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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 21:01:54 +02:00

(v2.1.1.9186) replace antibiotics with antimicrobials!

This commit is contained in:
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions

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@ -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()))
}
})