antimicrobial_selectors: Antimicrobial Selectors

In AMR: Antimicrobial Resistance Data Analysis

Antimicrobial Selectors

Description

These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base R, tidyverse, tidymodels, and data.table.

Simply puy, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class, code or name: column names "cefazolin", "kefzol", "CZO" and "J01DB04" would all be included in the following selection:

library(dplyr)
my_data_with_all_these_columns %>%
  select(cephalosporins())

Usage

aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

aminopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)

antifungals(only_sir_columns = FALSE, return_all = TRUE, ...)

antimycobacterials(only_sir_columns = FALSE, return_all = TRUE, ...)

betalactams(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

betalactams_with_inhibitor(only_sir_columns = FALSE, return_all = TRUE,
  ...)

carbapenems(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

cephalosporins(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

cephalosporins_1st(only_sir_columns = FALSE, return_all = TRUE, ...)

cephalosporins_2nd(only_sir_columns = FALSE, return_all = TRUE, ...)

cephalosporins_3rd(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

cephalosporins_4th(only_sir_columns = FALSE, return_all = TRUE, ...)

cephalosporins_5th(only_sir_columns = FALSE, return_all = TRUE, ...)

fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)

isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

lincosamides(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

lipoglycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)

macrolides(only_sir_columns = FALSE, return_all = TRUE, ...)

monobactams(only_sir_columns = FALSE, return_all = TRUE, ...)

nitrofurans(only_sir_columns = FALSE, return_all = TRUE, ...)

oxazolidinones(only_sir_columns = FALSE, return_all = TRUE, ...)

penicillins(only_sir_columns = FALSE, return_all = TRUE, ...)

phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)

polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)

streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)

sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)

tetracyclines(only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

trimethoprims(only_sir_columns = FALSE, return_all = TRUE, ...)

ureidopenicillins(only_sir_columns = FALSE, return_all = TRUE, ...)

amr_class(amr_class, only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

amr_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE,
  return_all = TRUE, ...)

administrable_per_os(only_sir_columns = FALSE, return_all = TRUE, ...)

administrable_iv(only_sir_columns = FALSE, return_all = TRUE, ...)

not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
  version_expected_phenotypes = 1.2, ...)

Arguments

only_sir_columns	A logical to indicate whether only antimicrobial columns must be included that were transformed to class sir on beforehand. Defaults to FALSE.
only_treatable	A logical to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is TRUE), such as gentamicin-high (GEH) and imipenem/EDTA (IPE).
return_all	A logical to indicate whether all matched columns must be returned (default is TRUE). With FALSE, only the first of each unique antimicrobial will be returned, e.g. if both columns "genta" and "gentamicin" exist in the data, only the first hit for gentamicin will be returned.
...	Ignored, only in place to allow future extensions.
amr_class	An antimicrobial class or a part of it, such as "carba" and "carbapenems". The columns group, atc_group1 and atc_group2 of the antimicrobials data set will be searched (case-insensitive) for this value.
filter	An expression to be evaluated in the antimicrobials data set, such as name %like% "trim".
col_mo	Column name of the names or codes of the microorganisms (see as.mo()) - the default is the first column of class mo. Values will be coerced using as.mo().
version_expected_phenotypes	The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".

Details

These functions can be used in data set calls for selecting columns and filtering rows. They work with base R, the Tidyverse, and data.table. They are heavily inspired by the Tidyverse selection helpers such as everything(), but are not limited to dplyr verbs. Nonetheless, they are very convenient to use with dplyr functions such as select(), filter() and summarise(), see Examples.

All selectors can also be used in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using antimicrobial selectors for predictive modelling.

All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the antimicrobials data set. This means that a selector such as aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.

The amr_class() function can be used to filter/select on a manually defined antimicrobial class. It searches for results in the antimicrobials data set within the columns group, atc_group1 and atc_group2.

The administrable_per_os() and administrable_iv() functions also rely on the antimicrobials data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the antimicrobials data set.

The amr_selector() function can be used to internally filter the antimicrobials data set on any results, see 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.

The not_intrinsic_resistant() function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of E. coli and K. pneumoniae and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies 'EUCAST Expected Resistant Phenotypes' v1.2 (2023) to determine intrinsic resistance, using the eucast_rules() function internally. Because of this determination, this function is quite slow in terms of performance.

Value

When used inside selecting or filtering, this returns a character vector of column names, with additional class "amr_selector". When used individually, this returns an 'ab' vector with all possible antimicrobials that the function would be able to select or filter.

Full list of supported (antimicrobial) classes

• aminoglycosides() can select:
  amikacin (AMK), amikacin/fosfomycin (AKF), 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)

• aminopenicillins() can select:
  amoxicillin (AMX) and ampicillin (AMP)

• antifungals() can select:
  amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)

• antimycobacterials() can select:
  4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), 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 (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)

• betalactams() can select:
  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), 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/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), 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 (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (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), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)

• betalactams_with_inhibitor() can select:
  amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)

• 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)

• cephalosporins() can select:
  cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), 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/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)

• cephalosporins_1st() can select:
  cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)

• cephalosporins_2nd() can select:
  cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)

• 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 screening test (CTX-S), 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)

• cephalosporins_4th() can select:
  cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)

• cephalosporins_5th() can select:
  ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)

• fluoroquinolones() can select:
  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)

• glycopeptides() can select:
  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)

• isoxazolylpenicillins() can select:
  cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)

• lincosamides() can select:
  clindamycin (CLI), lincomycin (LIN), and pirlimycin (PRL)

• lipoglycopeptides() can select:
  dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)

• macrolides() can select:
  acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)

• monobactams() can select:
  aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), carumonam (CAR), and tigemonam (TMN)

• nitrofurans() can select:
  furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)

• oxazolidinones() can select:
  cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)

• penicillins() can select:
  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)

• phenicols() can select:
  chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)

• polymyxins() can select:
  colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)

• quinolones() can select:
  besifloxacin (BES), cinoxacin (CIN), 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), flumequine (FLM), 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), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), 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), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), 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)

• rifamycins() can select:
  rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)

• streptogramins() can select:
  pristinamycin (PRI) and quinupristin/dalfopristin (QDA)

• sulfonamides() can select:
  brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)

• 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), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)

• trimethoprims() can select:
  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)

• ureidopenicillins() can select:
  azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)

Download Our Reference Data

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit our website for direct download links, or explore the actual files in our GitHub repository.

Examples

# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates


# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()


# Though they are primarily intended to use for selections and filters.
# Examples sections below are split into 'dplyr', 'base R', and 'data.table':


## Not run: 
# dplyr -------------------------------------------------------------------

library(dplyr, warn.conflicts = FALSE)

example_isolates %>% select(carbapenems())

# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates %>% select(mo, aminoglycosides())

# you can combine selectors like you are used with tidyverse
# e.g., for betalactams, but not the ones with an enzyme inhibitor:
example_isolates %>% select(betalactams(), -betalactams_with_inhibitor())

# select only antimicrobials with DDDs for oral treatment
example_isolates %>% select(administrable_per_os())

# get AMR for all aminoglycosides e.g., per ward:
example_isolates %>%
  group_by(ward) %>%
  summarise(across(aminoglycosides(),
                   resistance))

# You can combine selectors with '&' to be more specific:
example_isolates %>%
  select(penicillins() & administrable_per_os())

# get AMR for only drugs that matter - no intrinsic resistance:
example_isolates %>%
  filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
  group_by(ward) %>%
  summarise_at(not_intrinsic_resistant(),
               resistance)

# get susceptibility for antimicrobials whose name contains "trim":
example_isolates %>%
  filter(first_isolate()) %>%
  group_by(ward) %>%
  summarise(across(amr_selector(name %like% "trim"), susceptibility))

# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
example_isolates %>%
  select(carbapenems())

# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
example_isolates %>%
  select(mo, aminoglycosides())

# any() and all() work in dplyr's filter() too:
example_isolates %>%
  filter(
    any(aminoglycosides() == "R"),
    all(cephalosporins_2nd() == "R")
  )

# also works with c():
example_isolates %>%
  filter(any(c(carbapenems(), aminoglycosides()) == "R"))

# not setting any/all will automatically apply all():
example_isolates %>%
  filter(aminoglycosides() == "R")

# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
example_isolates %>%
  select(mo, amr_class("mycobact"))

# get bug/drug combinations for only glycopeptides in Gram-positives:
example_isolates %>%
  filter(mo_is_gram_positive()) %>%
  select(mo, glycopeptides()) %>%
  bug_drug_combinations() %>%
  format()

data.frame(
  some_column = "some_value",
  J01CA01 = "S"
) %>% # ATC code of ampicillin
  select(penicillins()) # only the 'J01CA01' column will be selected

# with recent versions of dplyr, this is all equal:
x <- example_isolates[carbapenems() == "R", ]
y <- example_isolates %>% filter(carbapenems() == "R")
z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == "R"))
identical(x, y) && identical(y, z)


## End(Not run)
# base R ------------------------------------------------------------------

# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]

# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]

# select only antimicrobials 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"))

# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
example_isolates[all(carbapenems()), ]

# filter with multiple antimicrobial selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]

# filter + select in one go: get penicillins in carbapenem-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()]

# amr_selector() applies a filter in the `antimicrobials` data set and is thus
# very flexible. For instance, to select antimicrobials with an oral DDD
# of at least 1 gram:
example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]


# data.table --------------------------------------------------------------

# data.table is supported as well, just use it in the same way as with
# base R, but add `with = FALSE` if using a single AB selector.

if (require("data.table")) {
  dt <- as.data.table(example_isolates)

  # this does not work, it returns column *names*
  dt[, carbapenems()]
}
if (require("data.table")) {
  # so `with = FALSE` is required
  dt[, carbapenems(), with = FALSE]
}

# for multiple selections or AB selectors, `with = FALSE` is not needed:
if (require("data.table")) {
  dt[, c("mo", aminoglycosides())]
}
if (require("data.table")) {
  dt[, c(carbapenems(), aminoglycosides())]
}

# row filters are also supported:
if (require("data.table")) {
  dt[any(carbapenems() == "S"), ]
}
if (require("data.table")) {
  dt[any(carbapenems() == "S"), penicillins(), with = FALSE]
}

AMR documentation built on June 8, 2025, 10:17 a.m.