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(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

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dr. M.S. (Matthijs) Berends
2026-03-09 11:57:36 +01:00
parent cba315c2e7
commit 353eaa3f38
21 changed files with 61 additions and 13 deletions
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16
data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R
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@@ -972,6 +972,17 @@ antimicrobials <- antimicrobials |>
select(1:4),
)
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(
antimicrobials |>
filter(ab == "NOV") |>
mutate(ab = "CLB",
cid = 54706138,
name = "Clorobiocin") |>
select(1:4),
)
# update ATC codes from WHOCC website -------------------------------------
library(rvest)
@@ -1171,6 +1182,11 @@ for (i in 1:nrow(antimicrobials)) {
antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc))
}
}
antimicrobials$group <- unname(antimicrobials$group)
antimicrobials$atc <- unname(antimicrobials$atc)
antimicrobials$abbreviations <- unname(antimicrobials$abbreviations)
antimicrobials$synonyms <- unname(antimicrobials$synonyms)
antimicrobials$loinc <- unname(antimicrobials$loinc)
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")