(v3.0.0.9019) Fixes #229, #230, #227, #225

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9018
+Version: 3.0.0.9019
-Date: 2025-08-07
+Date: 2025-09-01
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.0.9018
+# AMR 3.0.0.9019
 
 This is primarily a bugfix release, though we added one nice feature too.
 
@@ -15,11 +15,16 @@ This is primarily a bugfix release, though we added one nice feature too.
 * Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
 * Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
 * Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
-* Fixed `mdro()` to contain all reasons in verbose output (#227)
+* Fixed a bug the `antimicrobials` data set to remove statins (#229)
+* Fixed a bug in `mdro()` to make sure all genes specified in arguments are acknowledges
+* Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
 * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
 * Fixed some specific Dutch translations for antimicrobials
+* Added all reasons in verbose output of `mdro()` (#227)
 * Added `names` to `age_groups()` so that custom names can be given (#215)
 * Added note to `as.sir()` to make it explicit when higher-level taxonomic breakpoints are used (#218)
+* Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the `antimicrobials` data set (#225)
+* Updated Fosfomycin to be of antibiotic class 'Phosphonics' (#225)
 * Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms
 
 

R/mdro.R

@@ -174,48 +174,23 @@ mdro <- function(x = NULL,
   }
 
   # get gene values as TRUE/FALSE
-  if (is.character(esbl)) {
+  resolve_gene_var <- function(x, gene, varname) {
-    meet_criteria(esbl, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
+    if (is.character(gene)) {
-    esbl <- x[[esbl]]
+      meet_criteria(gene, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    meet_criteria(esbl, allow_class = "logical", allow_NA = TRUE)
+      gene <- x[[gene]]
-  } else if (length(esbl) == 1) {
+      meet_criteria(gene, allow_class = "logical", allow_NA = TRUE)
-    esbl <- rep(esbl, NROW(x))
+    } else if (length(gene) == 1) {
-  }
+      gene <- rep(gene, NROW(x))
-  if (is.character(carbapenemase)) {
+    }
-    meet_criteria(carbapenemase, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
+    x[[varname]] <- gene
-    carbapenemase <- x[[carbapenemase]]
+    x
-    meet_criteria(carbapenemase, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(carbapenemase) == 1) {
-    carbapenemase <- rep(carbapenemase, NROW(x))
-  }
-  if (is.character(mecA)) {
-    meet_criteria(mecA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecA <- x[[mecA]]
-    meet_criteria(mecA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecA) == 1) {
-    mecA <- rep(mecA, NROW(x))
-  }
-  if (is.character(mecC)) {
-    meet_criteria(mecC, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecC <- x[[mecC]]
-    meet_criteria(mecC, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecC) == 1) {
-    mecC <- rep(mecC, NROW(x))
-  }
-  if (is.character(vanA)) {
-    meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanA <- x[[vanA]]
-    meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanA) == 1) {
-    vanA <- rep(vanA, NROW(x))
-  }
-  if (is.character(vanB)) {
-    meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanB <- x[[vanB]]
-    meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanB) == 1) {
-    vanB <- rep(vanB, NROW(x))
   }
+  x <- resolve_gene_var(x, esbl, "esbl")
+  x <- resolve_gene_var(x, carbapenemase, "carbapenemase")
+  x <- resolve_gene_var(x, mecA, "mecA")
+  x <- resolve_gene_var(x, mecC, "mecC")
+  x <- resolve_gene_var(x, vanA, "vanA")
+  x <- resolve_gene_var(x, vanB, "vanB")
 
   info.bak <- info
   # don't throw info's more than once per call
@@ -1498,7 +1473,7 @@ mdro <- function(x = NULL,
     }
     trans_tbl(
       3, # positive
-      rows = which(x$order == "Enterobacterales" & esbl == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$esbl == TRUE),
       cols = "any",
       any_all = "any",
       reason = "Enterobacterales: ESBL"
@@ -1519,7 +1494,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x$order == "Enterobacterales" & carbapenemase == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$carbapenemase == TRUE),
       cols = "any",
       any_all = "any",
       reason = "Enterobacterales: carbapenemase"
@@ -1557,14 +1532,14 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       2, # unconfirmed
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(carbapenemase)),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(x$carbapenemase)),
       cols = carbapenems,
       any_all = "any",
       reason = "A. baumannii-calcoaceticus complex: potential carbapenemase"
     )
     trans_tbl(
       3,
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & carbapenemase == TRUE),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & x$carbapenemase == TRUE),
       cols = carbapenems,
       any_all = "any",
       reason = "A. baumannii-calcoaceticus complex: carbapenemase"
@@ -1574,6 +1549,7 @@ mdro <- function(x = NULL,
     x$psae <- 0
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R") | NA_as_FALSE(col_values(x, MEM) == "R"), 1, 0)
+    x$psae <- x$psae + ifelse(NA_as_FALSE(x$carbapenemase), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R") | NA_as_FALSE(col_values(x, CZA) == "R"), 1, 0)
     x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
@@ -1602,7 +1578,7 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (vanA == TRUE | vanB == TRUE)),
+      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (x$vanA == TRUE | x$vanB == TRUE)),
       cols = c(PEN, AMX, AMP, VAN),
       any_all = "any",
       reason = "E. faecium: vanA/vanB gene + penicillin group"
@@ -1611,14 +1587,14 @@ mdro <- function(x = NULL,
     # Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
     trans_tbl(
       2,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(x$mecA) | is.na(x$mecC))),
       cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
       any_all = "any",
       reason = "S. aureus complex: potential MRSA"
     )
     trans_tbl(
       3,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (x$mecA == TRUE | x$mecC == TRUE)),
       cols = "any",
       any_all = "any",
       reason = "S. aureus complex: mecA/mecC gene"
@@ -1899,7 +1875,10 @@ mdro <- function(x = NULL,
     # fill in empty reasons
     x$reason[is.na(x$reason)] <- "not covered by guideline"
     x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
+    # starting semicolons must be removed
     x$reason <- trimws(gsub("^;", "", x$reason))
+    # if criteria were not met initially, but later they were, then they have a following semicolon; remove the initial lack of meeting criteria
+    x$reason <- trimws(gsub("guideline criteria not met;", "", x$reason, fixed = TRUE))
     # format data set
     colnames(x)[colnames(x) == col_mo] <- "microorganism"
     x$microorganism <- mo_name(x$microorganism, language = NULL)

data-raw/ab.md5

@@ -1 +1 @@
-228840b3941753c4adee2b781d901590
+d12f1c78feaecbb4d1631f9c735ad49b

data-raw/datasets/antimicrobials.txt

@@ -116,7 +116,7 @@
 "CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"	"NA"			"NA"	"cefsulmid,cefsumido,cefsumidum"					"NA"
 "CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02,QJ01DI02"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
 "CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			"NA"	"NA"					"73604-1,73626-4,73649-6"
-"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
+"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cef,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
 "CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"			"cfav"	"avycaz,zavicefta"			6	"g"	"101483-6,73603-3,73625-6,73648-8,87734-0"
 "CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"czcl,tazcla,xtzl"	"NA"			6	"g"	"NA"
 "CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18,QJ01DD18"			"cefter"	"cefterame,cefteramum,ceftetrame"	0.4	"g"			"100047-0,76144-5"
@@ -162,7 +162,7 @@
 "CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01,QJ04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl,cyclos"	"cicloserina,closina,cyclorin,cycloserin,cycloserinum,farmiserina,levcicloserina,levcycloserine,levcycloserinum,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,wasserina"	0.75	"g"			"16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
 "DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04,QJ01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb,dalbav"	"dalbavancina,dalvance,xydalba,zeven"			1.5	"g"	"41688-3,41689-1,41690-9,41734-5"
 "DAN"	71335	"Danofloxacin"	"Fluoroquinolones"	"QJ01MA92"			"danofl"	"advocin,danofloxacine,danofloxacino,danofloxacinum"					"73601-7,73623-1,73646-2"
-"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"NA"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
+"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"dao"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
 "DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09,QJ01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt,dapt25,dapt50,daptom"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin"			0.28	"g"	"35787-1,35788-9,35789-7,41691-7"
 "DFX"	487101	"Delafloxacin"	"Fluoroquinolones"	"J01MA23,QJ01MA23"			"NA"	"baxdela,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	"88885-9,90447-4,93790-4"
 "DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06,QJ04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"deltyba"	0.2	"g"			"93851-4,96109-4"
@@ -184,7 +184,7 @@
 "ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13,QJ01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"xerava"			0.14	"g"	"100049-6,85423-2,93767-2"
 "ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03,QJ01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,ertape,etp"	"ertapenemsalt,invanz"			1	"g"	"101486-9,35799-6,35800-2,35801-0,35802-8"
 "ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,ery32,eryt,eryth"	"abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid"	2	"g"	1	"g"	"100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
-"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
+"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"emb,etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
 "ETI"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"J04AM03,QJ04AM03"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03,QJ04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi,ethion"	"aethionamidum,aetina,aetiva,amidazin,amidazine,atina,ethimide,ethina,ethinamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,trekator,trescatyl,trescazide,tubenamide,tubermin,tuberoid,tuberoson"	0.75	"g"			"16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
 "ETO"	6034	"Ethopabate"	"Other antibacterials"	"QP51AX17"			"NA"	"ethopabat"					"NA"
@@ -202,7 +202,7 @@
 "FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07,QJ01MB07"	"Quinolone antibacterials"	"Other quinolones"	"flumeq"	"apurone,fantacin,flumequina,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl"	1.2	"g"			"55675-3,55676-1,55677-9,55678-7"
 "FLR1"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"J01FA14,QJ01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar"	0.75	"g"			"NA"
 "FFL"	214356	"Fosfluconazole"	"Antifungals/antimycotics"	"NA"			"NA"	"fosfluconazol,procif,prodif"					"NA"
-"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
+"FOS"	446987	"Fosfomycin"	"Phosphonics"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
 "FMD"	572	"Fosmidomycin"	"Other antibacterials"	"NA"			"NA"	"fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum"					"NA"
 "FRM"	8378	"Framycetin"	"Aminoglycosides"	"D09AA01,QD09AA01,QJ01GB91,QR01AX08,QS01AA07,R01AX08,S01AA07"			"fram,framyc"	"actilin,actiline,antibiotique,bycomycin,enterfram,fradiomycin,fradiomycinum,framicetina,framidal,framycetine,framycetinum,framycin,framygen,francetin,jernadex,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycine,neomycinum,nivemycin,soframycin,soframycine"					"18926-6,257-6,258-4,259-2,260-0,55679-5"
 "FUR"	6870646	"Furazidin"	"Other antibacterials"	"J01XE03,QJ01XE03"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"akritoin,furagin,furaginum,furamag,furazidine,hydantoin"	0.3	"g"			"NA"
@@ -268,7 +268,7 @@
 "MET"	6087	"Meticillin"	"Beta-lactams/penicillins"	"J01CF03,QJ01CF03,QJ51CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"methic,meti"	"belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin"			4	"g"	"NA"
 "MTP"	68590	"Metioprim"	"Other antibacterials"	"NA"			"NA"	"methioprim,metioprima,metioprime,metioprimum"					"NA"
 "MXT"	3047729	"Metioxate"	"Fluoroquinolones"	"NA"			"NA"	"metioxato,metioxatum"					"NA"
-"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
+"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz,mtz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
 "MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10,QJ01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mezlo,mz"	"baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,mezlocillinum,multocillin"			6	"g"	"18947-2,330-1,331-9,332-7,333-5,3820-8,41702-2,54194-6,54195-3,54196-1"
 "MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"mezsul"	"NA"					"54194-6,54195-3,54196-1"
 "MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05,QJ02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica,micafu"	"fungard,funguard,micafungina,micafunginsalt,mycamine"			0.1	"g"	"53812-4,58418-5,65340-2,85048-7"
@@ -339,7 +339,7 @@
 "PMR"	5284447	"Pimaricin"	"Antifungals/antimycotics"	"NA"			"natamycin"	"delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin"					"NA"
 "PPA"	4831	"Pipemidic acid"	"Quinolones"	"J01MB04,QJ01MB04"	"Quinolone antibacterials"	"Other quinolones"	"pipaci,pipz,pizu"	"deblaston,dolcol,filtrax,karunomazin,memento,nuril,palin,pipedac,pipemid,pipemidate,pipemidic,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval"	0.8	"g"			"NA"
 "PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12,QJ01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pipera,pp"	"penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,tazocin"			14	"g"	"101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1"
-"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
+"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
 "TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"piptazobactam,tazonam,zobactin,zosyn"			14	"g"	"101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
 "PRC"	71978	"Piridicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"					"NA"
 "PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"	"QJ51FF90"			"pirlim"	"pirlimycina,pirlimycine,pirlimycinum,pirsue"					"35829-1,35830-9,35831-7"
@@ -370,7 +370,7 @@
 "RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02,QL01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali"	0.45	"g"			"NA"
 "RST"	33042	"Ribostamycin"	"Aminoglycosides"	"J01GB10,QJ01GB10"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"NA"	"exaluren,hetangmycin,ribastamin,ribostamicina,ribostamycine,ribostamycinum,vistamycin,xylostatin"			1	"g"	"NA"
 "RID1"	16659285	"Ridinilazole"	"Other antibacterials"	"NA"			"NA"	"ridinilazol"					"NA"
-"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
+"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rfb,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
 "RIF"	135398735	"Rifampicin"	"Antimycobacterials"	"J04AB02,QJ04AB02,QJ54AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa,rifamp"	"abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin"	0.6	"g"	0.6	"g"	"NA"
 "REI"	135483893	"Rifampicin/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM07,QJ04AM07"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"isonarif,rifamate,rifamazid"					"NA"
 "RFI"		"Rifampicin/isoniazid"	"Antimycobacterials"	"J04AM02,QJ04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
@@ -391,7 +391,6 @@
 "SRC"	54681908	"Sarecycline"	"Tetracyclines"	"J01AA14,QJ01AA14"	"Tetracyclines"	"Tetracyclines"	"NA"	"sareciclina,seysara"	0.1	"g"			"NA"
 "SRX"	9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"sarmoxillina,sarmoxilline,sarmoxillinum"					"NA"
 "SEC"	71815	"Secnidazole"	"Other antibacterials"	"P01AB07"			"NA"	"flagentyl,secnidal,secnidazolum,secnil,sindose,solosec"	2	"g"			"NA"
-"SMF"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"C10BA04,QC10BA04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	"NA"					"NA"
 "SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08,QJ01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso,sisomy"	"rickamicin,salvamina,sisomicina,sisomicine,sisomicinum,sisomin,sisomycin,sissomicin,sizomycin"			0.24	"g"	"18979-5,447-3,448-1,449-9,450-7,55714-0"
 "SIT"	461399	"Sitafloxacin"	"Fluoroquinolones"	"J01MA21,QJ01MA21"			"sitafl"	"gracevit"	0.1	"g"			"NA"
 "SDA"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"J04AA02,QJ04AA02"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	"NA"	"bactylan,lepasen,monopas,tubersan"	14	"g"	14	"g"	"NA"
@@ -495,4 +494,4 @@
 "VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03,QJ02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vorico,vrc"	"vfend,voriconazol,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
 "XBR"	72144	"Xibornol"	"Other antibacterials"	"J01XX02,QJ01XX02"	"Other antibacterials"	"Other antibacterials"	"NA"	"bactacine,bracen,nanbacine,xibornolo,xibornolum"					"NA"
 "ZID"	77846445	"Zidebactam"	"Other antibacterials"	"NA"			"NA"	"zidebactamsalt"					"NA"
-"ZFD"		"Zoliflodacin"		"NA"			"NA"	"NA"					"NA"
+"ZFD"		"Zoliflodacin"		"NA"			"zol"	"NA"					"NA"

man/antimicrobial_selectors.Rd

@@ -181,7 +181,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr 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)
 \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr 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)
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 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)
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 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), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), 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)
 \item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr 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)
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)

man/antimicrobials.Rd

@@ -5,9 +5,9 @@
 \alias{antimicrobials}
 \alias{antibiotics}
 \alias{antivirals}
-\title{Data Sets with 617 Antimicrobial Drugs}
+\title{Data Sets with 616 Antimicrobial Drugs}
 \format{
-\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 497 observations and 14 variables:}{
+\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
 \itemize{
 \item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
 \item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
@@ -50,7 +50,7 @@ LOINC:
 }
 }
 
-An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.
 
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }

man/custom_eucast_rules.Rd

@@ -103,7 +103,7 @@ These 35 antimicrobial groups are allowed in the rules (case-insensitive) and ca
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
-\item antimycobacterials\cr(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, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
+\item antimycobacterials\cr(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)
 \item betalactams\cr(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/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, 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, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
 \item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, 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)
 \item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)

man/custom_mdro_guideline.Rd

@@ -99,7 +99,7 @@ All 35 antimicrobial selectors are supported for use in the rules:
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
 \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin and ampicillin
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 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, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 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
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr 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/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, 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, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam
 \item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, 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
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem