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(v2.1.1.9141) new AMR selectors, eucast overwrite arg

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dr. M.S. (Matthijs) Berends
2025-02-07 18:01:22 +01:00
parent baea4323c7
commit 8ba2e4ed94
42 changed files with 282 additions and 197 deletions
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14
data-raw/_pre_commit_checks.R
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@ -402,13 +402,19 @@ pre_commit_lst$AB_FLUOROQUINOLONES <- antibiotics %>%
pre_commit_lst$AB_GLYCOPEPTIDES <- antibiotics %>%
filter(group %like% "glycopeptide") %>%
pull(ab)
pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antibiotics %>%
filter(name %like% "oxacillin|cloxacillin|dicloxacillin|flucloxacillin|meth?icillin") %>%
pull(ab)
pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
pre_commit_lst$AB_LINCOSAMIDES <- antibiotics %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin)" & name %unlike% "screening|inducible")) %>%
pull(ab)
pre_commit_lst$AB_MACROLIDES <- antibiotics %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)" & name %unlike% "screening|inducible")) %>%
pull(ab)
pre_commit_lst$AB_MONOBACTAMS <- antibiotics %>%
filter(group %like% "monobactam") %>%
pull(ab)
pre_commit_lst$AB_NITROFURANS <- antibiotics %>%
filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
@ -417,7 +423,7 @@ pre_commit_lst$AB_OXAZOLIDINONES <- antibiotics %>%
filter(group %like% "oxazolidinone") %>%
pull(ab)
pre_commit_lst$AB_PENICILLINS <- antibiotics %>%
filter(group %like% "penicillin") %>%
filter(group %like% "penicillin" & !(name %unlike% "/" & name %like% ".*bactam$")) %>%
pull(ab)
pre_commit_lst$AB_PHENICOLS <- antibiotics %>%
filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
@ -442,7 +448,7 @@ pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
filter(group %like% "trimethoprim") %>%
pull(ab)
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
pre_commit_lst$AB_BETALACTAMS <- c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS)
pre_commit_lst$AB_BETALACTAMS <- sort(c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS, pre_commit_lst$AB_MONOBACTAMS))
pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antibiotics %>%
filter(name %like% "/" & name %unlike% "EDTA" & ab %in% pre_commit_lst$AB_BETALACTAMS) %>%
pull(ab)