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(v1.3.0.9026) eucast expert rules 3.2

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dr. M.S. (Matthijs) Berends
2020-09-24 00:30:11 +02:00
parent a1411ddafc
commit c19095a3d5
107 changed files with 48638 additions and 3953 deletions
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25
data-raw/reproduction_of_antibiotics.R
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@ -543,6 +543,12 @@ old_sym <- old_sym[!old_sym %in% c("Cotrimoxazole", "Bactrimel")]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]] <- list(old_sym)
antibiotics[which(antibiotics$ab == "SXT"), "synonyms"][[1]] <- list(sort(unique(c(antibiotics[which(antibiotics$ab == "COL"), "synonyms"][[1]], "Cotrimoxazole", "Bactrimel", "Septra", "Bactrim", "Cotrimazole"))))
# Fix penicillins
antibiotics[which(antibiotics$ab == "PEN"), "abbreviations"][[1]] <- list(c("bepe", "pg", "pen", "peni", "peni g", "penicillin", "penicillin g"))
antibiotics[which(antibiotics$ab == "PEN"), "name"] <- "Benzylpenicillin"
antibiotics[which(antibiotics$ab == "PHN"), "abbreviations"][[1]] <- list(c("fepe", "peni v", "pv", "penicillin v", "PNV"))
antibiotics <- subset(antibiotics, antibiotics$ab != "PNV")
# New DDDs
antibiotics[which(antibiotics$ab == "PEN"), "iv_ddd"] <- 3.6
antibiotics[which(antibiotics$ab == "PEN"), "iv_units"] <- "g"
@ -594,6 +600,25 @@ antibiotics <- antibiotics %>%
name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)",
name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)",
TRUE ~ group))
antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones"
# update DDDs from WHOCC website
ddd_oral <- double(length = nrow(antibiotics))
ddd_iv <- double(length = nrow(antibiotics))
progress <- progress_ticker(nrow(antibiotics))
for (i in seq_len(nrow(antibiotics))) {
on.exit(close(progress))
progress$tick()
if (!is.na(antibiotics$atc[i])) {
ddd_oral[i] <- atc_online_ddd(antibiotics$atc[i], administration = "O")
ddd_iv[i] <- atc_online_ddd(antibiotics$atc[i], administration = "P") # parenteral
Sys.sleep(1)
}
}
ddd_oral[ddd_oral == 0] <- NA_real_
ddd_iv[ddd_iv == 0] <- NA_real_
antibiotics$oral_ddd <- ddd_oral
antibiotics$iv_ddd <- ddd_iv
# set as data.frame again
antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)