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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 14:21:48 +02:00

(v2.1.1.9041) antibiotics update

This commit is contained in:
2024-06-08 17:35:25 +02:00
parent e2acc513a5
commit af74e1d4f2
26 changed files with 110 additions and 67 deletions

View File

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