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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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8
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -30,9 +30,9 @@
library(AMR)
library(dplyr)
int_resis <- data.frame(mo = microorganisms$mo, stringsAsFactors = FALSE)
for (i in seq_len(nrow(antibiotics))) {
for (i in seq_len(nrow(antimicrobials))) {
int_resis$new <- as.sir("S")
colnames(int_resis)[ncol(int_resis)] <- antibiotics$ab[i]
colnames(int_resis)[ncol(int_resis)] <- antimicrobials$ab[i]
}
int_resis <- eucast_rules(int_resis,
@@ -49,14 +49,14 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.sir(x) | x == "R
select(mo, ab = name)
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
untreatable <- antimicrobials[which(antimicrobials$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
all(int_resis3$mo %in% microorganisms$mo)
all(int_resis3$ab %in% antibiotics$ab)
all(int_resis3$ab %in% antimicrobials$ab)
intrinsic_resistant <- df_remove_nonASCII(int_resis3)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")