Built site for AMR@3.0.1.9057: 0af3f84

2026-05-31 16:21:42 +02:00 · 2026-05-02 13:06:13 +00:00
parent 6fbd9e4b9f
commit 9447e0f2c2
107 changed files with 905 additions and 1160 deletions
--- a/reference/custom_interpretive_rules.md
+++ b/reference/custom_interpretive_rules.md
@@ -0,0 +1,551 @@
+# Define Custom Interpretive Rules
+
+Define custom interpretive rules for your organisation or specific
+analysis and use the output of this function in
+[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md).
+
+## Usage
+
+``` r
+custom_interpretive_rules(...)
+```
+
+## Arguments
+
+- ...:
+
+  Rules in [formula](https://rdrr.io/r/base/tilde.html) notation, see
+  below for instructions, and in *Examples*.
+
+## Value
+
+A [list](https://rdrr.io/r/base/list.html) containing the custom rules
+
+## Details
+
+Some organisations have their own adoption of interpretive rules. This
+function can be used to define custom rules to be used in the
+[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
+function.
+
+### Basics
+
+If you are familiar with the
+[`case_when()`](https://dplyr.tidyverse.org/reference/case-and-replace-when.html)
+function of the `dplyr` package, you will recognise the input method to
+set your own rules. Rules must be set using what R considers to be the
+'formula notation'. The rule itself is written *before* the tilde (`~`)
+and the consequence of the rule is written *after* the tilde:
+
+    x <- custom_interpretive_rules(TZP == "S" ~ aminopenicillins == "S",
+                                   TZP == "R" ~ aminopenicillins == "R")
+
+These are two custom interpretive rules: if TZP
+(piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and
+amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must
+be made "R". These rules can also be printed to the console, so it is
+immediately clear how they work:
+
+    x
+    #> A set of custom interpretive rules:
+    #>
+    #>   1. If TZP is "S" then set to  S :
+    #>      amoxicillin (AMX), ampicillin (AMP)
+    #>
+    #>   2. If TZP is "R" then set to  R :
+    #>      amoxicillin (AMX), ampicillin (AMP)
+
+The rules (the part *before* the tilde, in above example `TZP == "S"`
+and `TZP == "R"`) must be evaluable in your data set: it should be able
+to run as a filter in your data set without errors. This means for the
+above example that the column `TZP` must exist. We will create a sample
+data set and test the rules set:
+
+    df <- data.frame(mo = c("Escherichia coli", "Klebsiella pneumoniae"),
+                     TZP = as.sir("R"),
+                     ampi = as.sir("S"),
+                     cipro = as.sir("S"))
+    df
+    #>                      mo TZP ampi cipro
+    #> 1      Escherichia coli   R    S     S
+    #> 2 Klebsiella pneumoniae   R    S     S
+
+    interpretive_rules(df,
+                       rules = "custom",
+                       custom_rules = x,
+                       info = FALSE,
+                       overwrite = TRUE)
+    #>                      mo TZP ampi cipro
+    #> 1      Escherichia coli   R    R     S
+    #> 2 Klebsiella pneumoniae   R    R     S
+
+### Using taxonomic properties in rules
+
+There is one exception in columns used for the rules: all column names
+of the
+[microorganisms](https://amr-for-r.org/reference/microorganisms.md) data
+set can also be used, but do not have to exist in the data set. These
+column names are: `"mo"`, `"fullname"`, `"status"`, `"kingdom"`,
+`"phylum"`, `"class"`, `"order"`, `"family"`, `"genus"`, `"species"`,
+`"subspecies"`, `"rank"`, `"ref"`, `"oxygen_tolerance"`, `"source"`,
+`"lpsn"`, `"lpsn_parent"`, `"lpsn_renamed_to"`, `"mycobank"`,
+`"mycobank_parent"`, `"mycobank_renamed_to"`, `"gbif"`, `"gbif_parent"`,
+`"gbif_renamed_to"`, `"prevalence"`, and `"snomed"`. Thus, this next
+example will work as well, despite the fact that the `df` data set does
+not contain a column `genus`:
+
+    y <- custom_interpretive_rules(
+      TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
+      TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R"
+    )
+
+    interpretive_rules(df,
+                       rules = "custom",
+                       custom_rules = y,
+                       info = FALSE,
+                       overwrite = TRUE)
+    #>                      mo TZP ampi cipro
+    #> 1      Escherichia coli   R    S     S
+    #> 2 Klebsiella pneumoniae   R    R     S
+
+### Sharing rules among multiple users
+
+The rules set (the `y` object in this case) could be exported to a
+shared file location using
+[`saveRDS()`](https://rdrr.io/r/base/readRDS.html) if you collaborate
+with multiple users. The custom rules set could then be imported using
+[`readRDS()`](https://rdrr.io/r/base/readRDS.html).
+
+### Usage of multiple antimicrobials and antimicrobial group names
+
+You can define antimicrobial groups instead of single antimicrobials for
+the rule consequence, which is the part *after* the tilde (~). In the
+examples above, the antimicrobial group `aminopenicillins` includes both
+ampicillin and amoxicillin.
+
+Rules can also be applied to multiple antimicrobials and antimicrobial
+groups simultaneously. Use the [`c()`](https://rdrr.io/r/base/c.html)
+function to combine multiple antimicrobials. For instance, the following
+example sets all aminopenicillins and ureidopenicillins to "R" if column
+TZP (piperacillin/tazobactam) is "R":
+
+    x <- custom_interpretive_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R")
+    x
+    #> A set of custom interpretive rules:
+    #>
+    #>   1. If TZP is "R" then set to "R":
+    #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
+
+These 43 antimicrobial groups are allowed in the rules
+(case-insensitive) and can be used in any combination:
+
+- aminocoumarins  
+  (clorobiocin, novobiocin, and penicillin/novobiocin)
+
+- aminoglycosides  
+  (amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin,
+  bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high,
+  habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high,
+  kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin,
+  pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,
+  streptoduocin, streptomycin, streptomycin-high, tobramycin, and
+  tobramycin-high)
+
+- aminopenicillins  
+  (amoxicillin, amoxicillin/clavulanic acid, and ampicillin)
+
+- antifungals  
+  (amorolfine, amphotericin B, amphotericin B-high, anidulafungin,
+  butoconazole, caspofungin, ciclopirox, clotrimazole, econazole,
+  fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin,
+  ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole,
+  manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin,
+  posaconazole, rezafungin, ribociclib, sulconazole, terbinafine,
+  terconazole, and voriconazole)
+
+- antimycobacterials  
+  (4-aminosalicylic acid, calcium aminosalicylate, capreomycin,
+  clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid,
+  ethionamide, isoniazid,
+  isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide,
+  p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide,
+  rifabutin, rifampicin, rifampicin/ethambutol/isoniazid,
+  rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid,
+  rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium
+  aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone,
+  thioacetazone/isoniazid, tiocarlide, and viomycin)
+
+- betalactamase_inhibitors  
+  (amoxicillin/clavulanic acid, amoxicillin/sulbactam,
+  ampicillin/sulbactam, avibactam, aztreonam/avibactam,
+  aztreonam/nacubactam, cefepime/enmetazobactam, cefepime/nacubactam,
+  cefepime/taniborbactam, cefepime/tazobactam, cefepime/zidebactam,
+  cefoperazone/sulbactam, cefotaxime/sulbactam, ceftaroline/avibactam,
+  ceftazidime/avibactam, ceftibuten/avibactam, ceftolozane/tazobactam,
+  imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam,
+  mezlocillin/sulbactam, nacubactam, penicillin/sulbactam,
+  piperacillin/sulbactam, piperacillin/tazobactam, sulbactam,
+  sultamicillin, taniborbactam, tazobactam, ticarcillin/clavulanic acid,
+  xeruborbactam, and zidebactam)
+
+- betalactams  
+  (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam,
+  ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin,
+  azidocillin, azlocillin, aztreonam, aztreonam/avibactam,
+  aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin,
+  benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin
+  screening test, biapenem, carbenicillin, carindacillin, carumonam,
+  cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin,
+  cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene,
+  cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime,
+  cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam,
+  cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam,
+  cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol,
+  cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole,
+  cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam,
+  ceforanide, cefoselis, cefotaxime, cefotaxime screening test,
+  cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam,
+  cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test,
+  cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime,
+  cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil,
+  cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline,
+  ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam,
+  ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
+  ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
+  alapivoxil, ceftobiprole, ceftobiprole medocaril,
+  ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
+  inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin,
+  clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin,
+  ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA,
+  imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam,
+  meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin,
+  meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin,
+  oxacillin screening test, panipenem, penamecillin,
+  penicillin/novobiocin, penicillin/sulbactam, pheneticillin,
+  phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam,
+  piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam,
+  procaine benzylpenicillin, propicillin, razupenem, ritipenem,
+  ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin,
+  talampicillin, taniborbactam, tebipenem, temocillin, ticarcillin,
+  ticarcillin/clavulanic acid, and tigemonam)
+
+- betalactams_with_inhibitor  
+  (amoxicillin/clavulanic acid, amoxicillin/sulbactam,
+  ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam,
+  cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam,
+  cefepime/nacubactam, cefepime/taniborbactam, cefepime/tazobactam,
+  cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic
+  acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid,
+  ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic
+  acid, ceftibuten/avibactam, ceftolozane/tazobactam,
+  ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam,
+  meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam,
+  penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam,
+  piperacillin/tazobactam, and ticarcillin/clavulanic acid)
+
+- carbapenems  
+  (biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA,
+  imipenem/relebactam, meropenem, meropenem/nacubactam,
+  meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem
+  acoxil, taniborbactam, and tebipenem)
+
+- cephalosporins  
+  (cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine,
+  cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin,
+  cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren
+  pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid,
+  cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam,
+  cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet
+  pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime,
+  cefmetazole, cefodizime, cefonicid, cefoperazone,
+  cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime
+  screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam,
+  cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin
+  screening test, cefozopran, cefpimizole, cefpiramide, cefpirome,
+  cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid,
+  cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide,
+  ceftaroline, ceftaroline/avibactam, ceftazidime,
+  ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram
+  pivoxil, ceftezole, ceftibuten, ceftibuten/avibactam, ceftiofur,
+  ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole
+  medocaril, ceftolozane/tazobactam, ceftriaxone,
+  ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil,
+  cephradine, latamoxef, and loracarbef)
+
+- cephalosporins_1st  
+  (cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin,
+  cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole,
+  and cephradine)
+
+- cephalosporins_2nd  
+  (cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan,
+  cefotiam, cefoxitin, cefoxitin screening test, cefprozil, cefuroxime,
+  cefuroxime axetil, and loracarbef)
+
+- cephalosporins_3rd  
+  (cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren
+  pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime,
+  cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime,
+  cefotaxime screening test, cefotaxime/clavulanic acid,
+  cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole,
+  cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic
+  acid, cefsulodin, ceftazidime, ceftazidime/avibactam,
+  ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten,
+  ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime alapivoxil,
+  ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)
+
+- cephalosporins_4th  
+  (cefepime, cefepime/amikacin, cefepime/clavulanic acid,
+  cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam,
+  cefepime/tazobactam, cefepime/zidebactam, cefetecol, cefoselis,
+  cefozopran, cefpirome, and cefquinome)
+
+- cephalosporins_5th  
+  (ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole
+  medocaril, and ceftolozane/tazobactam)
+
+- cephalosporins_except_caz  
+  (cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine,
+  cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin,
+  cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren
+  pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid,
+  cefepime/enmetazobactam, cefepime/nacubactam, cefepime/taniborbactam,
+  cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet
+  pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime,
+  cefmetazole, cefodizime, cefonicid, cefoperazone,
+  cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime
+  screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam,
+  cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin
+  screening test, cefozopran, cefpimizole, cefpiramide, cefpirome,
+  cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid,
+  cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide,
+  ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam,
+  ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole,
+  ceftibuten, ceftibuten/avibactam, ceftiofur, ceftizoxime, ceftizoxime
+  alapivoxil, ceftobiprole, ceftobiprole medocaril,
+  ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase
+  inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and
+  loracarbef)
+
+- fluoroquinolones  
+  (besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole,
+  ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin,
+  danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin,
+  finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin,
+  grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole,
+  levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin,
+  moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline,
+  norfloxacin, norfloxacin screening test, norfloxacin/metronidazole,
+  norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin,
+  pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin,
+  premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin,
+  sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and
+  trovafloxacin)
+
+- fusidanes  
+  (fusidic acid)
+
+- glycopeptides  
+  (avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin,
+  ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin,
+  vancomycin, vancomycin-macromethod, and zorbamycin)
+
+- glycopeptides_except_lipo  
+  (avoparcin, bleomycin, norvancomycin, ramoplanin, teicoplanin,
+  teicoplanin-macromethod, vancomycin, vancomycin-macromethod, and
+  zorbamycin)
+
+- ionophores  
+  (lasalocid, monensin sodium, narasin, nystatin, and salinomycin)
+
+- isoxazolylpenicillins  
+  (cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin,
+  and oxacillin screening test)
+
+- lincosamides  
+  (clindamycin, clindamycin inducible screening test, lincomycin, and
+  pirlimycin)
+
+- lipoglycopeptides  
+  (dalbavancin, oritavancin, and telavancin)
+
+- macrolides  
+  (acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin,
+  clindamycin inducible screening test, dirithromycin, erythromycin,
+  flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin,
+  midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin,
+  primycin, rokitamycin, roxithromycin, solithromycin, spiramycin,
+  telithromycin, tildipirosin, tilmicosin, troleandomycin,
+  tulathromycin, tylosin, and tylvalosin)
+
+- monobactams  
+  (aztreonam, aztreonam/avibactam, aztreonam/nacubactam, carumonam, and
+  tigemonam)
+
+- nitrofurans  
+  (furazidin, furazolidone, nifurtoinol, nitrofurantoin, and
+  nitrofurazone)
+
+- oxazolidinones  
+  (cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)
+
+- penicillins  
+  (amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam,
+  ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin,
+  azidocillin, azlocillin, bacampicillin, benzathine benzylpenicillin,
+  benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin
+  screening test, carbenicillin, carindacillin, ciclacillin,
+  clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin,
+  hetacillin, lenampicillin, mecillinam, metampicillin, meticillin,
+  mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin
+  screening test, penamecillin, penicillin/novobiocin,
+  penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin,
+  piperacillin, piperacillin/sulbactam, piperacillin/tazobactam,
+  piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin,
+  propicillin, sarmoxicillin, sulbenicillin, sultamicillin,
+  talampicillin, temocillin, ticarcillin, and ticarcillin/clavulanic
+  acid)
+
+- peptides  
+  (avoparcin, bacitracin, bleomycin, dalbavancin, daptomycin,
+  norvancomycin, oritavancin, ramoplanin, teicoplanin,
+  teicoplanin-macromethod, telavancin, thiostrepton, vancomycin,
+  vancomycin-macromethod, and zorbamycin)
+
+- phenicols  
+  (chloramphenicol, florfenicol, and thiamphenicol)
+
+- phosphonics  
+  (amikacin/fosfomycin and fosfomycin)
+
+- pleuromutilins  
+  (retapamulin and tiamulin)
+
+- polymyxins  
+  (colistin, polymyxin B, and polymyxin B/polysorbate 80)
+
+- quinolones  
+  (besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole,
+  ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin,
+  danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin,
+  finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin,
+  gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin,
+  levofloxacin/ornidazole, levonadifloxacin, lomefloxacin,
+  marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin,
+  nalidixic acid, nalidixic acid screening test, nemonoxacin,
+  nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test,
+  norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin,
+  ofloxacin/ornidazole, orbifloxacin, oxolinic acid, ozenoxacin,
+  pazufloxacin, pefloxacin, pefloxacin screening test, pipemidic acid,
+  piromidic acid, pradofloxacin, premafloxacin, prulifloxacin,
+  rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin,
+  temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)
+
+- rifamycins  
+  (rifabutin, rifampicin, rifampicin/ethambutol/isoniazid,
+  rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid,
+  rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine)
+
+- spiropyrimidinetriones  
+  (zoliflodacin)
+
+- streptogramins  
+  (ostreogrycin, pristinamycin, quinupristin/dalfopristin, and
+  virginiamycine)
+
+- sulfonamides  
+  (isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
+  ormetroprim/sulfamethoxazole, sulfachlorpyridazine, sulfadiazine,
+  sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine,
+  sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole,
+  sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine,
+  sulfamerazine/trimethoprim, sulfamethazine, sulfamethizole,
+  sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine,
+  sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole,
+  sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole,
+  sulfapyridine, sulfasuccinamide, sulfathiazole, sulfathiourea,
+  sulfisoxazole, sulfonamide, and trimethoprim/sulfamethoxazole)
+
+- tetracyclines  
+  (cetocycline, chlortetracycline, clomocycline, demeclocycline,
+  doxycycline, eravacycline, lymecycline, metacycline, minocycline,
+  omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
+  sarecycline, tetracycline, tetracycline screening test,
+  tetracycline/oleandomycin, and tigecycline)
+
+- tetracyclines_except_tgc  
+  (cetocycline, chlortetracycline, clomocycline, demeclocycline,
+  doxycycline, eravacycline, lymecycline, metacycline, minocycline,
+  omadacycline, oxytetracycline, penimepicycline, rolitetracycline,
+  sarecycline, tetracycline, tetracycline screening test, and
+  tetracycline/oleandomycin)
+
+- trimethoprims  
+  (brodimoprim, iclaprim,
+  isoniazid/sulfamethoxazole/trimethoprim/pyridoxine,
+  ormetroprim/sulfamethoxazole, sulfadiazine, sulfadiazine/tetroxoprim,
+  sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine,
+  sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine,
+  sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim,
+  sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine,
+  sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim,
+  sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin,
+  sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea,
+  trimethoprim, and trimethoprim/sulfamethoxazole)
+
+- ureidopenicillins  
+  (azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)
+
+## Examples
+
+``` r
+x <- custom_interpretive_rules(
+  AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
+  AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I"
+)
+x
+#> A set of custom interpretive rules:
+#> 
+#>   1. If AMC is  R  and genus is "Klebsiella" then set to  R :
+#>      amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
+#> 
+#>   2. If AMC is  I  and genus is "Klebsiella" then set to  I :
+#>      amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
+
+# run the custom rule set (verbose = TRUE will return a logbook instead of the data set):
+eucast_rules(example_isolates,
+  rules = "custom",
+  custom_rules = x,
+  info = FALSE,
+  overwrite = TRUE,
+  verbose = TRUE
+)
+#> # A tibble: 8 × 9
+#>     row col   mo_fullname     old   new   rule  rule_group rule_name rule_source
+#>   <int> <chr> <chr>           <ord> <chr> <chr> <chr>      <chr>     <chr>      
+#> 1    33 AMP   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 2    33 AMX   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 3    34 AMP   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 4    34 AMX   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 5   531 AMP   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 6   531 AMX   Klebsiella pne… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 7  1485 AMP   Klebsiella oxy… R     I     "rep… Custom in… Custom i… Object 'x'…
+#> 8  1485 AMX   Klebsiella oxy… R     I     "rep… Custom in… Custom i… Object 'x'…
+
+# combine rule sets
+x2 <- c(
+  x,
+  custom_interpretive_rules(TZP == "R" ~ carbapenems == "R")
+)
+x2
+#> A set of custom interpretive rules:
+#> 
+#>   1. If AMC is  R  and genus is "Klebsiella" then set to  R :
+#>      amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
+#> 
+#>   2. If AMC is  I  and genus is "Klebsiella" then set to  I :
+#>      amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), ampicillin (AMP)
+#> 
+#>   3. If TZP is  R  then set to  R :
+#>      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), taniborbactam (TAN), tebipenem (TBP)
+```