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(v2.1.1.9192) fix fluoroquinolones and add bleomycin
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@ -397,7 +397,8 @@ pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
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pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
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filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
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# see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
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filter((group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|piromidic|pipemidic|rosoxacin") %>%
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pull(ab)
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pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
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filter(group %like% "glycopeptide") %>%
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@ -432,7 +433,7 @@ pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
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filter(group %like% "polymyxin") %>%
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pull(ab)
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pre_commit_lst$AB_QUINOLONES <- antimicrobials %>%
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filter(group %like% "quinolone") %>%
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filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") %>%
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pull(ab)
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pre_commit_lst$AB_RIFAMYCINS <- antimicrobials %>%
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filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
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