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(v2.1.1.9182) fix AMR selectors for tidymodels, add unit tests

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dr. M.S. (Matthijs) Berends
2025-03-03 12:59:27 +01:00
parent b85890449d
commit 9a9468fa84
16 changed files with 84 additions and 33 deletions
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46
tests/testthat/test-_misc.R
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@ -45,17 +45,47 @@ expect_equal(AMR:::trimws2(" test "), "test")
expect_equal(AMR:::trimws2(" test ", "l"), "test ")
expect_equal(AMR:::trimws2(" test ", "r"), " test")
# expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
# expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
# expect_warning(AMR:::get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(AMR:::get_column_abx(example_isolates, soft_dependencies = "FUS"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
# expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
# expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
}
# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
}
# test get_current_data() ----
is_right <- FALSE
check_df <- function(check_element, return_val = 0) {
is_right <<- FALSE
for (env in sys.frames()) {
if (!is.null(env[[check_element]]) && is.data.frame(env[[check_element]])) {
is_right <<- TRUE
}
}
return_val
}
df <- example_isolates[, check_df("x")]
expect_true(is_right, info = "the environmental data cannot be found for base/x")
df <- example_isolates[c(1:3), check_df("x")]
expect_true(is_right, info = "the environmental data cannot be found for base/x")
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
df <- example_isolates %>% select(mo, check_df("data123"))
expect_false(is_right, info = "just a check if non-sense is not being gathered by get_current_data()")
df <- example_isolates %>% select(mo, check_df(".data"))
expect_true(is_right, info = "the environmental data cannot be found for dplyr/select()")
df <- example_isolates %>% select_at(check_df(".tbl"))
expect_true(is_right, info = "the environmental data cannot be found for dplyr/select_at()")
}
if (AMR:::pkg_is_available("tidymodels", also_load = TRUE)) {
resistance_recipe <- recipe(mo ~ ., data = example_isolates) %>%
step_corr(check_df("training")) %>%
prep()
expect_true(is_right, info = "the environmental data cannot be found for tidymodels/prep()")
}