Nothing
# diagTab ----
test_that("diagTab function works as expected with default settings", {
data("qualData")
res <- qualData %>% diagTab(formula = ~ CandidateN + ComparativeN)
expect_s4_class(res, "MCTab")
expect_equal(matrix(res@tab), matrix(c(54, 8, 16, 122)))
expect_equal(res@levels, c("0", "1"))
})
test_that("diagTab function works as expected for qualitative performance", {
data("qualData")
res <- qualData %>%
diagTab(
formula = ~ CandidateN + ComparativeN,
levels = c(1, 0)
)
expect_equal(matrix(res@tab), matrix(c(122, 16, 8, 54)))
})
test_that("diagTab function works as expected for within-reader performance", {
data("PDL1RP")
res <- PDL1RP$wtn_reader %>%
diagTab(
formula = Order ~ Value,
bysort = "Sample",
levels = c("Positive", "Negative"),
rep = TRUE,
across = "Site"
)
expect_equal(matrix(res@tab), matrix(c(203, 17, 7, 223)))
})
test_that("diagTab function works as expected for between-reader performance", {
data("PDL1RP")
res <- PDL1RP$btw_reader %>%
diagTab(
formula = Reader ~ Value,
bysort = "Sample",
levels = c("Positive", "Negative"),
rep = TRUE,
across = "Site"
)
expect_equal(matrix(res@tab), matrix(c(200, 15, 7, 228)))
})
test_that("diagTab function works as expected for between-site performance", {
data("PDL1RP")
res <- PDL1RP$btw_site %>%
diagTab(
formula = Site ~ Value,
bysort = "Sample",
levels = c("Positive", "Negative"),
rep = TRUE
)
expect_equal(matrix(res@tab), matrix(c(201, 12, 4, 233)))
})
# getAccuracy ----
test_that("getAccuracy function works as expected with wilson method", {
data("qualData")
res <- qualData %>%
diagTab(
formula = ~ CandidateN + ComparativeN,
levels = c(1, 0)
) %>%
getAccuracy(ref = "r", r_ci = "wilson")
object <- matrix(
c(
"0.8841", "0.8200", "0.9274",
"0.8710", "0.7655", "0.9331",
"0.9385", "0.8833", "0.9685",
"0.7714", "0.6605", "0.8541",
"6.8514", "3.5785", "13.1181",
"0.1331", "0.0832", "0.2131"
),
nrow = 6, byrow = TRUE,
dimnames = list(
c("sens", "spec", "ppv", "npv", "plr", "nlr"),
ComparativeN = c("EST", "LowerCI", "UpperCI")
)
)
expect_equal(res, as.data.frame(object))
})
test_that("getAccuracy function works as expected without reference", {
data("qualData")
res <- qualData %>%
diagTab(
formula = ~ CandidateN + ComparativeN,
levels = c(1, 0)
) %>%
getAccuracy(ref = "nr", nr_ci = "wilson")
object <- matrix(
c(
"0.8841", "0.8200", "0.9274",
"0.8710", "0.7655", "0.9331",
"0.8800", "0.8277", "0.9180",
"0.7291", "0.6283", "0.8299"
),
nrow = 4, byrow = TRUE,
dimnames = list(
c("ppa", "npa", "opa", "kappa"),
ComparativeN = c("EST", "LowerCI", "UpperCI")
)
)
expect_equal(res, as.data.frame(object))
})
test_that("getAccuracy function works as expected with digits is 3", {
data("qualData")
res <- qualData %>%
diagTab(
formula = ~ CandidateN + ComparativeN,
levels = c(1, 0)
) %>%
getAccuracy(ref = "r", r_ci = "wilson", digits = 3)
object <- matrix(
c(
"0.884", "0.820", "0.927",
"0.871", "0.766", "0.933",
"0.938", "0.883", "0.968",
"0.771", "0.660", "0.854",
"6.851", "3.578", "13.118",
"0.133", "0.083", "0.213"
),
nrow = 6, byrow = TRUE,
dimnames = list(
c("sens", "spec", "ppv", "npv", "plr", "nlr"),
ComparativeN = c("EST", "LowerCI", "UpperCI")
)
)
expect_equal(res, as.data.frame(object))
})
test_that("getAccuracy function works as expected with between-readers precision", {
data("PDL1RP")
res <- PDL1RP$btw_reader %>%
diagTab(
formula = Reader ~ Value,
bysort = "Sample",
levels = c("Positive", "Negative"),
rep = TRUE,
across = "Site"
) %>%
getAccuracy(ref = "bnr", rng.seed = 12306)
object <- matrix(
c(
"0.9479", "0.9260", "0.9686",
"0.9540", "0.9342", "0.9730",
"0.9511", "0.9311", "0.9711"
),
nrow = 3, byrow = TRUE,
dimnames = list(
c("apa", "ana", "opa"),
ComparativeN = c("EST", "LowerCI", "UpperCI")
)
)
expect_equal(res, as.data.frame(object))
})
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