(v3.0.1.9033) add ionophores(), clorobiocin, aminocoumarins group

data-raw/_pre_commit_checks.R

@@ -369,6 +369,9 @@ pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
   filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
   pull(ab)
 pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
+pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
+  filter(name %like% "novobiocin|clorobiocin") %>%
+  pull(ab)
 pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
   filter(group %like% "antifungal") %>%
   pull(ab)
@@ -486,6 +489,18 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
 # this will be used for documentation:
 pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
 
+# Check that all AB_* groups with >= 4 members have a corresponding function
+for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
+  if (length(pre_commit_lst[[grp]]) >= 4) {
+    fn_name <- tolower(gsub("^AB_", "", grp))
+    if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
+      stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
+           " members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
+           call. = FALSE)
+    }
+  }
+}
+
 # Update the antimicrobials$group column
 usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
 prettify_group_name <- function(name) {
@@ -557,6 +572,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
                                       "Beta-lactams",
                                       "Beta-lactamase inhibitors",
                                       "Pleuromutilins",
+                                      "Aminocoumarins",
                                       "Other")
 if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
   stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))

data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R

@@ -972,6 +972,17 @@ antimicrobials <- antimicrobials |>
       select(1:4),
   )
 
+antimicrobials <- antimicrobials |>
+  mutate(ab = as.character(ab)) |>
+  bind_rows(
+    antimicrobials |>
+      filter(ab == "NOV") |>
+      mutate(ab = "CLB",
+             cid = 54706138,
+             name = "Clorobiocin") |>
+      select(1:4),
+  )
+
 # update ATC codes from WHOCC website -------------------------------------
 
 library(rvest)
@@ -1171,6 +1182,11 @@ for (i in 1:nrow(antimicrobials)) {
     antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc))
   }
 }
+antimicrobials$group <- unname(antimicrobials$group)
+antimicrobials$atc <- unname(antimicrobials$atc)
+antimicrobials$abbreviations <- unname(antimicrobials$abbreviations)
+antimicrobials$synonyms <- unname(antimicrobials$synonyms)
+antimicrobials$loinc <- unname(antimicrobials$loinc)
 
 
 usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")

data-raw/ab.md5

@@ -1 +1 @@
-147709d2fb1b31b013c6ffb387f4d3ba
+11aade8a39bfdff02d01fb52b04eacdc

data-raw/datasets/antimicrobials.txt

@@ -157,6 +157,7 @@
 "CLF1"	2799	"Clofoctol"	"Other"	"J01XX03,QJ01XX03"	"Other antibacterials"	"Other antibacterials"	"NA"	"clofoctolo,clofoctolum,gramplus,octofene,phenol"					"NA"
 "CLM"	71807	"Clometocillin"	"Penicillins,Beta-lactams"	"J01CE07,QJ01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen"	1	"g"			"NA"
 "CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11,QJ01AA11"	"Tetracyclines"	"Tetracyclines"	"NA"	"clomociclina,clomocyclinum,megaclor"	1	"g"			"NA"
+"CLB"	54706138	"Clorobiocin"	"Aminocoumarins"	"NA"			"NA"	"chlorobiocin"					"NA"
 "CTR"	2812	"Clotrimazole"	"Antifungals"	"A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90"			"clot"	"alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole"					"10653-4,10654-2,18909-2,54177-1,55663-9"
 "CLO"	6098	"Cloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF02,QJ01CF02,QJ51CF02,QS01AA90"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,cloxac"	"ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
 "COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,colist,cs,cst,ct"	"colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina"	9	"MU"	9	"MU"	"16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
@@ -307,7 +308,7 @@
 "NME"		"Norfloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA14,QJ01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NTI"		"Norfloxacin/tinidazole"	"Fluoroquinolones,Quinolones"	"J01RA13,QJ01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NVA"	10419027	"Norvancomycin"	"Glycopeptides,Peptides"	"NA"			"NA"	"NA"					"NA"
-"NOV"	54675769	"Novobiocin"	"Other"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
+"NOV"	54675769	"Novobiocin"	"Aminocoumarins"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
 "NYS"	6433272	"Nystatin"	"Ionophores,Antifungals"	"A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01"			"nyst,nystan"	"biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
 "OFX"	4583	"Ofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofloxa,ofx"	"exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
 "OOR"		"Ofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA09,QJ01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
@@ -332,7 +333,7 @@
 "PEF"	51081	"Pefloxacin"	"Fluoroquinolones,Quinolones"	"J01MA03,QJ01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl,perflo"	"labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
 "PEF-S"		"Pefloxacin screening test"	"Fluoroquinolones,Quinolones"	"NA"			"pef screen"	"NA"					"NA"
 "PNM"	10250769	"Penamecillin"	"Penicillins,Beta-lactams"	"J01CE06,QJ01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum"	1.05	"g"			"NA"
-"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
+"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams,Aminocoumarins"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
 "PSU"		"Penicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
 "PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10,QJ01AA10"	"Tetracyclines"	"Tetracyclines"	"NA"	"criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum"					"NA"
 "PIM"	65453	"Pentisomicin"	"Aminoglycosides"	"NA"			"NA"	"mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum"					"NA"