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(v0.7.1.9008) ab update

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dr. M.S. (Matthijs) Berends
2019-07-04 19:08:18 +02:00
parent c57ad26c5b
commit d9e257f8db
10 changed files with 19 additions and 12 deletions
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5
data-raw/reproduction_of_antibiotics.R
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@ -289,6 +289,8 @@ antibiotics <- filter(antibiotics, ab != "MOX")
antibiotics <- filter(antibiotics, ab != "RFP")
antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
# Rifampicin is better known as a drug than Rifampin (Rifampin is still listed as a brand name), so:
antibiotics[which(antibiotics$ab == "RIF"), "name"] <- "Rifampicin"
# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
antibiotics <- filter(antibiotics, ab != "PME")
antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
@ -300,8 +302,9 @@ 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"))
antibiotics <- antibiotics %>% arrange(name)
class(antibiotics$ab) <- "ab"
class(antibiotics$atc) <- "atc"
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, overwrite = TRUE)