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(v2.1.1.9192) fix fluoroquinolones and add bleomycin

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dr. M.S. (Matthijs) Berends
2025-03-10 17:04:35 +01:00
parent 32024e597a
commit 067a8aca66
26 changed files with 86 additions and 81 deletions
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data-raw/_pre_commit_checks.R
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@ -397,7 +397,8 @@ pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
# see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
filter((group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|piromidic|pipemidic|rosoxacin") %>%
pull(ab)
pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
filter(group %like% "glycopeptide") %>%
@ -432,7 +433,7 @@ pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
filter(group %like% "polymyxin") %>%
pull(ab)
pre_commit_lst$AB_QUINOLONES <- antimicrobials %>%
filter(group %like% "quinolone") %>%
filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") %>%
pull(ab)
pre_commit_lst$AB_RIFAMYCINS <- antimicrobials %>%
filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%