALCAT1, ~AVALCA1N, ~extra_var,
"01-701-1015", "Height", 147.32, "<160", 2, FALSE,
"01-701-1023", "Height", 162.56, ">=160", 1, TRUE,
"01-701-1028", "Height", 177.8, ">=160", 1, TRUE,
"01-701-1033", "Height", 175.26, ">=160", 1, TRUE,
"01-701-1034", "Height", NA, NA, NA, NA,
"01-701-1047", "Height", NA, NA, NA, NA,
"01-701-1097", "Height", 168.91, ">=160", 1, TRUE,
"01-701-1111", "Height", 158.24, "<160", 2, FALSE,
"01-701-1115", "Height", 181.61, ">=160", 1, TRUE,
"01-701-1118", "Height", 180.34, ">=160", 1, TRUE,
"01-701-1015", "Weight", 53.98, NA, NA, NA,
"01-701-1023", "Weight", 78.47, NA, NA, NA,
"01-701-1028", "Weight", 98.88, NA, NA, NA,
"01-701-1033", "Weight", 88.45, NA, NA, NA,
"01-701-1034", "Weight", NA, NA, NA, NA,
"01-701-1047", "Weight", NA, NA, NA, NA,
"01-701-1097", "Weight", 78.02, NA, NA, NA,
"01-701-1111", "Weight", 60.33, NA, NA, NA,
"01-701-1115", "Weight", 78.7, NA, NA, NA,
"01-701-1118", "Weight", 71.67, NA, NA, NA
)
expect_dfs_equal(
base = derive_vars_cat(advs, definition, by_vars = exprs(VSTEST)),
compare = expected_result,
keys = c("USUBJID", "VSTEST")
)
})
## Test 12: Wrong input for by_vars ----
test_that("derive_vars_cat Test 12: Wrong input for by_vars", {
# Define conditions
definition <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160", 2
)
expect_error(derive_vars_cat(advs, definition, by_vars = exprs(VSTEST == "Height")),
class = "assert_vars"
)
})
## Test 13: definition has wrong shape ----
test_that("derive_vars_cat Test 13: definition has wrong shape", {
# Define conditions
definition_wrong_shape <- exprs(
~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Height", AVAL >= 160, ">=160", 1,
"Height", AVAL < 160, "<160"
)
expect_snapshot_error(derive_vars_cat(advs, definition_wrong_shape, by_vars = exprs(VSTEST)))
})
## Test 14: two by_vars variables ----
test_that("derive_vars_cat Test 14: two by_vars variables", {
# Define conditions
definition <- exprs(
~VISIT, ~VSTEST, ~condition, ~AVALCAT1, ~AVALCA1N,
"Week 24", "Height", AVAL >= 160, ">=160", 1,
"Week 24", "Height", AVAL < 160, "<160", 2,
)
advs_visit <- advs %>% mutate(
VISIT = "Week 24"
)
expect_snapshot_error(derive_vars_cat(advs_visit, definition, by_vars = exprs(VSTEST, VISIT)))
})
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