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(v2.1.1.9041) antibiotics update

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dr. M.S. (Matthijs) Berends
2024-06-08 17:35:25 +02:00
parent e2acc513a5
commit af74e1d4f2
26 changed files with 110 additions and 67 deletions
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12
data-raw/reproduction_of_antibiotics.R
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@ -735,6 +735,18 @@ antibiotics <- antibiotics %>%
))
antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones"
# add clindamycin inducible screening
clin <- antibiotics |>
filter(ab == "FOX1") |>
mutate(ab = as.character("CLI1"),
name = "Clindamycin inducible screening",
group = "Macrolides/lincosamides")
antibiotics <- antibiotics |>
mutate(ab = as.character(ab)) |>
bind_rows(clin)
class(antibiotics$ab) <- c("ab", "character")
antibiotics[which(antibiotics$ab == "CLI1"), "abbreviations"][[1]] <- list(c("clindamycin inducible", "clinda inducible", "clin inducible"))
# add pretomanid
antibiotics <- antibiotics %>%
mutate(ab = as.character(ab)) %>%