diff --git a/DESCRIPTION b/DESCRIPTION index 1c9b06c04..de8d80492 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 3.0.1.9032 -Date: 2026-03-08 +Version: 3.0.1.9033 +Date: 2026-03-09 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 diff --git a/NAMESPACE b/NAMESPACE index f46c1a138..91808bf54 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -248,6 +248,7 @@ export(glycopeptides) export(guess_ab_col) export(inner_join_microorganisms) export(interpretive_rules) +export(ionophores) export(is.ab) export(is.av) export(is.disk) diff --git a/NEWS.md b/NEWS.md index cd249636d..c6ecbb237 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9032 +# AMR 3.0.1.9033 ### New * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes` @@ -8,7 +8,7 @@ - `all_mic()`, `all_mic_predictors()` - `all_disk()`, `all_disk_predictors()` * Data set `esbl_isolates` to practise with AMR modelling -* AMR selectors `peptides()`, `phosphonics()` and `spiropyrimidinetriones()` +* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()` * Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions. - `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254) - This transforms the output from S/R to WT/NWT @@ -32,10 +32,10 @@ ### Updates * `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable). * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly. +* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`) * `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255) * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246) * `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246) -* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`) * Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244) * Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243) * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"` diff --git a/R/amr_selectors.R b/R/amr_selectors.R index 48ed5bccd..1d3d99b99 100755 --- a/R/amr_selectors.R +++ b/R/amr_selectors.R @@ -352,6 +352,14 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) { amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all) } +#' @rdname antimicrobial_selectors +#' @export +ionophores <- function(only_sir_columns = FALSE, return_all = TRUE, ...) { + meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) + meet_criteria(return_all, allow_class = "logical", has_length = 1) + amr_select_exec("ionophores", only_sir_columns = only_sir_columns, return_all = return_all) +} + #' @rdname antimicrobial_selectors #' @export isoxazolylpenicillins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) { diff --git a/R/sysdata.rda b/R/sysdata.rda index bdfeb1314..d7eacd65f 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 538bed043..aa3b9d2bc 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -369,6 +369,9 @@ pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>% filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>% pull(ab) pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC")) +pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>% + filter(name %like% "novobiocin|clorobiocin") %>% + pull(ab) pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>% filter(group %like% "antifungal") %>% pull(ab) @@ -486,6 +489,18 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>% # this will be used for documentation: pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"]) +# Check that all AB_* groups with >= 4 members have a corresponding function +for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) { + if (length(pre_commit_lst[[grp]]) >= 4) { + fn_name <- tolower(gsub("^AB_", "", grp)) + if (!fn_name %in% ls(envir = asNamespace("AMR"))) { + stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]), + " members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.", + call. = FALSE) + } + } +} + # Update the antimicrobials$group column usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors") prettify_group_name <- function(name) { @@ -557,6 +572,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins", "Beta-lactams", "Beta-lactamase inhibitors", "Pleuromutilins", + "Aminocoumarins", "Other") if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) { stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", ")) diff --git a/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R b/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R index 51e361460..8d494e710 100644 --- a/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R +++ b/data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R @@ -972,6 +972,17 @@ antimicrobials <- antimicrobials |> select(1:4), ) +antimicrobials <- antimicrobials |> + mutate(ab = as.character(ab)) |> + bind_rows( + antimicrobials |> + filter(ab == "NOV") |> + mutate(ab = "CLB", + cid = 54706138, + name = "Clorobiocin") |> + select(1:4), + ) + # update ATC codes from WHOCC website ------------------------------------- library(rvest) @@ -1171,6 +1182,11 @@ for (i in 1:nrow(antimicrobials)) { antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc)) } } +antimicrobials$group <- unname(antimicrobials$group) +antimicrobials$atc <- unname(antimicrobials$atc) +antimicrobials$abbreviations <- unname(antimicrobials$abbreviations) +antimicrobials$synonyms <- unname(antimicrobials$synonyms) +antimicrobials$loinc <- unname(antimicrobials$loinc) usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz") diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index 922e2efe5..985903b74 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -147709d2fb1b31b013c6ffb387f4d3ba +11aade8a39bfdff02d01fb52b04eacdc diff --git a/data-raw/datasets/antimicrobials.dta b/data-raw/datasets/antimicrobials.dta index a717b8d30..a2481f7d0 100644 Binary files a/data-raw/datasets/antimicrobials.dta and b/data-raw/datasets/antimicrobials.dta differ diff --git a/data-raw/datasets/antimicrobials.feather b/data-raw/datasets/antimicrobials.feather index 7a2652b31..49d0d53e1 100644 Binary files a/data-raw/datasets/antimicrobials.feather and b/data-raw/datasets/antimicrobials.feather differ diff --git a/data-raw/datasets/antimicrobials.parquet b/data-raw/datasets/antimicrobials.parquet index f68438fbf..866100ada 100644 Binary files a/data-raw/datasets/antimicrobials.parquet and b/data-raw/datasets/antimicrobials.parquet differ diff --git a/data-raw/datasets/antimicrobials.rds b/data-raw/datasets/antimicrobials.rds index 190c8eadf..5d94a84ae 100644 Binary files a/data-raw/datasets/antimicrobials.rds and b/data-raw/datasets/antimicrobials.rds differ diff --git a/data-raw/datasets/antimicrobials.sav b/data-raw/datasets/antimicrobials.sav index 0332b5fa5..e088f6bca 100644 Binary files a/data-raw/datasets/antimicrobials.sav and b/data-raw/datasets/antimicrobials.sav differ diff --git a/data-raw/datasets/antimicrobials.txt b/data-raw/datasets/antimicrobials.txt index 35700db21..b3680a643 100644 --- a/data-raw/datasets/antimicrobials.txt +++ b/data-raw/datasets/antimicrobials.txt @@ -157,6 +157,7 @@ "CLF1" 2799 "Clofoctol" "Other" "J01XX03,QJ01XX03" "Other antibacterials" "Other antibacterials" "NA" "clofoctolo,clofoctolum,gramplus,octofene,phenol" "NA" "CLM" 71807 "Clometocillin" "Penicillins,Beta-lactams" "J01CE07,QJ01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen" 1 "g" "NA" "CLM1" 54680675 "Clomocycline" "Tetracyclines" "J01AA11,QJ01AA11" "Tetracyclines" "Tetracyclines" "NA" "clomociclina,clomocyclinum,megaclor" 1 "g" "NA" +"CLB" 54706138 "Clorobiocin" "Aminocoumarins" "NA" "NA" "chlorobiocin" "NA" "CTR" 2812 "Clotrimazole" "Antifungals" "A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90" "clot" "alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole" "10653-4,10654-2,18909-2,54177-1,55663-9" "CLO" 6098 "Cloxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF02,QJ01CF02,QJ51CF02,QS01AA90" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,cloxac" "ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen" 2 "g" 2 "g" "16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7" "COL" 5311054 "Colistin" "Polymyxins" "A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01" "Other antibacterials" "Polymyxins" "cl,coli,colist,cs,cst,ct" "colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina" 9 "MU" 9 "MU" "16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6" @@ -307,7 +308,7 @@ "NME" "Norfloxacin/metronidazole" "Fluoroquinolones,Quinolones" "J01RA14,QJ01RA14" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" "NTI" "Norfloxacin/tinidazole" "Fluoroquinolones,Quinolones" "J01RA13,QJ01RA13" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" "NVA" 10419027 "Norvancomycin" "Glycopeptides,Peptides" "NA" "NA" "NA" "NA" -"NOV" 54675769 "Novobiocin" "Other" "QJ01XX95" "novo,novobi" "albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3" +"NOV" 54675769 "Novobiocin" "Aminocoumarins" "QJ01XX95" "novo,novobi" "albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3" "NYS" 6433272 "Nystatin" "Ionophores,Antifungals" "A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01" "nyst,nystan" "biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex" 1.5 "MU" "10697-1,10698-9,18958-9,35824-2,55689-4" "OFX" 4583 "Ofloxacin" "Fluoroquinolones,Quinolones" "J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16" "Quinolone antibacterials" "Fluoroquinolones" "of,ofl,oflo,ofloxa,ofx" "exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin" 0.4 "g" 0.4 "g" "18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8" "OOR" "Ofloxacin/ornidazole" "Fluoroquinolones,Quinolones" "J01RA09,QJ01RA09" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA" @@ -332,7 +333,7 @@ "PEF" 51081 "Pefloxacin" "Fluoroquinolones,Quinolones" "J01MA03,QJ01MA03" "Quinolone antibacterials" "Fluoroquinolones" "pefl,perflo" "labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox" 0.8 "g" 0.8 "g" "18963-9,35828-3,390-5,3906-5,7040-9" "PEF-S" "Pefloxacin screening test" "Fluoroquinolones,Quinolones" "NA" "pef screen" "NA" "NA" "PNM" 10250769 "Penamecillin" "Penicillins,Beta-lactams" "J01CE06,QJ01CE06" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum" 1.05 "g" "NA" -"PNO" "Penicillin/novobiocin" "Penicillins,Beta-lactams" "NA" "pennov" "NA" "35872-1,35873-9,35874-7" +"PNO" "Penicillin/novobiocin" "Penicillins,Beta-lactams,Aminocoumarins" "NA" "pennov" "NA" "35872-1,35873-9,35874-7" "PSU" "Penicillin/sulbactam" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" "NA" "PNM1" 54686187 "Penimepicycline" "Tetracyclines" "J01AA10,QJ01AA10" "Tetracyclines" "Tetracyclines" "NA" "criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum" "NA" "PIM" 65453 "Pentisomicin" "Aminoglycosides" "NA" "NA" "mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum" "NA" diff --git a/data-raw/datasets/antimicrobials.xlsx b/data-raw/datasets/antimicrobials.xlsx index 6a7a3b6fb..21bc7e64a 100644 Binary files a/data-raw/datasets/antimicrobials.xlsx and b/data-raw/datasets/antimicrobials.xlsx differ diff --git a/data/antibiotics.rda b/data/antibiotics.rda index 31f6ebe26..9a9e74d3d 100644 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/data/antimicrobials.rda b/data/antimicrobials.rda index 6f9b65732..f5953720f 100644 Binary files a/data/antimicrobials.rda and b/data/antimicrobials.rda differ diff --git a/man/antimicrobial_selectors.Rd b/man/antimicrobial_selectors.Rd index fd4f7825f..68b567102 100644 --- a/man/antimicrobial_selectors.Rd +++ b/man/antimicrobial_selectors.Rd @@ -17,6 +17,7 @@ \alias{cephalosporins_5th} \alias{fluoroquinolones} \alias{glycopeptides} +\alias{ionophores} \alias{isoxazolylpenicillins} \alias{lincosamides} \alias{lipoglycopeptides} @@ -81,6 +82,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE, glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...) +ionophores(only_sir_columns = FALSE, return_all = TRUE, ...) + isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) @@ -202,6 +205,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT) \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA) \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR) +\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL) \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S) \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL) \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV) diff --git a/man/antimicrobials.Rd b/man/antimicrobials.Rd index 467e53cf0..a67bc0559 100644 --- a/man/antimicrobials.Rd +++ b/man/antimicrobials.Rd @@ -5,9 +5,9 @@ \alias{antimicrobials} \alias{antibiotics} \alias{antivirals} -\title{Data Sets with 624 Antimicrobial Drugs} +\title{Data Sets with 625 Antimicrobial Drugs} \format{ -\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 504 observations and 14 variables:}{ +\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 505 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 504 rows and 14 columns. +An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 505 rows and 14 columns. An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns. } diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index b4d86f6cf..1dcc03020 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -98,8 +98,9 @@ x #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP) }\if{html}{\out{}} -These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination: +These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination: \itemize{ +\item aminocoumarins\cr(clorobiocin, novobiocin, and penicillin/novobiocin) \item aminoglycosides\cr(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) \item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, 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) diff --git a/man/custom_mdro_guideline.Rd b/man/custom_mdro_guideline.Rd index d2114e855..83fea9f46 100644 --- a/man/custom_mdro_guideline.Rd +++ b/man/custom_mdro_guideline.Rd @@ -94,7 +94,7 @@ You can define antimicrobial groups instead of single antimicrobials for the rul ) }\if{html}{\out{}} -All 42 antimicrobial selectors are supported for use in the rules: +All 43 antimicrobial selectors are supported for use in the rules: \itemize{ \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, kasugamycin, 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, amoxicillin/clavulanic acid, and ampicillin @@ -111,6 +111,7 @@ All 42 antimicrobial selectors are supported for use in the rules: \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr 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 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin +\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid, monensin sodium, narasin, nystatin, and salinomycin \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin