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(v2.1.1.9192) fix fluoroquinolones and add bleomycin

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dr. M.S. (Matthijs) Berends committed 2025-03-10 17:04:35 +01:00
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man/AMR-deprecated.Rd
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@@ -8,7 +8,7 @@
\alias{ab_selector}
\title{Deprecated Functions}
\format{
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 487 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 488 rows and 14 columns.
}
\usage{
ab_class(...)
man/antimicrobial_selectors.Rd
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@@ -182,8 +182,8 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), and oxacillin (OXA)
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), lincomycin (LIN), and pirlimycin (PRL)
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)
man/antimicrobials.Rd
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@@ -4,9 +4,9 @@
\name{antimicrobials}
\alias{antimicrobials}
\alias{antivirals}
\title{Data Sets with 607 Antimicrobial Drugs}
\title{Data Sets with 608 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 487 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 488 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimcrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
man/custom_eucast_rules.Rd
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@@ -102,9 +102,9 @@ These 34 antimicrobial groups are allowed in the rules (case-insensitive) and ca
\item cephalosporins_4th\cr(cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)
\item cephalosporins_5th\cr(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)
\item cephalosporins_except_caz\cr(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)
\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
\item glycopeptides\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
\item glycopeptides_except_lipo\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
\item fluoroquinolones\cr(besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
\item glycopeptides\cr(avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)
\item glycopeptides_except_lipo\cr(avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)
\item isoxazolylpenicillins\cr(cloxacillin, dicloxacillin, flucloxacillin, meticillin, and oxacillin)
\item lincosamides\cr(clindamycin, lincomycin, and pirlimycin)
\item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin)
man/eucast_rules.Rd
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@@ -99,7 +99,7 @@ To define antimicrobials column names, leave as it is to determine it automatica
The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no}{S01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA06&showdescription=no}{J01RA06}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD09&showdescriLine truncated
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no}{S01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA06&showdescription=no}{J01RA06}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescripLine truncated
}
\section{Reference Data Publicly Available}{
man/mdro.Rd
+1 -1
View File
@@ -182,7 +182,7 @@ To define antimicrobials column names, leave as it is to determine it automatica
The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no}{S01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA06&showdescription=no}{J01RA06}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD09&showdescriLine truncated
Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=S01AE08&showdescription=no}{S01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA06&showdescription=no}{J01RA06}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescripLine truncated
}
\section{Interpretation of SIR}{