mirror of
https://github.com/msberends/AMR.git
synced 2025-07-11 09:41:57 +02:00
(v2.1.1.9186) replace antibiotics with antimicrobials!
This commit is contained in:
@ -27,83 +27,85 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
|
||||
expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
|
||||
expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))
|
||||
test_that("count works", {
|
||||
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
|
||||
expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
|
||||
expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))
|
||||
|
||||
# AMX resistance in `example_isolates`
|
||||
expect_equal(count_R(example_isolates$AMX), 804)
|
||||
expect_equal(count_I(example_isolates$AMX), 3)
|
||||
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
|
||||
expect_equal(
|
||||
count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
|
||||
suppressWarnings(count_IR(example_isolates$AMX))
|
||||
)
|
||||
expect_equal(
|
||||
suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
|
||||
count_SI(example_isolates$AMX)
|
||||
)
|
||||
|
||||
# warning for speed loss
|
||||
# expect_warning(count_resistant(as.character(example_isolates$AMC)))
|
||||
|
||||
# expect_warning(count_resistant(example_isolates$AMC, as.character(example_isolates$GEN)))
|
||||
|
||||
# check for errors
|
||||
expect_error(count_resistant("test", minimum = "test"))
|
||||
expect_error(count_resistant("test", as_percent = "test"))
|
||||
expect_error(count_susceptible("test", minimum = "test"))
|
||||
expect_error(count_susceptible("test", as_percent = "test"))
|
||||
|
||||
expect_error(count_df(c("A", "B", "C")))
|
||||
expect_error(count_df(example_isolates[, "date", drop = TRUE]))
|
||||
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
|
||||
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
|
||||
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
|
||||
expect_identical(
|
||||
example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
|
||||
example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
|
||||
example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)
|
||||
# AMX resistance in `example_isolates`
|
||||
expect_equal(count_R(example_isolates$AMX), 804)
|
||||
expect_equal(count_I(example_isolates$AMX), 3)
|
||||
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
|
||||
expect_equal(
|
||||
count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
|
||||
suppressWarnings(count_IR(example_isolates$AMX))
|
||||
)
|
||||
expect_equal(
|
||||
suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
|
||||
count_SI(example_isolates$AMX)
|
||||
)
|
||||
|
||||
# count of cases
|
||||
expect_equal(
|
||||
example_isolates %>%
|
||||
# warning for speed loss
|
||||
# expect_warning(count_resistant(as.character(example_isolates$AMC)))
|
||||
|
||||
# expect_warning(count_resistant(example_isolates$AMC, as.character(example_isolates$GEN)))
|
||||
|
||||
# check for errors
|
||||
expect_error(count_resistant("test", minimum = "test"))
|
||||
expect_error(count_resistant("test", as_percent = "test"))
|
||||
expect_error(count_susceptible("test", minimum = "test"))
|
||||
expect_error(count_susceptible("test", as_percent = "test"))
|
||||
|
||||
expect_error(count_df(c("A", "B", "C")))
|
||||
expect_error(count_df(example_isolates[, "date", drop = TRUE]))
|
||||
|
||||
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
|
||||
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
|
||||
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
|
||||
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
|
||||
expect_identical(
|
||||
example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
|
||||
example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
|
||||
example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)
|
||||
)
|
||||
|
||||
# count of cases
|
||||
expect_equal(
|
||||
example_isolates %>%
|
||||
group_by(ward) %>%
|
||||
summarise(
|
||||
cipro = count_susceptible(CIP),
|
||||
genta = count_susceptible(GEN),
|
||||
combination = count_susceptible(CIP, GEN)
|
||||
) %>%
|
||||
pull(combination),
|
||||
c(946, 428, 94)
|
||||
)
|
||||
|
||||
# count_df
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
|
||||
c(
|
||||
example_isolates$AMX %>% count_susceptible(),
|
||||
example_isolates$AMX %>% count_resistant()
|
||||
)
|
||||
)
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
|
||||
c(
|
||||
suppressWarnings(example_isolates$AMX %>% count_S()),
|
||||
example_isolates$AMX %>% count_I(),
|
||||
example_isolates$AMX %>% count_R()
|
||||
)
|
||||
)
|
||||
|
||||
# grouping in sir_calc_df() (= backbone of sir_df())
|
||||
expect_true("ward" %in% (example_isolates %>%
|
||||
group_by(ward) %>%
|
||||
summarise(
|
||||
cipro = count_susceptible(CIP),
|
||||
genta = count_susceptible(GEN),
|
||||
combination = count_susceptible(CIP, GEN)
|
||||
) %>%
|
||||
pull(combination),
|
||||
c(946, 428, 94)
|
||||
)
|
||||
|
||||
# count_df
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
|
||||
c(
|
||||
example_isolates$AMX %>% count_susceptible(),
|
||||
example_isolates$AMX %>% count_resistant()
|
||||
)
|
||||
)
|
||||
expect_equal(
|
||||
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
|
||||
c(
|
||||
suppressWarnings(example_isolates$AMX %>% count_S()),
|
||||
example_isolates$AMX %>% count_I(),
|
||||
example_isolates$AMX %>% count_R()
|
||||
)
|
||||
)
|
||||
|
||||
# grouping in sir_calc_df() (= backbone of sir_df())
|
||||
expect_true("ward" %in% (example_isolates %>%
|
||||
group_by(ward) %>%
|
||||
select(ward, AMX, CIP, gender) %>%
|
||||
sir_df() %>%
|
||||
colnames()))
|
||||
}
|
||||
select(ward, AMX, CIP, gender) %>%
|
||||
sir_df() %>%
|
||||
colnames()))
|
||||
}
|
||||
})
|
||||
|
||||
Reference in New Issue
Block a user