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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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8
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -33,7 +33,7 @@ for (i in seq_len(nrow(antibiotics))) {
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
is.na(have_these_values) & reference.version == 3.2),
is.na(have_these_values) & reference.version == 3.3),
info = FALSE)
int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>%
@@ -41,6 +41,12 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R
filter(value == "R") %>%
select(microorganism, antibiotic = name)
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening"), "name", drop = TRUE]
int_resis2 <- int_resis2 %>%
filter(!antibiotic %in% untreatable) %>%
arrange(microorganism, antibiotic)
int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)