Nothing
context("eGFR")
test_that("creatinine_mgdl_to_uM", {
expect_equal(creatinine_mgdl_to_uM(scr_mgdl = 1), 88.4017, tol = 0.0001)
expect_warning(creatinine_mgdl_to_uM(scr_mgdl = 0.01))
})
test_that("Values that are likely to be already uM give a warning.", {
expect_warning(creatinine_mgdl_to_uM(scr_mgdl = 80))
})
test_that("egfr expected errors", {
expect_error(egfr())
expect_error(egfr(scr_uM = 1))
expect_error(egfr(age_y = 1))
expect_error(egfr(scr_uM = 1, age_y = 1, height_m = 1))
expect_error(egfr(scr_uM = 1, age_y = 1, height_m = 1, male = TRUE))
})
test_that("egfr automatic selection", {
suppressWarnings({
mdrd <- egfr_mdrd(
scr_uM = rep(240, 4),
age_y = rep(60, 4),
male = c(TRUE, TRUE, FALSE, FALSE),
black = c(TRUE, FALSE, TRUE, FALSE)
)
egfr_auto <- egfr(
scr_uM = c(rep(80, 8), rep(240, 4)),
age_y = c(rep(1, 4), rep(60, 8)),
height_m = rep(1, 12),
male = rep(c(TRUE, TRUE, FALSE, FALSE), 3),
black = rep(c(TRUE, FALSE, TRUE, FALSE), 3)
)
})
expect_equal(
egfr_auto,
c(
egfr_bedside_schwartz(
scr_uM = rep(80, 4),
height_m = rep(1, 4)
),
egfr_ckdepi(
scr_uM = rep(80, 4),
age_y = rep(60, 4),
male = c(TRUE, TRUE, FALSE, FALSE),
black = c(TRUE, FALSE, TRUE, FALSE)
),
mdrd
),
info = "eGFR method selection chooses the correct method for the data."
)
})
test_that("egfr combination of MDRD and CKD-EPI", {
suppressWarnings(
mdrd <- egfr_mdrd(scr_uM = 120, age_y = 75, male = TRUE, black = TRUE)
)
expect_equal(
expect_warning(
egfr(scr_uM = 120, age_y = 75, height_m = 1, male = TRUE, black = TRUE),
regexp = "neither"),
mean(
c(
egfr_ckdepi(scr_uM = 120, age_y = 75, male = TRUE, black = TRUE,
warn_mdrd_preferred = FALSE),
mdrd
)
),
info = "Neither value preferred, use the average"
)
expect_equal(
expect_warning(
egfr(scr_uM = 140, age_y = 20, height_m = 1, male = TRUE, black = FALSE),
regexp = "both"
),
mean(
c(
egfr_ckdepi(scr_uM = 140, age_y = 20, male = TRUE, black = FALSE,
warn_mdrd_preferred = FALSE),
egfr_mdrd(scr_uM = 140, age_y = 20, male = TRUE, black = FALSE)
)
),
info = "Both value preferred, use the average"
)
})
test_that("egfr_bedside_schwartz", {
expect_equal(egfr_bedside_schwartz(scr_uM = 80, height_m = 1),
36.2 * 100 / 80)
expect_warning(egfr_bedside_schwartz(scr_uM = 1, height_m = 1))
expect_warning(egfr_bedside_schwartz(scr_uM = 80, height_m = 100))
})
test_that("Ensure all 4 combinations of male / black work with egfr_ckdepi", {
expect_equal(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = TRUE, black = TRUE),
141 *
min(80 / 79.6, 1) ^ (-0.411) *
max(80 / 79.6, 1) ^ (-1.209) *
0.993 ^ 20 *
1 *
1.159
)
expect_equal(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = TRUE, black = FALSE),
141 *
min(80 / 79.6, 1) ^ (-0.411) *
max(80 / 79.6, 1) ^ (-1.209) *
0.993 ^ 20 *
1 *
1
)
expect_equal(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = FALSE, black = TRUE),
141 *
min(80 / 61.9, 1) ^ (-0.329) *
max(80 / 61.9, 1) ^ (-1.209) *
0.993 ^ 20 *
1.018 *
1.159
)
expect_equal(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = FALSE, black = FALSE),
141 *
min(80 / 61.9, 1) ^ (-0.329) *
max(80 / 61.9, 1) ^ (-1.209) *
0.993 ^ 20 *
1.018 *
1
)
})
test_that("Combinations of vector inputs for egfr_ckdepi", {
# Same male / female, black / not black
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, TRUE),
black = c(TRUE, TRUE)),
141 *
c(1, 60 / 79.6) ^ (-0.411) * # male
c(80 / 79.6, 1) ^ (-1.209) * # male
1 * # male
0.993 ^ 20 *
1.159 # black
)
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(FALSE, FALSE),
black = c(TRUE, TRUE)),
141 *
c(1, 60 / 61.9) ^ (-0.329) * # female
c(80 / 61.9, 1) ^ (-1.209) * # female
1.018 * # female
0.993 ^ 20 *
1.159 # black
)
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, TRUE),
black = c(FALSE, FALSE)),
141 *
c(1, 60 / 79.6) ^ (-0.411) * # male
c(80 / 79.6, 1) ^ (-1.209) * # male
1 * # male
0.993 ^ 20 *
1 # not black
)
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, TRUE),
black = c(FALSE, FALSE)),
141 *
c(1, 60 / 79.6) ^ (-0.411) * # male
c(80 / 79.6, 1) ^ (-1.209) * # male
1 * # male
0.993 ^ 20 *
1 # not black
)
# Different male / female, same black / not black
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, FALSE),
black = c(TRUE, TRUE)),
141 *
c(1, 60 / 61.9) ^ c(-0.411, -0.329) *
c(80 / 79.6, 1) ^ (-1.209) *
c(1, 1.018) *
0.993 ^ 20 *
1.159 # black
)
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(FALSE, TRUE),
black = c(FALSE, FALSE)),
141 *
c(1, 60 / 79.6) ^ c(-0.329, -0.411) *
c(80 / 61.9, 1) ^ (-1.209) *
c(1.018, 1) *
0.993 ^ 20 *
1 # not black
)
# Same male / female, different black / not black
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, TRUE),
black = c(FALSE, TRUE)),
141 *
c(1, 60 / 79.6) ^ (-0.411) * # male
c(80 / 79.6, 1) ^ (-1.209) * # male
1 * # male
0.993 ^ 20 *
c(1, 1.159)
)
expect_equal(
egfr_ckdepi(scr_uM = c(80, 60), age_y = c(20, 20), male = c(TRUE, TRUE),
black = c(TRUE, FALSE)),
141 *
c(1, 60 / 79.6) ^ (-0.411) * # male
c(80 / 79.6, 1) ^ (-1.209) * # male
1 * # male
0.993 ^ 20 *
c(1.159, 1)
)
})
test_that("egfr_cockcroft_gault", {
expect_warning(
egfr_cockcroft_gault(scr_uM = 80, age_y = 20, weight_kg = 70, male = TRUE,
idms_assay = FALSE),
regexp = "not recommended",
info = "Cockcroft-Gault is never recommended"
)
expect_equal(
expect_warning(egfr_cockcroft_gault(scr_uM = 80, age_y = 20, weight_kg = 70,
male = TRUE)),
(140 - 20) *
70 *
1 / # male
#0.85 / # female
(72 * 113.12 / 10000 * 80)
)
expect_equal(
expect_warning(egfr_cockcroft_gault(scr_uM = 80, age_y = 20, weight_kg = 70,
male = FALSE)),
(140 - 20) *
70 *
#1 / # male
0.85 / # female
(72 * 113.12 / 10000 * 80)
)
expect_equal(
expect_warning(
egfr_cockcroft_gault(scr_uM = c(80, 80), age_y = c(20, 20),
weight_kg = c(70, 70), male = c(FALSE, TRUE))),
(140 - 20) *
70 *
c(0.85, 1) /
(72 * 113.12 / 10000 * 80)
)
})
test_that("egfr_mdrd warning about output range", {
expect_warning(
egfr_mdrd(
scr_uM = 80,
age_y = 20,
male = TRUE,
black = TRUE,
idms_assay = TRUE,
warn_ckdepi_preferred = TRUE
),
regexp = "CKD-EPI is recommended",
fixed = TRUE
)
expect_silent(
egfr_mdrd(
scr_uM = 80,
age_y = 20,
male = TRUE,
black = TRUE,
idms_assay = TRUE,
warn_ckdepi_preferred = FALSE
)
)
})
test_that("egfr_mdrd scalar accuracy", {
expect_equal(
egfr_mdrd(
scr_uM = 240,
age_y = 20,
male = TRUE,
black = TRUE,
idms_assay = TRUE,
warn_ckdepi_preferred = TRUE
),
32788 *
175 / 186 * # idms
# 1 * # not idms
240 ^ (-1.154) *
20 ^ (-0.203) *
1.212 * # black
# 1 * # not black
1 # male
# 0.742 # female
)
expect_equal(
egfr_mdrd(
scr_uM = 240,
age_y = 20,
male = FALSE,
black = TRUE,
idms_assay = TRUE,
warn_ckdepi_preferred = TRUE
),
32788 *
175 / 186 * # idms
# 1 * # not idms
240 ^ (-1.154) *
20 ^ (-0.203) *
1.212 * # black
# 1 * # not black
#1 # male
0.742 # female
)
expect_equal(
egfr_mdrd(
scr_uM = 240,
age_y = 20,
male = TRUE,
black = FALSE,
idms_assay = TRUE,
warn_ckdepi_preferred = TRUE
),
32788 *
175 / 186 * # idms
# 1 * # not idms
240 ^ (-1.154) *
20 ^ (-0.203) *
# 1.212 * # black
1 * # not black
1 # male
# 0.742 # female
)
expect_equal(
egfr_mdrd(
scr_uM = 240,
age_y = 20,
male = TRUE,
black = TRUE,
idms_assay = FALSE,
warn_ckdepi_preferred = TRUE
),
32788 *
# 175 / 186 * # idms
1 * # not idms
240 ^ (-1.154) *
20 ^ (-0.203) *
1.212 * # black
# 1 * # not black
1 # male
# 0.742 # female
)
})
test_that("egfr calcs warn or adjust correctly with IDMS-calibrated assays", {
expect_warning(
egfr_bedside_schwartz(scr_uM = 80, height_m = 1, idms_assay = FALSE),
regexp = "IDMS"
)
expect_silent(
egfr_bedside_schwartz(scr_uM = 80, height_m = 1, idms_assay = TRUE)
)
expect_warning(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = TRUE, black = TRUE,
idms_assay = FALSE),
regexp = "IDMS"
)
expect_silent(
egfr_ckdepi(scr_uM = 80, age_y = 20, male = TRUE, black = TRUE,
idms_assay = TRUE)
)
expect_warning(
egfr_cockcroft_gault(scr_uM = 80, age_y = 20, weight_kg = 70, male = TRUE),
regexp = "IDMS"
)
expect_warning(
egfr_cockcroft_gault(scr_uM = 80, age_y = 20, weight_kg = 70, male = TRUE,
idms_assay = FALSE),
regexp = "not recommended",
all = TRUE
)
expect_silent(
egfr_mdrd(scr_uM = 240, age_y = 20, male = TRUE, black = TRUE,
idms_assay = TRUE)
)
expect_silent(
egfr_mdrd(scr_uM = 240, age_y = 20, male = TRUE, black = TRUE,
idms_assay = FALSE)
)
expect_true(
egfr_mdrd(scr_uM = 240, age_y = 20, male = TRUE, black = TRUE,
idms_assay = TRUE) !=
egfr_mdrd(scr_uM = 240, age_y = 20, male = TRUE, black = TRUE,
idms_assay = FALSE)
)
})
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