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(v2.1.1.9226) update intrinsic_resistant, unit test fixes

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dr. M.S. (Matthijs) Berends
2025-03-27 15:20:22 +01:00
parent e6f88241b2
commit 969a42cc8c
29 changed files with 139318 additions and 244254 deletions
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8
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -38,8 +38,9 @@ for (i in seq_len(nrow(antimicrobials))) {
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(
AMR:::EUCAST_RULES_DF,
is.na(have_these_values) & reference.version == 3.3
is.na(have_these_values) & reference.rule_group == "Expected phenotypes" & reference.version == 1.2
),
overwrite = TRUE,
info = FALSE
)
@@ -52,13 +53,14 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.sir(x) | x == "R
untreatable <- antimicrobials[which(antimicrobials$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
# takes ages with filter()..., weird
int_resis3 <- int_resis2[which(!int_resis2$ab %in% untreatable), ]
class(int_resis3$ab) <- c("ab", "character")
int_resis3$ab <- as.ab(int_resis3$ab)
int_resis3
all(int_resis3$mo %in% microorganisms$mo)
all(int_resis3$ab %in% antimicrobials$ab)
intrinsic_resistant <- df_remove_nonASCII(int_resis3)
intrinsic_resistant <- int_resis3
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
rm(intrinsic_resistant)