diff --git a/DESCRIPTION b/DESCRIPTION index a108c602..4b92b609 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9047 +Version: 2.1.1.9048 Date: 2024-06-13 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 59627cb0..3c7875fe 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9047 +# AMR 2.1.1.9048 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)* diff --git a/R/aa_globals.R b/R/aa_globals.R index ba55480d..dd983efc 100755 --- a/R/aa_globals.R +++ b/R/aa_globals.R @@ -161,6 +161,7 @@ globalVariables(c( "microorganisms", "microorganisms.codes", "mo", + "n", "name", "new", "numerator", @@ -186,8 +187,10 @@ globalVariables(c( "total", "txt", "type", + "uti_index", "value", "varname", + "x", "xvar", "y", "year", diff --git a/R/sir.R b/R/sir.R index cefb7fed..3ce6fc4a 100755 --- a/R/sir.R +++ b/R/sir.R @@ -362,10 +362,16 @@ as.sir.default <- function(x, x[x.bak == 2] <- "I" x[x.bak == 3] <- "R" } - } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "SDD", "I", "R", "N", NA_character_))) { + } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) { x[x.bak == "1"] <- "S" x[x.bak == "2"] <- "I" x[x.bak == "3"] <- "R" + } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "4", "5", "S", "SDD", "I", "R", "N", NA_character_))) { + x[x.bak == "1"] <- "S" + x[x.bak == "2"] <- "SDD" + x[x.bak == "3"] <- "I" + x[x.bak == "4"] <- "R" + x[x.bak == "5"] <- "N" } else if (!all(is.na(x)) && !identical(levels(x), c("S", "SDD", "I", "R", "N")) && !all(x %in% c("S", "SDD", "I", "R", "N", NA))) { if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) { # check if they are actually MICs or disks @@ -1133,7 +1139,7 @@ as_sir_method <- function(method_short, if (all(uti_current == FALSE, na.rm = TRUE)) { breakpoints_current <- breakpoints_current %pm>% # this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE - pm_mutate(uti_index = ifelse(uti == FALSE, 1, + pm_mutate(uti_index = ifelse(is.na(uti) & uti == FALSE, 1, ifelse(is.na(uti), 2, 3))) %pm>% # be as specific as possible (i.e. prefer species over genus): @@ -1170,22 +1176,22 @@ as_sir_method <- function(method_short, } else { site <- paste0("body site '", site, "'") } - if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_coerced)) { + if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) { # only UTI breakpoints available warning_("in `as.sir()`: interpretation of ", font_bold(ab_formatted), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See `?as.sir`.") rise_warning <- TRUE - } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_coerced)) { + } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) { # both UTI and Non-UTI breakpoints available msgs <- c(msgs, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`.")) breakpoints_current <- breakpoints_current %pm>% pm_filter(uti == FALSE) - } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_coerced)) { + } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) { # breakpoints for multiple body sites available msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ".")) } # first check if mo is intrinsic resistant - if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_coerced) %in% AMR_env$intrinsic_resistant) { + if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_current) %in% AMR_env$intrinsic_resistant) { msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, "")) new_sir <- rep(as.sir("R"), length(rows)) } else if (nrow(breakpoints_current) == 0) { diff --git a/R/sysdata.rda b/R/sysdata.rda index ee918470..df810d0d 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/vctrs.R b/R/vctrs.R index dd86f5c3..db8855cd 100755 --- a/R/vctrs.R +++ b/R/vctrs.R @@ -179,10 +179,13 @@ vec_arith.mic <- function(op, x, y, ...) { # S3: sir ---- vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") { - x + NA_sir_[0] } vec_ptype2.sir.sir <- function(x, y, ...) { - x + NA_sir_[0] +} +vec_ptype2.character.sir <- function(x, y, ...) { + NA_sir_[0] } vec_cast.character.sir <- function(x, to, ...) { as.character(x) diff --git a/R/zzz.R b/R/zzz.R index 6399a473..8af3068b 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -176,6 +176,7 @@ AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %o # S3: sir s3_register("vctrs::vec_ptype2", "sir.default") s3_register("vctrs::vec_ptype2", "sir.sir") + s3_register("vctrs::vec_ptype2", "character.sir") s3_register("vctrs::vec_cast", "character.sir") s3_register("vctrs::vec_cast", "sir.character") diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index 3d39d280..c4d8b529 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -3e7a1cbb21b49cdc7626ea3016a017cc +4e536434d1301bedaec0e856c74cded8 diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index 132bec46..3b0df444 100644 Binary files a/data-raw/antibiotics.dta and b/data-raw/antibiotics.dta differ diff --git a/data-raw/antibiotics.feather b/data-raw/antibiotics.feather index 83695f8e..0f296293 100644 Binary files a/data-raw/antibiotics.feather and b/data-raw/antibiotics.feather differ diff --git a/data-raw/antibiotics.rds b/data-raw/antibiotics.rds index 22c42faa..cf13ab0b 100644 Binary files a/data-raw/antibiotics.rds and b/data-raw/antibiotics.rds differ diff --git a/data-raw/antibiotics.sav b/data-raw/antibiotics.sav index 6ab74931..7ad2bc02 100644 Binary files a/data-raw/antibiotics.sav and b/data-raw/antibiotics.sav differ diff --git a/data-raw/antibiotics.txt b/data-raw/antibiotics.txt index 9e1718cc..f3e97728 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -9,7 +9,7 @@ "AMC" 23665637 "Amoxicillin/clavulanic acid" "Beta-lactams/penicillins" "J01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/c,amcl,aml,aug,xl" "amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,augmentan,augmentin,augmentin xr,augmentine,auspilic,clamentin,clamobit,clavamox,clavinex,clavoxilin plus,clavulin,clavumox,coamoxiclav,eumetinex,kmoxilin,spectramox,spektramox,synulox,viaclav,xiclav" 1.5 "g" 3 "g" "" "AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "NA" "" "" "55614-2,55615-9,55616-7" "AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "A01AB04,A07AA07,G01AA03,J02AA01" "Antimycotics for systemic use" "Antibiotics" "amf,amfb,amph" "abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon" 40 "mg" 210 "mg" "16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1" -"AMH" "Amphotericin B-high" "Aminoglycosides" "NA" "amfo b high,amhl,ampho b high,amphotericin high" "" "" +"AMH" "Amphotericin B-high" "Antifungals/antimycotics" "NA" "amfo b high,amhl,ampho b high,amphotericin high" "" "" "AMP" 6249 "Ampicillin" "Beta-lactams/penicillins" "J01CA01,S01AA19" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "am,amp,ampi" "acillin,adobacillin,amblosin,amcill,amfipen,amfipen v,amipenix s,ampichel,ampicil,ampicilina,ampicillin,ampicillin a,ampicillin acid,ampicillin anhydrate,ampicillin anhydrous,ampicillin base,ampicillin hydrate,ampicillin sodium,ampicillina,ampicilline,ampicillinum,ampicin,ampifarm,ampikel,ampimed,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,anhydrous ampicillin,austrapen,binotal,bonapicillin,britacil,campicillin,copharcilin,delcillin,deripen,divercillin,doktacillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,olin kid,omnipen,orbicilina,pen a oral,pen ampil,penbristol,penbritin,penbritin paediatric,penbritin syrup,penbrock,penicline,penimic,pensyn,pentrex,pentrexl,pentrexyl,pentritin,pfizerpen a,polycillin,polyflex,ponecil,princillin,principen,qidamp,racenacillin,redicilin,rosampline,roscillin,semicillin,semicillin r,servicillin,sumipanto,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,viccillin s,vidocillin,wypicil" 2 "g" 6 "g" "101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5" "SAM" 119561 "Ampicillin/sulbactam" "Beta-lactams/penicillins" "J01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/s,ab,ams,amsu,apsu,sam" "sulacillin" 6 "g" "101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7" "AMR" 73341 "Amprolium" "Other antibacterials" "QP51BX02" "" "amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid" "" diff --git a/data-raw/antibiotics.xlsx b/data-raw/antibiotics.xlsx index e1f07d0f..e0eae581 100644 Binary files a/data-raw/antibiotics.xlsx and b/data-raw/antibiotics.xlsx differ diff --git a/data-raw/antibiotics.xpt b/data-raw/antibiotics.xpt index 35f126cd..905a58c7 100644 Binary files a/data-raw/antibiotics.xpt and b/data-raw/antibiotics.xpt differ diff --git a/data/antibiotics.rda b/data/antibiotics.rda index c3bf6e4e..ec8c76a5 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/inst/tinytest/test-sir.R b/inst/tinytest/test-sir.R index 89d3c502..7e437add 100644 --- a/inst/tinytest/test-sir.R +++ b/inst/tinytest/test-sir.R @@ -92,6 +92,12 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) { mutate(MEM = as.sir(ifelse(AMC == "S", "S", MEM))) %>% pull(MEM) %>% is.sir()) + + expect_true(example_isolates %>% + select(AMC, MEM) %>% + mutate(MEM = if_else(AMC == "S", "S", MEM)) %>% + pull(MEM) %>% + is.sir()) } if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) { expect_inherits( diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 1b5c7880..7134a7a4 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -144,9 +144,9 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c \section{Full list of supported (antibiotic) classes}{ \itemize{ -\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH) +\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 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) +\item \code{\link[=antifungals]{antifungals()}} can select: \cr 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[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), 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) \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) diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index 7e5608db..f3cb5e17 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -88,9 +88,9 @@ x These 30 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination: \itemize{ -\item aminoglycosides\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, 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 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(amphotericin B, 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 antifungals\cr(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 betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, 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, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, 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)