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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47
This commit is contained in:
@@ -3,8 +3,13 @@
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\name{antibiotic_class_selectors}
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\alias{antibiotic_class_selectors}
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\alias{ab_class}
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\alias{ab_selector}
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\alias{administrable_per_os}
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\alias{administrable_iv}
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\alias{aminoglycosides}
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\alias{aminopenicillins}
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\alias{antifungals}
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\alias{antimycobacterials}
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\alias{betalactams}
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\alias{carbapenems}
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\alias{cephalosporins}
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@@ -24,15 +29,26 @@
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\alias{streptogramins}
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\alias{quinolones}
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\alias{tetracyclines}
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\alias{trimethoprims}
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\alias{ureidopenicillins}
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\title{Antibiotic Class Selectors}
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\title{Antibiotic Selectors}
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\usage{
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ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE)
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ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE)
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administrable_per_os(only_rsi_columns = FALSE)
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administrable_iv(only_rsi_columns = FALSE)
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aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE)
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aminopenicillins(only_rsi_columns = FALSE)
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antifungals(only_rsi_columns = FALSE)
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antimycobacterials(only_rsi_columns = FALSE)
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betalactams(only_rsi_columns = FALSE, only_treatable = TRUE)
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carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE)
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@@ -71,6 +87,8 @@ quinolones(only_rsi_columns = FALSE)
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tetracyclines(only_rsi_columns = FALSE)
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trimethoprims(only_rsi_columns = FALSE)
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ureidopenicillins(only_rsi_columns = FALSE)
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}
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\arguments{
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@@ -79,40 +97,54 @@ ureidopenicillins(only_rsi_columns = FALSE)
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\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
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\item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
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\item{filter}{an \link{expression} to be evaluated in the \link{antibiotics} data set, such as \code{name \%like\% "trim"}}
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}
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\value{
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(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
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}
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\description{
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These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
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These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by \code{\link[=cephalosporins]{cephalosporins()}}.
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}
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\details{
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These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.
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All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the \code{\link[=ab_class]{ab_class()}} function to filter/select on a manually defined antibiotic class.
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All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the \link{antibiotics} data set. This means that a selector such as \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
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The \code{\link[=ab_class]{ab_class()}} function can be used to filter/select on a manually defined antibiotic class. It searches for results in the \link{antibiotics} data set within the columns \code{name}, \code{atc_group1} and \code{atc_group2}.
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The \code{\link[=ab_selector]{ab_selector()}} function can be used to internally filter the \link{antibiotics} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
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The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[=administrable_iv]{administrable_iv()}} functions also rely on the \link{antibiotics} data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the \link{antibiotics} data set.
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}
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\section{Full list of supported agents}{
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\section{Full list of supported (antibiotic) classes}{
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\itemize{
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\item \code{aminoglycosides()} can select amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)
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\item \code{aminopenicillins()} can select amoxicillin (AMX) and ampicillin (AMP)
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\item \code{betalactams()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
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\item \code{carbapenems()} can select biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
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\item \code{cephalosporins()} can select cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
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\item \code{cephalosporins_1st()} can select cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)
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\item \code{cephalosporins_2nd()} can select cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
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\item \code{cephalosporins_3rd()} can select 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) and latamoxef (LTM)
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\item \code{cephalosporins_4th()} can select cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO) and cefquinome (CEQ)
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\item \code{cephalosporins_5th()} can select ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI) and ceftolozane/tazobactam (CZT)
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\item \code{fluoroquinolones()} can select 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), 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)
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\item \code{glycopeptides()} can select avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN) and vancomycin-macromethod (VAM)
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\item \code{lincosamides()} can select acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
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\item \code{lipoglycopeptides()} can select dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)
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\item \code{macrolides()} can select acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
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\item \code{oxazolidinones()} can select cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)
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\item \code{penicillins()} can select amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
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\item \code{polymyxins()} can select colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)
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\item \code{streptogramins()} can select pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
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\item \code{quinolones()} can select besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
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\item \code{tetracyclines()} can select cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)
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\item \code{ureidopenicillins()} can select azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)
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\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB) and tobramycin-high (TOH)
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\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
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\item \code{\link[=antifungals]{antifungals()}} can select: \cr 5-fluorocytosine (FCT), amphotericin B (AMB), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), micafungin (MIF), miconazole (MCZ), nystatin (NYS), pimaricin (Natamycin) (PMR), posaconazole (POS), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC) and voriconazole (VOR)
|
||||
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (Tuberactinomycin) (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), prothionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone/isoniazid (THI1), tiocarlide (TCR) and viomycin (VIO)
|
||||
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (Amdinocillin) (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA) and tebipenem (TBP)
|
||||
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefaloridine (RID), cefamandole (MAN), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (Cefcatacol) (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/enzyme inhibitor (CEI), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), cefuroxime (CXM), cefuroxime axetil (CXA), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP), cephradine (CED), latamoxef (LTM) and loracarbef (LOR)
|
||||
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefaloridine (RID), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephalexin (LEX), cephalothin (CEP), cephapirin (HAP) and cephradine (CED)
|
||||
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA) and loracarbef (LOR)
|
||||
\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) and latamoxef (LTM)
|
||||
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (Cefcatacol) (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), ceftolozane/enzyme inhibitor (CEI) 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), 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[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (Leucomycin) (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
|
||||
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI) and telavancin (TLV)
|
||||
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (Leucomycin) (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL) and tylvalosin (TYL1)
|
||||
\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD) and thiacetazone (THA)
|
||||
\item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (Amdinocillin) (MEC), metampicillin (MTM), methicillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), phenethicillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC) and ticarcillin/clavulanic acid (TCC)
|
||||
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB) and polymyxin B/polysorbate 80 (POP)
|
||||
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX) and trovafloxacin (TVA)
|
||||
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
|
||||
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), tetracycline (TCY) and tigecycline (TGC)
|
||||
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP) and trimethoprim/sulfamethoxazole (SXT)
|
||||
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP) and piperacillin/tazobactam (TZP)
|
||||
}
|
||||
}
|
||||
|
||||
@@ -146,6 +178,9 @@ example_isolates[, carbapenems()]
|
||||
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
|
||||
example_isolates[, c("mo", aminoglycosides())]
|
||||
|
||||
# select only antibiotic columns with DDDs for oral treatment
|
||||
example_isolates[, administrable_per_os()]
|
||||
|
||||
# filter using any() or all()
|
||||
example_isolates[any(carbapenems() == "R"), ]
|
||||
subset(example_isolates, any(carbapenems() == "R"))
|
||||
@@ -160,6 +195,13 @@ example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
|
||||
# filter + select in one go: get penicillins in carbapenems-resistant strains
|
||||
example_isolates[any(carbapenems() == "R"), penicillins()]
|
||||
|
||||
# You can combine selectors with '&' to be more specific. For example,
|
||||
# penicillins() would select benzylpenicillin ('peni G') and
|
||||
# administrable_per_os() would select erythromycin. Yet, when combined these
|
||||
# drugs are both omitted since benzylpenicillin is not administrable per os
|
||||
# and erythromycin is not a penicillin:
|
||||
example_isolates[, penicillins() & administrable_per_os()]
|
||||
|
||||
|
||||
# dplyr -------------------------------------------------------------------
|
||||
\donttest{
|
||||
@@ -169,6 +211,16 @@ if (require("dplyr")) {
|
||||
example_isolates \%>\%
|
||||
group_by(hospital_id) \%>\%
|
||||
summarise(across(aminoglycosides(), resistance))
|
||||
|
||||
# You can combine selectors with '&' to be more specific:
|
||||
example_isolates \%>\%
|
||||
select(penicillins() & administrable_per_os())
|
||||
|
||||
# get susceptibility for antibiotics whose name contains "trim":
|
||||
example_isolates \%>\%
|
||||
filter(first_isolate()) \%>\%
|
||||
group_by(hospital_id) \%>\%
|
||||
summarise(across(ab_selector(name \%like\% "trim"), susceptibility))
|
||||
|
||||
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
||||
example_isolates \%>\%
|
||||
|
||||
Reference in New Issue
Block a user