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(v2.1.1.9041) antibiotics update
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@ -181,10 +181,10 @@ AB_AMINOGLYCOSIDES <- antibiotics %>%
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filter(group %like% "aminoglycoside") %>%
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pull(ab)
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AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
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AB_ANTIFUNGALS <- AMR_env$AB_lookup %>%
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AB_ANTIFUNGALS <- antibiotics %>%
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filter(group %like% "antifungal") %>%
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pull(ab)
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AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>%
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AB_ANTIMYCOBACTERIALS <- antibiotics %>%
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filter(group %like% "antimycobacterial") %>%
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pull(ab)
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AB_CARBAPENEMS <- antibiotics %>%
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@ -221,7 +221,10 @@ AB_LINCOSAMIDES <- antibiotics %>%
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filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
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pull(ab)
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AB_MACROLIDES <- antibiotics %>%
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filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>%
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filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
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pull(ab)
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AB_NITROFURANS <- antibiotics %>%
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filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
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pull(ab)
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AB_OXAZOLIDINONES <- antibiotics %>%
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filter(group %like% "oxazolidinone") %>%
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@ -235,6 +238,9 @@ AB_POLYMYXINS <- antibiotics %>%
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AB_QUINOLONES <- antibiotics %>%
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filter(group %like% "quinolone") %>%
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pull(ab)
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AB_RIFAMYCINS <- antibiotics %>%
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filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
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pull(ab)
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AB_STREPTOGRAMINS <- antibiotics %>%
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filter(atc_group2 %like% "streptogramin") %>%
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pull(ab)
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@ -310,10 +316,12 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
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AB_GLYCOPEPTIDES_EXCEPT_LIPO,
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AB_LINCOSAMIDES,
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AB_MACROLIDES,
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AB_NITROFURANS,
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AB_OXAZOLIDINONES,
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AB_PENICILLINS,
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AB_POLYMYXINS,
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AB_QUINOLONES,
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AB_RIFAMYCINS,
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AB_STREPTOGRAMINS,
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AB_TETRACYCLINES,
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AB_TETRACYCLINES_EXCEPT_TGC,
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