Skip to contents

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 drug, 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 cephalosporins().

Usage

ab_class(ab_class, only_sir_columns = FALSE, only_treatable = TRUE, ...)

ab_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE, ...)

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

aminopenicillins(only_sir_columns = FALSE, ...)

antifungals(only_sir_columns = FALSE, ...)

antimycobacterials(only_sir_columns = FALSE, ...)

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

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

cephalosporins(only_sir_columns = FALSE, ...)

cephalosporins_1st(only_sir_columns = FALSE, ...)

cephalosporins_2nd(only_sir_columns = FALSE, ...)

cephalosporins_3rd(only_sir_columns = FALSE, ...)

cephalosporins_4th(only_sir_columns = FALSE, ...)

cephalosporins_5th(only_sir_columns = FALSE, ...)

fluoroquinolones(only_sir_columns = FALSE, ...)

glycopeptides(only_sir_columns = FALSE, ...)

lincosamides(only_sir_columns = FALSE, ...)

lipoglycopeptides(only_sir_columns = FALSE, ...)

macrolides(only_sir_columns = FALSE, ...)

oxazolidinones(only_sir_columns = FALSE, ...)

penicillins(only_sir_columns = FALSE, ...)

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

streptogramins(only_sir_columns = FALSE, ...)

quinolones(only_sir_columns = FALSE, ...)

tetracyclines(only_sir_columns = FALSE, ...)

trimethoprims(only_sir_columns = FALSE, ...)

ureidopenicillins(only_sir_columns = FALSE, ...)

administrable_per_os(only_sir_columns = FALSE, ...)

administrable_iv(only_sir_columns = FALSE, ...)

not_intrinsic_resistant(
  only_sir_columns = FALSE,
  col_mo = NULL,
  version_expertrules = 3.3,
  ...
)

Arguments

ab_class

an antimicrobial class or a part of it, such as "carba" and "carbapenems". The columns group, atc_group1 and atc_group2 of the antibiotics data set will be searched (case-insensitive) for this value.

only_sir_columns

a logical to indicate whether only columns of class sir must be selected (default is FALSE), see as.sir()

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)

...

ignored, only in place to allow future extensions

filter

an expression to be evaluated in the antibiotics 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_expertrules

the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".

Value

(internally) a character vector of column names, with additional class "ab_selector"

Details

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

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 antibiotics data set. This means that a selector such as aminoglycosides() will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.

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

The ab_selector() function can be used to internally filter the antibiotics 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 administrable_per_os() and administrable_iv() functions also rely on the antibiotics data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the antibiotics data set.

The not_intrinsic_resistant() function can be used to only select antibiotic columns 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 Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021) to determine intrinsic resistance, using the eucast_rules() function internally. Because of this determination, this function is quite slow in terms of performance.

Full list of supported (antibiotic) classes

  • 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)

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

  • antifungals() can select:
    amphotericin B (AMB), 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), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), 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/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (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/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), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), 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), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), 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/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (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/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 (FOX1), 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/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/clavulanic acid (CPC), cefepime/tazobactam (FPT), 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), 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)

  • 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)

  • lincosamides() can select:
    acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)

  • 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), 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)

  • 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), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), 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), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), 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), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)

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

  • 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), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), 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)

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

  • 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), 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)

Reference Data Publicly Available

All data sets in this AMR package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

Examples

# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
example_isolates
#> # A tibble: 2,000 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   
#>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   
#>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   
#>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   
#>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   
#>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   
#>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    
#>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    
#>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   
#> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   
#> # … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,
#> #   TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,
#> #   CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>,
#> #   TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>,
#> #   MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>,
#> #   ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,
#> #   CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>

# base R ------------------------------------------------------------------

# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 2,000 × 2
#>    IPM   MEM  
#>    <sir> <sir>
#>  1 NA    NA   
#>  2 NA    NA   
#>  3 NA    NA   
#>  4 NA    NA   
#>  5 NA    NA   
#>  6 NA    NA   
#>  7 NA    NA   
#>  8 NA    NA   
#>  9 NA    NA   
#> 10 NA    NA   
#> # … with 1,990 more rows

# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 2,000 × 5
#>    mo           GEN   TOB   AMK   KAN  
#>    <mo>         <sir> <sir> <sir> <sir>
#>  1 B_ESCHR_COLI NA    NA    NA    NA   
#>  2 B_ESCHR_COLI NA    NA    NA    NA   
#>  3 B_STPHY_EPDR NA    NA    NA    NA   
#>  4 B_STPHY_EPDR NA    NA    NA    NA   
#>  5 B_STPHY_EPDR NA    NA    NA    NA   
#>  6 B_STPHY_EPDR NA    NA    NA    NA   
#>  7 B_STPHY_AURS NA    S     NA    NA   
#>  8 B_STPHY_AURS NA    S     NA    NA   
#>  9 B_STPHY_EPDR NA    NA    NA    NA   
#> 10 B_STPHY_EPDR NA    NA    NA    NA   
#> # … with 1,990 more rows

# select only antibiotic columns with DDDs for oral treatment
example_isolates[, administrable_per_os()]
#> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC'
#>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#>   (rifampicin)
#> # A tibble: 2,000 × 23
#>    OXA   FLC   AMX   AMC   AMP   CXM   KAN   TMP   NIT   FOS   LNZ   CIP   MFX  
#>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#>  1 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA   
#>  2 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA   
#>  3 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA   
#>  4 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA   
#>  5 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA   
#>  6 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA   
#>  7 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA   
#>  8 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA   
#>  9 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    S     NA   
#> 10 NA    S     NA    NA    NA    S     NA    S     NA    NA    NA    S     NA   
#> # … with 1,990 more rows, and 10 more variables: VAN <sir>, TCY <sir>,
#> #   DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, RIF <sir>

# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 55 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R    
#>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA   
#>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA   
#>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA   
#> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA   
#> # … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>
subset(example_isolates, any(carbapenems() == "R"))
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 55 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R    
#>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA   
#>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA   
#>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA   
#> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA   
#> # … with 45 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>

# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 962 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   
#>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   
#>  3 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   
#>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   
#>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    
#>  6 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    
#>  7 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    
#>  8 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R    
#>  9 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R    
#> 10 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R    
#> # … with 952 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>
example_isolates[all(carbapenems()), ]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "S", "I" or "R"
#> # A tibble: 756 × 46
#>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir>
#>  1 2002-04-14 F30196     73 M      Outpat… B_STRPT_GRPB  S     NA    S     S    
#>  2 2003-04-08 114570     74 M      ICU     B_STRPT_PYGN  S     NA    S     S    
#>  3 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S    
#>  4 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S    
#>  5 2003-08-14 F71508      0 F      Clinic… B_STRPT_GRPB  S     NA    S     S    
#>  6 2003-10-16 650870     63 F      ICU     B_ESCHR_COLI  R     NA    NA    R    
#>  7 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R    
#>  8 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R    
#>  9 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA   
#> 10 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA   
#> # … with 746 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>

# filter with multiple antibiotic selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 26 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R    
#>  2 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  3 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  4 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  5 2008-12-06 501361     43 F      Clinical B_STNTR_MLTP R     NA    NA    R    
#>  6 2011-05-09 207325     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#>  7 2012-03-12 582258     80 M      ICU      B_STPHY_CONS R     R     R     R    
#>  8 2012-05-19 C25552     89 F      Outpati… B_STPHY_CONS R     R     R     R    
#>  9 2012-07-17 F05015     83 M      ICU      B_STPHY_CONS R     R     R     R    
#> 10 2012-07-20 404299     66 F      Clinical B_STPHY_CONS R     R     R     R    
#> # … with 16 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>

# filter + select in one go: get penicillins in carbapenems-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'
#>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#>   (piperacillin/tazobactam)
#> # A tibble: 55 × 7
#>    PEN   OXA   FLC   AMX   AMC   AMP   TZP  
#>    <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#>  1 NA    NA    NA    NA    NA    NA    NA   
#>  2 NA    NA    NA    NA    NA    NA    NA   
#>  3 R     NA    NA    R     R     R     R    
#>  4 NA    NA    NA    NA    NA    NA    R    
#>  5 NA    NA    NA    NA    NA    NA    R    
#>  6 NA    NA    NA    NA    NA    NA    R    
#>  7 NA    NA    NA    NA    NA    NA    R    
#>  8 NA    NA    NA    NA    NA    NA    R    
#>  9 R     NA    NA    NA    S     NA    S    
#> 10 R     NA    NA    NA    S     NA    S    
#> # … with 45 more rows

# 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()]
#> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'
#>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#>   (piperacillin/tazobactam)
#> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC'
#>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#>   (rifampicin)
#> # A tibble: 2,000 × 5
#>    OXA   FLC   AMX   AMC   AMP  
#>    <sir> <sir> <sir> <sir> <sir>
#>  1 NA    NA    NA    I     NA   
#>  2 NA    NA    NA    I     NA   
#>  3 NA    R     NA    NA    NA   
#>  4 NA    R     NA    NA    NA   
#>  5 NA    R     NA    NA    NA   
#>  6 NA    R     NA    NA    NA   
#>  7 NA    S     R     S     R    
#>  8 NA    S     R     S     R    
#>  9 NA    R     NA    NA    NA   
#> 10 NA    S     NA    NA    NA   
#> # … with 1,990 more rows

# ab_selector() applies a filter in the `antibiotics` data set and is thus very
# flexible. For instance, to select antibiotic columns with an oral DDD of at
# least 1 gram:
example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
#> ℹ For ab_selector(oral_ddd > 1 & oral_units == "g") using columns 'OXA'
#>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS'
#>   (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin),
#>   'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol)
#> # A tibble: 2,000 × 13
#>    OXA   FLC   AMX   AMC   AMP   KAN   FOS   LNZ   VAN   ERY   CLI   MTR   CHL  
#>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir>
#>  1 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA   
#>  2 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA   
#>  3 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA   
#>  4 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA   
#>  5 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA   
#>  6 NA    R     NA    NA    NA    NA    NA    NA    S     R     R     NA    NA   
#>  7 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA   
#>  8 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA   
#>  9 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA   
#> 10 NA    S     NA    NA    NA    NA    NA    NA    S     S     NA    NA    NA   
#> # … with 1,990 more rows

# dplyr -------------------------------------------------------------------
# \donttest{
if (require("dplyr")) {
  # get AMR for all aminoglycosides e.g., per ward:
  example_isolates %>%
    group_by(ward) %>%
    summarise(across(aminoglycosides(), resistance))
}
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> Warning: There was 1 warning in `summarise()`.
#>  In argument: `across(aminoglycosides(), resistance)`.
#>  In group 3: `ward = "Outpatient"`.
#> Caused by warning:
#> ! Introducing NA: only 23 results available for KAN in group: ward =
#> "Outpatient" (minimum = 30).
#> # A tibble: 3 × 5
#>   ward         GEN   TOB   AMK   KAN
#>   <chr>      <dbl> <dbl> <dbl> <dbl>
#> 1 Clinical   0.229 0.315 0.626     1
#> 2 ICU        0.290 0.400 0.662     1
#> 3 Outpatient 0.2   0.368 0.605    NA
if (require("dplyr")) {
  # You can combine selectors with '&' to be more specific:
  example_isolates %>%
    select(penicillins() & administrable_per_os())
}
#> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'
#>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'
#>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'
#>   (piperacillin/tazobactam)
#> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC'
#>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid),
#>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP'
#>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ'
#>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN'
#>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY'
#>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR'
#>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF'
#>   (rifampicin)
#> # A tibble: 2,000 × 5
#>    OXA   FLC   AMX   AMC   AMP  
#>    <sir> <sir> <sir> <sir> <sir>
#>  1 NA    NA    NA    I     NA   
#>  2 NA    NA    NA    I     NA   
#>  3 NA    R     NA    NA    NA   
#>  4 NA    R     NA    NA    NA   
#>  5 NA    R     NA    NA    NA   
#>  6 NA    R     NA    NA    NA   
#>  7 NA    S     R     S     R    
#>  8 NA    S     R     S     R    
#>  9 NA    R     NA    NA    NA   
#> 10 NA    S     NA    NA    NA   
#> # … with 1,990 more rows
if (require("dplyr")) {
  # get AMR for only drugs that matter - no intrinsic resistance:
  example_isolates %>%
    filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
    group_by(ward) %>%
    summarise(across(not_intrinsic_resistant(), resistance))
}
#> ℹ Using column 'mo' as input for mo_genus()
#> ℹ For not_intrinsic_resistant() removing columns 'PEN'
#>   (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC'
#>   (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM'
#>   (azithromycin), and 'RIF' (rifampicin)
#> Warning: There were 52 warnings in `summarise()`.
#> The first warning was:
#>  In argument: `across(not_intrinsic_resistant(), resistance)`.
#>  In group 1: `ward = "Clinical"`.
#> Caused by warning:
#> ! Introducing NA: no results available for OXA in group: ward = "Clinical"
#> (minimum = 30).
#>  Run `dplyr::last_dplyr_warnings()` to see the 51 remaining warnings.
#> # A tibble: 3 × 33
#>   ward    OXA   FLC    AMX    AMC    AMP     TZP     CZO     FEP     CXM     FOX
#>   <chr> <dbl> <dbl>  <dbl>  <dbl>  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#> 1 Clin…    NA    NA  0.606  0.121  0.606  0.0504  0.0656  0.0159  0.0622  0.0648
#> 2 ICU      NA    NA  0.535  0.172  0.535  0.119  NA       0.0722  0.0828  0.0992
#> 3 Outp…    NA    NA NA     NA     NA     NA      NA      NA      NA      NA     
#> # … with 22 more variables: CTX <dbl>, CAZ <dbl>, CRO <dbl>, GEN <dbl>,
#> #   TOB <dbl>, AMK <dbl>, KAN <dbl>, TMP <dbl>, SXT <dbl>, NIT <dbl>,
#> #   FOS <dbl>, CIP <dbl>, MFX <dbl>, TCY <dbl>, TGC <dbl>, DOX <dbl>,
#> #   IPM <dbl>, MEM <dbl>, MTR <dbl>, CHL <dbl>, COL <dbl>, MUP <dbl>
if (require("dplyr")) {
  # get susceptibility for antibiotics whose name contains "trim":
  example_isolates %>%
    filter(first_isolate()) %>%
    group_by(ward) %>%
    summarise(across(ab_selector(name %like% "trim"), susceptibility))
}
#> ℹ For ab_selector(name %like% "trim") using columns 'TMP' (trimethoprim)
#>   and 'SXT' (trimethoprim/sulfamethoxazole)
#> # A tibble: 3 × 3
#>   ward         TMP   SXT
#>   <chr>      <dbl> <dbl>
#> 1 Clinical   0.627 0.808
#> 2 ICU        0.549 0.778
#> 3 Outpatient 0.667 0.821
if (require("dplyr")) {
  # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
  example_isolates %>%
    select(carbapenems())
}
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> # A tibble: 2,000 × 2
#>    IPM   MEM  
#>    <sir> <sir>
#>  1 NA    NA   
#>  2 NA    NA   
#>  3 NA    NA   
#>  4 NA    NA   
#>  5 NA    NA   
#>  6 NA    NA   
#>  7 NA    NA   
#>  8 NA    NA   
#>  9 NA    NA   
#> 10 NA    NA   
#> # … with 1,990 more rows
if (require("dplyr")) {
  # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
  example_isolates %>%
    select(mo, aminoglycosides())
}
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 2,000 × 5
#>    mo           GEN   TOB   AMK   KAN  
#>    <mo>         <sir> <sir> <sir> <sir>
#>  1 B_ESCHR_COLI NA    NA    NA    NA   
#>  2 B_ESCHR_COLI NA    NA    NA    NA   
#>  3 B_STPHY_EPDR NA    NA    NA    NA   
#>  4 B_STPHY_EPDR NA    NA    NA    NA   
#>  5 B_STPHY_EPDR NA    NA    NA    NA   
#>  6 B_STPHY_EPDR NA    NA    NA    NA   
#>  7 B_STPHY_AURS NA    S     NA    NA   
#>  8 B_STPHY_AURS NA    S     NA    NA   
#>  9 B_STPHY_EPDR NA    NA    NA    NA   
#> 10 B_STPHY_EPDR NA    NA    NA    NA   
#> # … with 1,990 more rows
if (require("dplyr")) {
  # any() and all() work in dplyr's filter() too:
  example_isolates %>%
    filter(
      any(aminoglycosides() == "R"),
      all(cephalosporins_2nd() == "R")
    )
}
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ For cephalosporins_2nd() using columns 'CXM' (cefuroxime) and 'FOX'
#>   (cefoxitin)
#> # A tibble: 112 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R    
#>  3 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
#>  4 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   
#>  5 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   
#>  6 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R    
#>  7 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R    
#>  8 2003-08-13 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
#>  9 2003-09-05 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
#> 10 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA   
#> # … with 102 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>
if (require("dplyr")) {
  # also works with c():
  example_isolates %>%
    filter(any(c(carbapenems(), aminoglycosides()) == "R"))
}
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> # A tibble: 531 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R    
#>  3 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  4 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S    
#>  5 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
#>  6 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S    
#>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  8 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S    
#> 10 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S    
#> # … with 521 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>
if (require("dplyr")) {
  # not setting any/all will automatically apply all():
  example_isolates %>%
    filter(aminoglycosides() == "R")
}
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
#>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
#> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around all() or
#>   any() to prevent this note.
#> # A tibble: 427 × 46
#>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  
#>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir>
#>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA   
#>  2 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  3 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S    
#>  4 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA   
#>  5 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S    
#>  6 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R    
#>  8 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S    
#>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S    
#> 10 2002-05-16 D25302     65 F      ICU      B_STRPT_ANGN S     NA    NA    S    
#> # … with 417 more rows, and 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>,
#> #   CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>,
#> #   CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>,
#> #   SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>,
#> #   VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>,
#> #   CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,
#> #   COL <sir>, MUP <sir>, RIF <sir>
if (require("dplyr")) {
  # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
  example_isolates %>%
    select(mo, ab_class("mycobact"))
}
#> ℹ For ab_class("mycobact") using column 'RIF' (rifampicin)
#> # A tibble: 2,000 × 2
#>    mo           RIF  
#>    <mo>         <sir>
#>  1 B_ESCHR_COLI R    
#>  2 B_ESCHR_COLI R    
#>  3 B_STPHY_EPDR NA   
#>  4 B_STPHY_EPDR NA   
#>  5 B_STPHY_EPDR NA   
#>  6 B_STPHY_EPDR NA   
#>  7 B_STPHY_AURS NA   
#>  8 B_STPHY_AURS NA   
#>  9 B_STPHY_EPDR NA   
#> 10 B_STPHY_EPDR NA   
#> # … with 1,990 more rows
if (require("dplyr")) {
  # get bug/drug combinations for only glycopeptides in Gram-positives:
  example_isolates %>%
    filter(mo_is_gram_positive()) %>%
    select(mo, glycopeptides()) %>%
    bug_drug_combinations() %>%
    format()
}
#> ℹ Using column 'mo' as input for mo_is_gram_positive()
#> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC'
#>   (teicoplanin)
#> # A tibble: 2 × 8
#>   Group           Drug             CoNS  E. fa…¹ S. au…² S. ep…³ S. ho…⁴ S. pn…⁵
#>   <chr>           <chr>            <chr> <chr>   <chr>   <chr>   <chr>   <chr>  
#> 1 "Glycopeptides" Teicoplanin (TE… ""    ""      " 0.0%… "64.1%… " 6.8%… ""     
#> 2 ""              Vancomycin (VAN… " 0.… " 0.0%… " 0.0%… " 0.0%… " 0.0%… " 0.0%…
#> # … with abbreviated variable names ¹​`E. faecalis`, ²​`S. aureus`,
#> #   ³​`S. epidermidis`, ⁴​`S. hominis`, ⁵​`S. pneumoniae`
if (require("dplyr")) {
  data.frame(
    some_column = "some_value",
    J01CA01 = "S"
  ) %>% # ATC code of ampicillin
    select(penicillins()) # only the 'J01CA01' column will be selected
}
#> ℹ For penicillins() using column 'J01CA01' (ampicillin)
#>   J01CA01
#> 1       S
if (require("dplyr")) {
  # 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)
}
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to
#>   prevent this note.
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to
#>   prevent this note.
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> [1] TRUE
# }