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(v2.1.1.9199) fix eucast

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-14 13:43:22 +01:00
parent e134e01418
commit 58d7aa8790
57 changed files with 143 additions and 122 deletions
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19
tests/testthat/test-eucast_rules.R
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@@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
test_that("eucast_rules works", {
test_that("test-eucast_rules.R", {
# thoroughly check input table
expect_equal(
colnames(AMR:::EUCAST_RULES_DF),
@@ -42,8 +42,14 @@ test_that("eucast_rules works", {
)
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned, keep_synonyms = TRUE, language = NULL)))
expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
MOs_test <- suppressWarnings(
trimws(paste(
mo_genus(MOs_mentioned, keep_synonyms = TRUE, language = NULL),
mo_species(MOs_mentioned, keep_synonyms = TRUE, language = NULL)
))
)
MOs_test[MOs_test == ""] <- mo_fullname(MOs_mentioned[MOs_test == ""], keep_synonyms = TRUE, language = NULL)
expect_equal(MOs_mentioned, MOs_test)
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))
@@ -108,7 +114,7 @@ test_that("eucast_rules works", {
TIC = as.sir("R"),
PIP = as.sir("S")
) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE, overwrite = TRUE) %>%
pull(PIP) %>%
unique() %>%
as.character()
@@ -127,6 +133,7 @@ test_that("eucast_rules works", {
stringsAsFactors = FALSE
),
version_expertrules = 3.1,
overwrite = TRUE,
only_sir_columns = FALSE
)$CLR))
b <- example_isolates$ERY
@@ -168,6 +175,7 @@ test_that("eucast_rules works", {
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = TRUE,
overwrite = TRUE,
info = FALSE
)$cefotax,
as.sir(c("S", "R"))
@@ -180,6 +188,7 @@ test_that("eucast_rules works", {
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NA,
overwrite = TRUE,
info = FALSE
)$cefotax,
as.sir(c("S", NA))
@@ -192,6 +201,7 @@ test_that("eucast_rules works", {
cefotax = as.sir(c("S", "S"))
),
ampc_cephalosporin_resistance = NULL,
overwrite = TRUE,
info = FALSE
)$cefotax,
as.sir(c("S", "S"))
@@ -218,6 +228,7 @@ test_that("eucast_rules works", {
rules = "custom",
custom_rules = x,
info = FALSE,
overwrite = TRUE,
verbose = TRUE
)),
8,