mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:46:11 +01:00
add unit tests
This commit is contained in:
parent
a5a4354651
commit
967ee86757
@ -18,6 +18,7 @@ test_that("G-test works", {
|
||||
expected = 0.01787343,
|
||||
tolerance = 0.00000001)
|
||||
|
||||
|
||||
# INDEPENDENCE
|
||||
|
||||
x <- matrix(data = round(runif(4) * 100000, 0),
|
||||
@ -26,4 +27,8 @@ test_that("G-test works", {
|
||||
expect_lt(g.test(x)$p.value,
|
||||
1)
|
||||
|
||||
expect_warning(g.test(x = c(772, 1611, 737),
|
||||
y = c(780, 1560, 780),
|
||||
rescale.p = TRUE))
|
||||
|
||||
})
|
||||
|
@ -35,12 +35,56 @@ test_that("resistance works", {
|
||||
|
||||
})
|
||||
|
||||
test_that("old rsi works", {
|
||||
# amox resistance in `septic_patients` should be around 53.86%
|
||||
expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
|
||||
expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
|
||||
expect_equal(rsi_df(septic_patients,
|
||||
ab = "amox",
|
||||
info = TRUE),
|
||||
0.5756,
|
||||
tolerance = 0.0001)
|
||||
# pita+genta susceptibility around 98.09%
|
||||
expect_equal(rsi(septic_patients$pita,
|
||||
septic_patients$gent,
|
||||
interpretation = "S",
|
||||
info = TRUE),
|
||||
0.9809,
|
||||
tolerance = 0.0001)
|
||||
expect_equal(rsi_df(septic_patients,
|
||||
ab = c("pita", "gent"),
|
||||
interpretation = "S",
|
||||
info = TRUE),
|
||||
0.9809,
|
||||
tolerance = 0.0001)
|
||||
# more than 2 not allowed
|
||||
expect_error(rsi_df(septic_patients,
|
||||
ab = c("mero", "pita", "gent"),
|
||||
interpretation = "IS",
|
||||
info = TRUE))
|
||||
|
||||
# count of cases
|
||||
expect_equal(septic_patients %>%
|
||||
group_by(hospital_id) %>%
|
||||
summarise(cipro_S = rsi(cipr, interpretation = "S",
|
||||
as_percent = TRUE, warning = FALSE),
|
||||
cipro_n = n_rsi(cipr),
|
||||
genta_S = rsi(gent, interpretation = "S",
|
||||
as_percent = TRUE, warning = FALSE),
|
||||
genta_n = n_rsi(gent),
|
||||
combination_S = rsi(cipr, gent, interpretation = "S",
|
||||
as_percent = TRUE, warning = FALSE),
|
||||
combination_n = n_rsi(cipr, gent)) %>%
|
||||
pull(combination_n),
|
||||
c(138, 474, 170, 464, 183))
|
||||
})
|
||||
|
||||
test_that("prediction of rsi works", {
|
||||
amox_R <- septic_patients %>%
|
||||
filter(bactid == "ESCCOL") %>%
|
||||
rsi_predict(col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = FALSE) %>%
|
||||
info = TRUE) %>%
|
||||
pull("probR")
|
||||
# amox resistance will decrease using dataset `septic_patients`
|
||||
expect_true(amox_R[2] > amox_R[20])
|
||||
@ -65,13 +109,13 @@ test_that("prediction of rsi works", {
|
||||
model = "INVALID MODEL",
|
||||
col_ab = "amox",
|
||||
col_date = "date",
|
||||
info = FALSE))
|
||||
info = TRUE))
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
col_ab = "NOT EXISTING COLUMN",
|
||||
col_date = "date",
|
||||
info = FALSE))
|
||||
info = TRUE))
|
||||
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
|
||||
col_ab = "amox",
|
||||
col_date = "NOT EXISTING COLUMN",
|
||||
info = FALSE))
|
||||
info = TRUE))
|
||||
})
|
||||
|
Loading…
Reference in New Issue
Block a user