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(v1.6.0.9041) filter_ab_class() fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-16 10:50:00 +02:00
parent 00496e45b7
commit 916df6e90c
41 changed files with 142 additions and 133 deletions
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10
inst/tinytest/test-eucast_rules.R
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@ -24,15 +24,15 @@
# ==================================================================== #
# thoroughly check input table
expect_equal(colnames(eucast_rules_file),
expect_equal(colnames(AMR:::eucast_rules_file),
c("if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group",
"reference.version",
"note"))
MOs_mentioned <- unique(eucast_rules_file$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_mentioned <- unique(AMR:::eucast_rules_file$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
@ -71,7 +71,7 @@ b <- data.frame(mo = c("Staphylococcus aureus",
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
if (suppressWarnings(require("dplyr"))) {
if (pkg_is_available("dplyr")) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
@ -109,7 +109,7 @@ expect_equal(
"S")
# also test norf
if (suppressWarnings(require("dplyr"))) {
if (pkg_is_available("dplyr")) {
expect_stdout(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}