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(v0.8.0.9004) added MDR guideline by Magiorakos et al.

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dr. M.S. (Matthijs) Berends
2019-10-26 21:56:41 +02:00
parent c01dc8a5b7
commit d2e8249edd
20 changed files with 605 additions and 118 deletions
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13
data-raw/reproduction_of_antibiotics.R
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@ -305,9 +305,18 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti
antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
# High level Gentamcin and Streptomycin
antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl"))
antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl"))
antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
# add imi to imipenem
antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi"))
## new ATC codes
# ceftaroline
antibiotics[which(antibiotics$ab == "CPT"), "atc"] <- "J01DI02"
# faropenem
antibiotics[which(antibiotics$ab == "FAR"), "atc"] <- "J01DI03"
# ceftobiprole
antibiotics[which(antibiotics$ab == "BPR"), "atc"] <- "J01DI01"
antibiotics <- antibiotics %>% arrange(name)