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

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dr. M.S. (Matthijs) Berends
2026-03-09 11:57:36 +01:00
parent cba315c2e7
commit 353eaa3f38
21 changed files with 61 additions and 13 deletions
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4
man/antimicrobial_selectors.Rd
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@@ -17,6 +17,7 @@
\alias{cephalosporins_5th}
\alias{fluoroquinolones}
\alias{glycopeptides}
\alias{ionophores}
\alias{isoxazolylpenicillins}
\alias{lincosamides}
\alias{lipoglycopeptides}
@@ -81,6 +82,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@@ -202,6 +205,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\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), 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), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), 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), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)

6
man/antimicrobials.Rd
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@@ -5,9 +5,9 @@
\alias{antimicrobials}
\alias{antibiotics}
\alias{antivirals}
\title{Data Sets with 624 Antimicrobial Drugs}
\title{Data Sets with 625 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 504 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 505 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimicrobial 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.}}
@@ -50,7 +50,7 @@ LOINC:
}
}
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 504 rows and 14 columns.
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 505 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
}

3
man/custom_eucast_rules.Rd
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@@ -98,8 +98,9 @@ x
#> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
}\if{html}{\out{</div>}}
These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
\itemize{
\item aminocoumarins\cr(clorobiocin, novobiocin, and penicillin/novobiocin)
\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
\item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, and ampicillin)
\item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)

3
man/custom_mdro_guideline.Rd
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@@ -94,7 +94,7 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
)
}\if{html}{\out{</div>}}
All 42 antimicrobial selectors are supported for use in the rules:
All 43 antimicrobial selectors are supported for use in the rules:
\itemize{
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, and ampicillin
@@ -111,6 +111,7 @@ All 42 antimicrobial selectors are supported for use in the rules:
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin
\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid, monensin sodium, narasin, nystatin, and salinomycin
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin