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updated taxonomy

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dr. M.S. (Matthijs) Berends
2022-12-12 00:14:56 +01:00
parent eed1c14b96
commit 8da2467209
46 changed files with 132944 additions and 57370 deletions
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14
data-raw/reproduction_of_intrinsic_resistant.R
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@@ -50,13 +50,17 @@ int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R
# remove lab drugs
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
int_resis2 <- int_resis2 %>%
filter(!ab %in% untreatable) %>%
arrange(mo, ab)
# takes ages with filter()..., weird
int_resis3 <- int_resis2[which(!int_resis2$ab %in% untreatable), ]
class(int_resis3$ab) <- c("ab", "character")
int_resis3
intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
all(int_resis3$mo %in% microorganisms$mo)
all(int_resis3$ab %in% antibiotics$ab)
intrinsic_resistant <- df_remove_nonASCII(int_resis3)
usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")
rm(intrinsic_resistant)
# AFTER THIS:
# DO NOT FORGET TO UPDATE THE VERSION NUMBER IN mo_is_intrinsic_resistant()
# DO NOT FORGET TO UPDATE THE VERSION NUMBER IN mo_is_intrinsic_resistant() AND R/data.R