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(v3.0.1.9028) fix unique CIDs
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Package: AMR
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Version: 3.0.1.9027
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Version: 3.0.1.9028
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Date: 2026-03-06
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 3.0.1.9027
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# AMR 3.0.1.9028
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### New
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* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
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@@ -65,6 +65,7 @@
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#' ab_synonyms("AMX")
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#' ab_tradenames("AMX")
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#' ab_group("AMX")
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#' ab_group("AMX", all_groups = TRUE) # most specific to most general
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#' ab_atc_group1("AMX")
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#' ab_atc_group2("AMX")
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#' ab_url("AMX")
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@@ -163,7 +164,7 @@ ab_tradenames <- function(x, ...) {
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}
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#' @rdname ab_property
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#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most distinctive group name.
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#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most specific group name.
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#' @export
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ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
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meet_criteria(x, allow_NA = TRUE)
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"CHL" 5959 "Chloramphenicol" "Phenicols" "D06AX02,D10AF03,G01AA05,J01BA01,QD06AX02,QD10AF03,QG01AA05,QJ01BA01,QJ51BA01,QS01AA01,QS02AA01,QS03AA08,S01AA01,S02AA01,S03AA08" "Amphenicols" "Amphenicols" "c,chl,chlo,chlora,cl" "alficetyn,ambofen,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocide,chlorocin,chlorocol,chlorofair,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chlorovules,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextramycin,dextromycetin,doctamicina,econochlor,embacetin,emetren,enteromycetin,erbaplast,ertilen,farmicetina,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,intramycetin,isicetin,ismicetina,isophenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromisan,loromisin,mastiphen,maybridge,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,petnamycetin,quemicetina,rivomycin,romphenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,viceton" 3 "g" 3 "g" "15101-9,16603-3,16604-1,172-7,173-5,174-3,175-0,18903-5,25247-8,29214-4,29346-4,29347-2,3455-3,7001-1"
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"CTE" 54675777 "Chlortetracycline" "Tetracyclines" "A01AB21,D06AA02,J01AA03,QA01AB21,QD06AA02,QG51AA08,QJ01AA03,QJ51AA03,QS01AA02,S01AA02" "Tetracyclines" "Tetracyclines" "chltet" "acronize,alexomycin,aueromycin,aureocarmyl,aureociclina,aureocina,aureocycline,aureomycin,aureomykoin,aurofac,auxeomycin,biomitsin,biomycin,chlormax,chlorotetracycline,chlortetracyclinum,chrysomykine,clorocipan,clortetraciclina,clortetrin,declomycin,declostatin,deganol,demeclor,demeplus,demetraciclina,demetraclin,detracin,detravis,diuciclin,duomycin,elkamicina,flamycin,isphamycin,ledermicina,ledermycin,ledermycine,mexocine,novotriclina,pennchlor,perciclina,periciclina,sumaclina,uromycin,veraciclina" 1 "g" "176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
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"CIC" 19003 "Ciclacillin" "Penicillins,Beta-lactams" "NA" "cyclac" "bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital" "NA"
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"CIX" 47472 "Ciclopirox" "Antifungals" "D01AE14,G01AX12,QD01AE14,QG01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "NA" "NA"
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"CIX" "Ciclopirox" "Antifungals" "D01AE14,G01AX12,QD01AE14,QG01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "NA" "NA"
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"CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06,QJ01MB06" "Quinolone antibacterials" "Other quinolones" "cino,cinoxa,cnox" "cinobac,cinobactin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm" 1 "g" "180-0,181-8,182-6,183-4,18905-0,55656-3"
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"CIP" 2764 "Ciprofloxacin" "Fluoroquinolones,Quinolones" "J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07" "Quinolone antibacterials" "Fluoroquinolones" "ci,cip,cipr,ciprof,cp" "alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,zumaflox" 1 "g" 0.8 "g" "101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
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"CIM" "Ciprofloxacin/metronidazole" "Fluoroquinolones,Quinolones" "J01RA10,QJ01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
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@@ -293,7 +293,7 @@
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"NAL-S" "Nalidixic acid screening test" "Quinolones" "NA" "nal screen" "NA" "NA"
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"NAR" 65452 "Narasin" "Ionophores" "QP51BB04" "narasi" "monteban,narasine,narasino,narasinum,skycis" "87570-8"
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"NEM" 11993740 "Nemonoxacin" "Fluoroquinolones,Quinolones" "J01MB08,QJ01MB08" "Quinolone antibacterials" "Other quinolones" "NA" "NA" "NA"
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"NEO" 8378 "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom,neomyc" "NA" 5 "g" 1 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
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"NEO" "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom,neomyc" "NA" 5 "g" 1 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
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"NET" 441306 "Netilmicin" "Aminoglycosides" "J01GB07,QJ01GB07,QS01AA23,S01AA23" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti,netilm" "netillin,netilmicina,netilmicine,netilmicinum,netilyn,netira,netromicine,netromycin,nettacin,ntromicine,ntromycin,vectacin,zetamicin" 0.35 "g" 0.35 "g" "18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
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"NIC" 9507 "Nicarbazin" "Other" "NA" "NA" "nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin" "NA"
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"NIF" 71946 "Nifuroquine" "Fluoroquinolones,Quinolones" "NA" "NA" "abimasten,nifuroquina,nifuroquinum,quinaldofur" "NA"
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@@ -325,7 +325,7 @@
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"OXO" 4628 "Oxolinic acid" "Quinolones" "J01MB05,QJ01MB05" "Quinolone antibacterials" "Other quinolones" "oxoaci" "aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid" 1 "g" "NA"
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"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "A01AB25,D06AA03,G01AA07,J01AA06,QA01AB25,QD06AA03,QG01AA07,QG51AA01,QJ01AA06,QJ51AA06,QS01AA04,S01AA04" "Tetracyclines" "Tetracyclines" "oxytet" "achromycin,actisite,adamycin,artomycin,berkmycen,biostat,bristacycline,cancycline,cyclopar,dabicycline,diacycine,dumocyclin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hostacycline,hydroxytetracyclinum,lenocycline,macocyn,medamycin,mephacyclin,nitox,oksisyklin,ossitetraciclina,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxymycin,oxypam,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracyclinum,paltet,partrex,pennox,piracaps,proteroxyna,qidtet,quadracycline,quatrex,remicyclin,retet,ricycline,riomitsin,ryomycin,solkaciclina,stevacin,stilciclina,subamycin,sumycin,supramycin,sustamycin,tarocyn,tarosin,tefilin,teline,telotrex,teravit,terrafungine,terramitsin,terramycine,tetrabakat,tetrabid,tetrablet,tetracaps,tetracompren,tetrakap,tetralution,tetramavan,tetramed,tetran,tetrosol,topicycline,triphacyclin,unicin,ursocyclin,ursocycline,vetquamycin" 1 "g" 1 "g" "17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
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"OZN" "Ozenoxacin" "Quinolones" "D06AX14,QD06AX14" "NA" "NA" "NA"
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"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "NA" "pasraa" "NA" "NA"
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"PAS" "P-aminosalicylic acid" "Antimycobacterials" "NA" "pasraa" "NA" "NA"
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"PAN" 72015 "Panipenem" "Carbapenems,Beta-lactams" "NA" "NA" "carbenin,panipenemum,penipanem" "100056-1,53823-1"
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"PAR" 165580 "Paromomycin" "Other" "A07AA06,QA07AA06,QJ01GB92" "NA" "aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum" 3 "g" "51719-3,53824-9,55700-9,55701-7,55702-5"
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"PAZ" 65957 "Pazufloxacin" "Fluoroquinolones,Quinolones" "J01MA18,QJ01MA18" "Quinolone antibacterials" "Fluoroquinolones" "NA" "pazufloxacine,pazufloxacino,pazufloxacinum" 1 "g" "NA"
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@@ -423,7 +423,7 @@
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"SZO" 187764 "Sulfamazone" "Trimethoprims,Sulfonamides" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA"
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"SLF3" 5325 "Sulfamerazine" "Trimethoprims,Sulfonamides" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA"
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"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
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"SUM" 5327 "Sulfamethazine" "Sulfonamides" "NA" "NA" "NA" "87592-2"
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"SUM" "Sulfamethazine" "Sulfonamides" "NA" "NA" "NA" "87592-2"
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"SLF4" 5328 "Sulfamethizole" "Trimethoprims,Sulfonamides" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3"
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"SMX" 5329 "Sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak" 2 "g" "10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
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"SLF5" 5330 "Sulfamethoxypyridazine" "Trimethoprims,Sulfonamides" "J01ED05,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA"
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@@ -439,7 +439,7 @@
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"SNA" 60582 "Sulfasuccinamide" "Sulfonamides" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA"
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"SUT" 5340 "Sulfathiazole" "Trimethoprims,Sulfonamides" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7"
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"SLF13" 3000579 "Sulfathiourea" "Trimethoprims,Sulfonamides" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA"
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"SOX" 5344 "Sulfisoxazole" "Sulfonamides" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
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"SOX" "Sulfisoxazole" "Sulfonamides" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
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"SSS" 86225 "Sulfonamide" "Sulfonamides" "NA" "sfna,sulami" "NA" "17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
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"SLP" 9950244 "Sulopenem" "Other" "NA" "sulope" "orlynvah" "55289-3,55290-1,55291-9"
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"SLT6" 444022 "Sultamicillin" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA"
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@@ -465,7 +465,7 @@
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"TET" 65450 "Tetroxoprim" "Other" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA"
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"THA" 9568512 "Thiacetazone" "Oxazolidinones" "NA" "NA" "acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin" "32384-0,54184-7,54204-3"
|
||||
"THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8"
|
||||
"TAT" 9568512 "Thioacetazone" "Antimycobacterials" "J04AK07,QJ04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" "NA"
|
||||
"TAT" "Thioacetazone" "Antimycobacterials" "J04AK07,QJ04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" "NA"
|
||||
"THI1" "Thioacetazone/isoniazid" "Antimycobacterials" "J04AM04,QJ04AM04" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
|
||||
"THS" 16129666 "Thiostrepton" "Peptides" "NA" "NA" "alaninamide,bryamycin,gargon,pharmakon,prestwick,sporangiomycin,thiactin,tiostrepton" "NA"
|
||||
"TIA" 656958 "Tiamulin" "Pleuromutilins" "QJ01XQ01" "tiamul" "denagard,thiamutilin,tiamulina,tiamuline,tiamulinum" "35846-5,35847-3,35848-1,87589-8"
|
||||
@@ -496,7 +496,7 @@
|
||||
"VAN" 14969 "Vancomycin" "Glycopeptides,Peptides" "A07AA09,J01XA01,QA07AA09,QJ01XA01,QS01AA28,S01AA28" "Other antibacterials" "Glycopeptide antibacterials" "va,van,vanc,vancom" "vancocin,vancoled,vancomicina,vancomycine,vancomycinum" 2 "g" 2 "g" "13586-3,13587-1,19000-9,20578-1,23615-8,25228-8,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,523-1,524-9,525-6,526-4,59381-4,7059-9,92241-9,97657-1"
|
||||
"VAM" "Vancomycin-macromethod" "Glycopeptides,Peptides" "NA" "NA" "NA" "NA"
|
||||
"VIO" 135398671 "Viomycin" "Antimycobacterials" "NA" "NA" "florimycin,floromycin,vioactane,viocin,viomicin,viomicina,viomycine,viomycinum" "19001-7,23616-6,527-2,528-0,529-8,530-6"
|
||||
"VIR" 11979535 "Virginiamycine" "Streptogramins" "NA" "NA" "NA" "NA"
|
||||
"VIR" "Virginiamycine" "Streptogramins" "NA" "NA" "NA" "NA"
|
||||
"VOR" 71616 "Voriconazole" "Antifungals" "J02AC03,QJ02AC03" "Antimycotics for systemic use" "Triazole derivatives" "vori,vorico,vrc" "vfend,voriconazol,voriconazolum,voriconzole,vorikonazole" 0.4 "g" 0.4 "g" "32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
|
||||
"XER" 140830474 "Xeruborbactam" "Beta-lactamase inhibitors" "NA" "NA" "benzo,borate" "NA"
|
||||
"XBR" 72144 "Xibornol" "Other" "J01XX02,QJ01XX02" "Other antibacterials" "Other antibacterials" "NA" "bactacine,bracen,nanbacine,xibornolo,xibornolum" "NA"
|
||||
|
||||
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@@ -59,7 +59,7 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
|
||||
|
||||
\item{...}{In case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}.}
|
||||
|
||||
\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most distinctive group name.}
|
||||
\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most specific group name.}
|
||||
|
||||
\item{only_first}{A \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).}
|
||||
|
||||
@@ -116,6 +116,7 @@ ab_cid("AMX")
|
||||
ab_synonyms("AMX")
|
||||
ab_tradenames("AMX")
|
||||
ab_group("AMX")
|
||||
ab_group("AMX", all_groups = TRUE) # most specific to most general
|
||||
ab_atc_group1("AMX")
|
||||
ab_atc_group2("AMX")
|
||||
ab_url("AMX")
|
||||
|
||||
@@ -35,7 +35,7 @@ test_that("test-data.R", {
|
||||
expect_identical(class(microorganisms$mo), c("mo", "character"))
|
||||
expect_identical(nrow(antimicrobials), length(unique(AMR::antimicrobials$ab)))
|
||||
expect_identical(class(AMR::antimicrobials$ab), c("ab", "character"))
|
||||
|
||||
expect_identical(nrow(antimicrobials[!is.na(antimicrobials$cid), ]), length(unique(AMR::antimicrobials$cid[!is.na(antimicrobials$cid)])), label = "nr of rows with CIDs", expected.label = "unique nr of CIDs")
|
||||
|
||||
# check cross table reference
|
||||
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
|
||||
|
||||
Reference in New Issue
Block a user