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(v1.3.0.9026) eucast expert rules 3.2

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-24 00:30:11 +02:00
parent a1411ddafc
commit c19095a3d5
107 changed files with 48638 additions and 3953 deletions
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12
tests/testthat/test-eucast_rules.R
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@ -31,7 +31,12 @@ test_that("EUCAST rules work", {
"and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group",
"reference.version"))
"reference.version",
"note"))
MOs_mentioned <- unique(eucast_rules_file$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!is_possibly_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
expect_length(MOs_mentioned[MOs_test != MOs_mentioned], 0)
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))
@ -72,7 +77,7 @@ test_that("EUCAST rules work", {
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo") %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
@ -85,7 +90,8 @@ test_that("EUCAST rules work", {
ERY = example_isolates$ERY,
AZM = as.rsi("R"),
CLR = as.rsi("R"),
stringsAsFactors = FALSE))$CLR
stringsAsFactors = FALSE),
version_expertrules = 3.1)$CLR
b <- example_isolates$ERY
expect_identical(a[!is.na(b)],
b[!is.na(b)])