diff --git a/.github/prehooks/commit-msg b/.github/prehooks/commit-msg index 825e67cd..c3a4a69b 100755 --- a/.github/prehooks/commit-msg +++ b/.github/prehooks/commit-msg @@ -28,7 +28,6 @@ # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # -#!/bin/bash ####################################### # This script runs on commit-msg hook # @@ -56,6 +55,3 @@ fi # Prepend the version number to the commit message echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE" - -# Print the updated commit message for verification -echo "Updated commit message: $(cat "$COMMIT_MSG_FILE")" diff --git a/.github/prehooks/pre-commit b/.github/prehooks/pre-commit index 987029e5..36dfc7ed 100755 --- a/.github/prehooks/pre-commit +++ b/.github/prehooks/pre-commit @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/bash # ==================================================================== # # TITLE: # @@ -118,9 +118,4 @@ if [ -e "NEWS.md" ]; then else echo "- no NEWS.md found!" fi - -# set the version number as an environment variable for the commit-msg hook -export COMMIT_VERSION=$currentversion -echo "- exported COMMIT_VERSION=${currentversion} for the commit-msg hook" - echo "" diff --git a/DESCRIPTION b/DESCRIPTION index 3c7fabbc..9b7c96aa 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 2.1.1.9040 -Date: 2024-06-07 +Version: 2.1.1.9041 +Date: 2024-06-08 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 b1e7296e..d048d2c6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -286,6 +286,7 @@ export(mo_url) export(mo_year) export(mrgn) export(n_sir) +export(nitrofurans) export(not_intrinsic_resistant) export(oxazolidinones) export(pca) @@ -305,6 +306,7 @@ export(rescale_mic) export(reset_AMR_locale) export(resistance) export(resistance_predict) +export(rifamycins) export(right_join_microorganisms) export(scale_colour_mic) export(scale_fill_mic) diff --git a/NEWS.md b/NEWS.md index 404bc9b0..4eb686c3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9040 +# AMR 2.1.1.9041 *(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!)* @@ -22,6 +22,8 @@ This package now supports not only tools for AMR data analysis in clinical setti ## Changed * For SIR interpretation, it is now possible to use column names for argument `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users. +* Extended the antibiotic selectors with `nitrofurans()` and `rifamycins()` +* Added "clindamycin inducible screening" as `CLI1` to the `antibiotics` data set. Since clindamycin is a lincosamide, the antibiotic selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antibiotic selectors that contain non-treatable drugs) * For MICs: * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960) * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions. @@ -36,6 +38,7 @@ This package now supports not only tools for AMR data analysis in clinical setti * Fix for using a manual value for `mo_transform` in `antibiogram()` * Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high) * Improved overall algorithm of `as.ab()` for better performance and accuracy +* When using antibiotic selectors such as `aminoglycosides()` that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using `only_treatable = FALSE` ## Other * Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input diff --git a/R/ab_selectors.R b/R/ab_selectors.R index a7bcb727..db8d8e2f 100755 --- a/R/ab_selectors.R +++ b/R/ab_selectors.R @@ -367,9 +367,10 @@ glycopeptides <- function(only_sir_columns = FALSE, ...) { #' @rdname antibiotic_class_selectors #' @export -lincosamides <- function(only_sir_columns = FALSE, ...) { +lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) { meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) - ab_select_exec("lincosamides", only_sir_columns = only_sir_columns) + meet_criteria(only_treatable, allow_class = "logical", has_length = 1) + ab_select_exec("lincosamides", only_sir_columns = only_sir_columns, only_treatable = only_treatable) } #' @rdname antibiotic_class_selectors @@ -386,6 +387,13 @@ macrolides <- function(only_sir_columns = FALSE, ...) { ab_select_exec("macrolides", only_sir_columns = only_sir_columns) } +#' @rdname antibiotic_class_selectors +#' @export +nitrofurans <- function(only_sir_columns = FALSE, ...) { + meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) + ab_select_exec("nitrofurans", only_sir_columns = only_sir_columns) +} + #' @rdname antibiotic_class_selectors #' @export oxazolidinones <- function(only_sir_columns = FALSE, ...) { @@ -410,16 +418,23 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) { #' @rdname antibiotic_class_selectors #' @export -streptogramins <- function(only_sir_columns = FALSE, ...) { +quinolones <- function(only_sir_columns = FALSE, ...) { meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) - ab_select_exec("streptogramins", only_sir_columns = only_sir_columns) + ab_select_exec("quinolones", only_sir_columns = only_sir_columns) } #' @rdname antibiotic_class_selectors #' @export -quinolones <- function(only_sir_columns = FALSE, ...) { +rifamycins <- function(only_sir_columns = FALSE, ...) { meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) - ab_select_exec("quinolones", only_sir_columns = only_sir_columns) + ab_select_exec("rifamycins", only_sir_columns = only_sir_columns) +} + +#' @rdname antibiotic_class_selectors +#' @export +streptogramins <- function(only_sir_columns = FALSE, ...) { + meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) + ab_select_exec("streptogramins", only_sir_columns = only_sir_columns) } #' @rdname antibiotic_class_selectors @@ -579,9 +594,9 @@ ab_select_exec <- function(function_name, # untreatable drugs if (only_treatable == TRUE) { - untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE] + untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE] if (any(untreatable %in% names(ab_in_data))) { - if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) { + if (message_not_thrown_before(function_name, "ab_class", "untreatable")) { warning_( "in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ", vector_and( @@ -591,8 +606,7 @@ ab_select_exec <- function(function_name, ), quotes = FALSE, sort = TRUE - ), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ", - "This warning will be shown once per session." + ), ". They can be included using `", function_name, "(only_treatable = FALSE)`." ) } ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable] diff --git a/R/mic.R b/R/mic.R index 5c7efa03..d6259a34 100644 --- a/R/mic.R +++ b/R/mic.R @@ -43,6 +43,9 @@ VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)), c("<", "<=", "", ">=", ">"), paste0, VALID_MIC_LEVELS))) +COMMON_MIC_VALUES <- c(0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064, + 0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32, + 64, 128, 256, 512, 1024) #' Transform Input to Minimum Inhibitory Concentrations (MIC) #' @@ -300,10 +303,10 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) { } # create a manual factor with levels only within desired range - expanded <- range_as_table(x, - expand = TRUE, - keep_operators = ifelse(keep_operators == "edges", "none", keep_operators), - mic_range = mic_range) + expanded <- plotrange_as_table(x, + expand = TRUE, + keep_operators = ifelse(keep_operators == "edges", "none", keep_operators), + mic_range = mic_range) if (keep_operators == "edges") { names(expanded)[1] <- paste0("<=", names(expanded)[1]) names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)]) diff --git a/R/plot.R b/R/plot.R index 8cf4ab65..1907aafd 100755 --- a/R/plot.R +++ b/R/plot.R @@ -195,7 +195,7 @@ plot.mic <- function(x, } main <- gsub(" +", " ", paste0(main, collapse = " ")) - x <- range_as_table(x, expand = expand) + x <- plotrange_as_table(x, expand = expand) cols_sub <- plot_colours_subtitle_guideline( x = x, mo = mo, @@ -327,7 +327,7 @@ autoplot.mic <- function(object, } object <- as.mic(object) # make sure that currently implemented MIC levels are used - x <- range_as_table(object, expand = expand) + x <- plotrange_as_table(object, expand = expand) cols_sub <- plot_colours_subtitle_guideline( x = x, mo = mo, @@ -392,7 +392,7 @@ autoplot.mic <- function(object, fortify.mic <- function(object, ...) { object <- as.mic(object) # make sure that currently implemented MIC levels are used stats::setNames( - as.data.frame(range_as_table(object, expand = FALSE)), + as.data.frame(plotrange_as_table(object, expand = FALSE)), c("x", "y") ) } @@ -430,7 +430,7 @@ plot.disk <- function(x, } main <- gsub(" +", " ", paste0(main, collapse = " ")) - x <- range_as_table(x, expand = expand) + x <- plotrange_as_table(x, expand = expand) cols_sub <- plot_colours_subtitle_guideline( x = x, mo = mo, @@ -559,7 +559,7 @@ autoplot.disk <- function(object, title <- gsub(" +", " ", paste0(title, collapse = " ")) } - x <- range_as_table(object, expand = expand) + x <- plotrange_as_table(object, expand = expand) cols_sub <- plot_colours_subtitle_guideline( x = x, mo = mo, @@ -624,7 +624,7 @@ autoplot.disk <- function(object, # will be exported using s3_register() in R/zzz.R fortify.disk <- function(object, ...) { stats::setNames( - as.data.frame(range_as_table(object, expand = FALSE)), + as.data.frame(plotrange_as_table(object, expand = FALSE)), c("x", "y") ) } @@ -789,26 +789,15 @@ fortify.sir <- function(object, ...) { ) } -range_as_table <- function(x, expand, keep_operators = "all", mic_range = NULL) { +plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NULL) { x <- x[!is.na(x)] if (is.mic(x)) { x <- as.mic(x, keep_operators = keep_operators) if (expand == TRUE) { - # expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print - extra_range <- max(x) - min_range <- min(x) - if (!is.null(mic_range)) { - if (!is.na(mic_range[2])) { - extra_range <- as.mic(mic_range[2]) * 2 - } - if (!is.na(mic_range[1])) { - min_range <- as.mic(mic_range[1]) - } - } - extra_range <- extra_range / 2 - while (min(extra_range) / 2 > min_range) { - extra_range <- c(min(extra_range) / 2, extra_range) - } + # expand range for MIC by adding common intermediate factors levels + extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)] + # remove the ones that are in 25% range of user values + extra_range <- extra_range[!vapply(FUN.VALUE = logical(1), extra_range, function(r) any(abs(r - x) / x < 0.25, na.rm = TRUE))] nms <- extra_range extra_range <- rep(0, length(extra_range)) names(extra_range) <- nms diff --git a/R/sysdata.rda b/R/sysdata.rda index 098bcaf7..62861360 100755 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/translate.R b/R/translate.R index 71b38b78..b4e72a95 100755 --- a/R/translate.R +++ b/R/translate.R @@ -244,6 +244,7 @@ translate_into_language <- function(from, # starting with longest pattern, since more general translations are shorter, such as 'Group' order(nchar(df_trans$pattern), decreasing = TRUE), function(i) { + if (df_trans$pattern[i] %like% "[/]") return(df_trans$pattern[i]) from_unique_translated <<- gsub( pattern = df_trans$pattern[i], replacement = df_trans[i, lang, drop = TRUE], diff --git a/data-raw/_pre_commit_checks.R b/data-raw/_pre_commit_checks.R index 8b43fc67..470b7e5a 100644 --- a/data-raw/_pre_commit_checks.R +++ b/data-raw/_pre_commit_checks.R @@ -181,10 +181,10 @@ AB_AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab) AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX")) -AB_ANTIFUNGALS <- AMR_env$AB_lookup %>% +AB_ANTIFUNGALS <- antibiotics %>% filter(group %like% "antifungal") %>% pull(ab) -AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>% +AB_ANTIMYCOBACTERIALS <- antibiotics %>% filter(group %like% "antimycobacterial") %>% pull(ab) AB_CARBAPENEMS <- antibiotics %>% @@ -221,7 +221,10 @@ AB_LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab) AB_MACROLIDES <- antibiotics %>% - filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% + filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>% + pull(ab) +AB_NITROFURANS <- antibiotics %>% + filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>% pull(ab) AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% @@ -235,6 +238,9 @@ AB_POLYMYXINS <- antibiotics %>% AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab) +AB_RIFAMYCINS <- antibiotics %>% + filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>% + pull(ab) AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab) @@ -310,10 +316,12 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF, AB_GLYCOPEPTIDES_EXCEPT_LIPO, AB_LINCOSAMIDES, AB_MACROLIDES, + AB_NITROFURANS, AB_OXAZOLIDINONES, AB_PENICILLINS, AB_POLYMYXINS, AB_QUINOLONES, + AB_RIFAMYCINS, AB_STREPTOGRAMINS, AB_TETRACYCLINES, AB_TETRACYCLINES_EXCEPT_TGC, diff --git a/data-raw/ab.md5 b/data-raw/ab.md5 index 473f317d..3d39d280 100644 --- a/data-raw/ab.md5 +++ b/data-raw/ab.md5 @@ -1 +1 @@ -85e31c828b6f1795c8cb18b568f15c3e +3e7a1cbb21b49cdc7626ea3016a017cc diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index d3c43005..132bec46 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 36d26ebb..83695f8e 100644 Binary files a/data-raw/antibiotics.feather and b/data-raw/antibiotics.feather differ diff --git a/data-raw/antibiotics.parquet b/data-raw/antibiotics.parquet index 0d4181bd..e69de29b 100644 Binary files a/data-raw/antibiotics.parquet and b/data-raw/antibiotics.parquet differ diff --git a/data-raw/antibiotics.rds b/data-raw/antibiotics.rds index 6eafceff..22c42faa 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 a6319390..6ab74931 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 34fd6781..9e1718cc 100644 --- a/data-raw/antibiotics.txt +++ b/data-raw/antibiotics.txt @@ -137,13 +137,14 @@ "CIX" 47472 "Ciclopirox" "Antifungals/antimycotics" "D01AE14,G01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "butaconazole,butoconazol,butoconazole,butoconazolum,ciclodan,ciclopirox,ciclopirox gel,ciclopirox olamin,ciclopiroxum,compositenstarke,dahlin,femstat,gynofort,loprox,loprox cream,loprox gel,penlac,polyfructosanum,stieprox" "" "CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06" "Quinolone antibacterials" "Other quinolones" "cino,cnox" "azolinic acid,cinobac,cinobactin,cinoxacin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm" 1 "g" "180-0,181-8,182-6,183-4,18905-0,55656-3" "CIP" 2764 "Ciprofloxacin" "Quinolones" "J01MA02,S01AE03,S02AA15,S03AA07" "Quinolone antibacterials" "Fluoroquinolones" "ci,cip,cipr,cp" "alcon cilox,auripro,bacquinor,baflox,baycip,bernoflox,cetraxal,ciflox,cifloxin,ciloxan,ciplus,ciprecu,ciprine,ciprinol,cipro i.v.,cipro iv,cipro xl,cipro xr,ciprobay,ciprobay uro,ciprocinol,ciprodar,ciproflox,ciprofloxacin,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprogis,ciprolin,ciprolon,cipromycin,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citopcin,corsacin,cyprobay,fimoflox,flociprin,ipiflox,italnik,linhaliq,otiprio,probiox,proflaxin,quinolid,quintor,rancif,roxytal,septicide,sophixin ofteno,spitacin,superocin,velmonit,velomonit,zumaflox" 1 "g" 0.8 "g" "101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9" -"CIM" "Ciprofloxacin/metronidazole" "Other antibacterials" "J01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" -"CIO" "Ciprofloxacin/ornidazole" "Other antibacterials" "J01RA12" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" -"CIT" "Ciprofloxacin/tinidazole" "Other antibacterials" "J01RA11" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" +"CIM" "Ciprofloxacin/metronidazole" "Quinolones" "J01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" +"CIO" "Ciprofloxacin/ornidazole" "Quinolones" "J01RA12" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" +"CIT" "Ciprofloxacin/tinidazole" "Quinolones" "J01RA11" "Combinations of antibacterials" "Combinations of antibacterials" "" "" "" "CLR" 84029 "Clarithromycin" "Macrolides/lincosamides" "J01FA09" "Macrolides, lincosamides and streptogramins" "Macrolides" "ch,cla,clar,clm,clr" "abbotic,astromen,biaxin,biaxin filmtab,biaxin hp,biaxin xl,biaxin xl filmtab,bicrolid,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycin,clarithromycine,clarithromycinum,claritromicina,clathromycin,crixan,cyllid,cyllind,fromilid,heliclar,klabax,klacid,klaciped,klaricid,klaricid h.p,klaricid h.p.,klaricid pediatric,klaricid xl,klarid,klarin,kofron,mabicrol,macladin,maclar,prevpac,veclam,vikrol,zeclar" 0.5 "g" 1 "g" "100048-8,16619-9,16620-7,188-3,189-1,18907-6,190-9,191-7,20375-2,23619-0,25190-0,25191-8,25192-6,25253-6,34638-7,43987-7,43990-1,43991-9,7003-7,80559-8,89485-7" "CLA1" 5280980 "Clavulanic acid" "Other antibacterials" "NA" "" "acide clavulanique,acido clavulanico,acidum clavulanicum,clavulanate,clavulanate acid,clavulanate lithium,clavulanateacid,clavulanic acid,clavulansaeure,clavulansaure,clavulinic acid,clavulox,serdaxin,sodium clavulanate" "" "CLX" 60063 "Clinafloxacin" "Quinolones" "NA" "" "clinafloxacin" "32376-6,33284-1,35785-5,35786-3,7004-5" "CLI" 446598 "Clindamycin" "Macrolides/lincosamides" "D10AF01,G01AA10,J01FF01" "Macrolides, lincosamides and streptogramins" "Lincosamides" "cc,cd,cli,clin,cm,da" "antirobe,chlolincocin,clindaderm,clindamicina,clindamycin,clindamycine,clindamycinum,clinimycin,dalacin c,dalacine,klimicin,sobelin" 1.2 "g" 1.8 "g" "16621-5,16622-3,18908-4,192-5,193-3,194-1,195-8,25249-4,3486-8,42720-3,55657-1,55658-9,55659-7,55660-5,61188-9,7005-2" +"CLI1" "Clindamycin inducible screening" "Macrolides/lincosamides" "NA" "clindamycin inducible,clinda inducible,clin inducible" "" "" "CLF" 2794 "Clofazimine" "Antimycobacterials" "J04BA01" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof" "chlofazimine,clofazimin,clofazimina,clofazimine,clofaziminum,colfazimine,lampren,lamprene,riminophenazine" 0.1 "g" "16623-1,20376-0,23620-8,23627-3,43986-9,43988-5,43989-3,55661-3,55662-1,96108-6" "CLF1" 2799 "Clofoctol" "Other antibacterials" "J01XX03" "Other antibacterials" "Other antibacterials" "" "clofoctol,clofoctolo,clofoctolum,gramplus,octofene" "" "CLM" 71807 "Clometocillin" "Beta-lactams/penicillins" "J01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "" "chlomethocillin,clometacillin,clometocilina,clometocillin,clometocilline,clometocillinum,rixapen" 1 "g" "" diff --git a/data-raw/antibiotics.xlsx b/data-raw/antibiotics.xlsx index 7c0459f3..e1f07d0f 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 f4c9c10f..35f126cd 100644 Binary files a/data-raw/antibiotics.xpt and b/data-raw/antibiotics.xpt differ diff --git a/data-raw/reproduction_of_antibiotics.R b/data-raw/reproduction_of_antibiotics.R index 36cac087..9c06b89c 100644 --- a/data-raw/reproduction_of_antibiotics.R +++ b/data-raw/reproduction_of_antibiotics.R @@ -735,6 +735,18 @@ antibiotics <- antibiotics %>% )) antibiotics[which(antibiotics$ab %in% c("CYC", "LNZ", "THA", "TZD")), "group"] <- "Oxazolidinones" +# add clindamycin inducible screening +clin <- antibiotics |> + filter(ab == "FOX1") |> + mutate(ab = as.character("CLI1"), + name = "Clindamycin inducible screening", + group = "Macrolides/lincosamides") +antibiotics <- antibiotics |> + mutate(ab = as.character(ab)) |> + bind_rows(clin) +class(antibiotics$ab) <- c("ab", "character") +antibiotics[which(antibiotics$ab == "CLI1"), "abbreviations"][[1]] <- list(c("clindamycin inducible", "clinda inducible", "clin inducible")) + # add pretomanid antibiotics <- antibiotics %>% mutate(ab = as.character(ab)) %>% diff --git a/data-raw/translations.tsv b/data-raw/translations.tsv index db3cd856..e46ed171 100644 --- a/data-raw/translations.tsv +++ b/data-raw/translations.tsv @@ -73,6 +73,7 @@ Bacitracin FALSE TRUE TRUE FALSE 阿奇霉素 Bacitracin Bacitracin Bacitracine Benzathine benzylpenicillin FALSE TRUE TRUE FALSE 苄丝肼青霉素 Benzathine benzylpenicillin Benzathinbenzylpenicillin Benzylpenicillinebenzathine Bentsatiinibentsyylipenisilliini Benzathine benzylpénicilline Benzathin-Benzylpenicillin Βενζαθίνη βενζυλπενικιλλίνη Benzatina benzilpenicillina ベンズシン・ベンジルペニシリン Benzathine benzylpenicillin Benzylpenicylina benzylowa Benzatina benzatina benzilpenicilina Benzatină benzilpenicilină Бензатин бензилпенициллин Bencilpenicilina benzatínica Benzathinbenzylpenicillin Benzatin benzilpenisilin Бензатину бензилпеніцилін Benzathine phenoxymethylpenicillin FALSE TRUE TRUE FALSE 苄星苯氧甲基青霉素 Benzatinový fenoxymethylpenicilin Benzathinfenoxymethylpenicillin Fenoxymethylpenicillinebenzathine Bentsatiinifenoksimetyylipenisilliini Phénoxyméthylpénicilline benzathine Benzathin-Phenoxymethylpenicillin Βενζαθίνη φαινοξυμεθυλοπενικιλλίνη Benzatina fenossimetilpenicillina ベンザチンフェノキシメチルペニシリン Benzathine fenoksymetylpenicillin Fenoksymetylopenicylina benzylowa Benzatina fenoximetilpenicilina Benzatină fenoximetilpenicilină Бензатин феноксиметилпенициллин Fenoximetilpenicilina benzatínica Bensathinfenoximetylpenicillin Benzatin fenoksimetilpenisilin Бензатину феноксиметилпеніцилін Benzylpenicillin FALSE TRUE TRUE FALSE 苄基青霉素 Benzylpenicilin Benzylpenicillin Benzylpenicilline Bentsyylipenisilliini Benzylpénicilline Benzylpenicillin Βενζυλοπενικιλλίνη Benzilpenicillina ベンジルペニシリン Benzylpenicillin Benzylpenicylina Benzilpenicilina Benzilpenicilină Бензилпенициллин Bencilpenicilina Bensylpenicillin Benzilpenisilin Бензилпеніцилін +Cadazolid FALSE TRUE TRUE FALSE 卡达唑利德 Kadazolid Cadazolid Cadazolid Kadazolid Cadazolid Cadazolid Καδαζολίδη Cadazolid カダゾリド Cadazolid Kadazolid Cadazolid Cadazolid Кадазолид Cadazolid Cadazolid Cadazolid Кадазолід Calcium aminosalicylate FALSE TRUE TRUE FALSE 氨基水杨酸钙 Aminosalicylát vápenatý Calciumaminosalicylat Aminosalicylzuur Kalsiumaminosalisylaatti Aminosalicylate de calcium Kalzium-Aminosalicylat Αμινοσαλικυλικό ασβέστιο Calcio aminosalicilato アミノサリチル酸カルシウム Kalsiumaminosalicylat Aminosalicylan wapnia Aminosalicilato de cálcio Aminosalicilat de calciu Аминосалицилат кальция Aminosalicilato de calcio Kalciumaminosalicylat Kalsiyum aminosalisilat Кальцію аміносаліцилат Capreomycin FALSE TRUE TRUE FALSE 氨水杨酸钙 Kapreomycin Capreomycin Capreomycine Kapreomysiini Capréomycine Capreomycin Καπρεομυκίνη Capreomicina カプレオマイシン Capreomycin Kapreomycyna Capreomicina Capreomicină Капреомицин Capreomicina Kapreomycin Kapreomisin Капреоміцин Carbenicillin FALSE TRUE TRUE FALSE 羧基青霉素 Karbenicilin Carbenicillin Carbenicilline Karbenisilliini Carbénicilline Carbenicillin Καρβενικιλλίνη Carbenicillina カルベニシリン Karbenicillin Karbenicylina Carbenicilina Carbenicilină Карбенициллин Carbenicilina Karbenicillin Karbenisilin Карбеніцилін @@ -110,14 +111,19 @@ Chloramphenicol FALSE TRUE TRUE FALSE 氯霉素 Chloramfenikol Kloramfenicol Chl Chlortetracycline FALSE TRUE TRUE FALSE 金霉素 Chlortetracyklin Chlortetracyclin Chloortetracycline Klortetasykliini Chlortétracycline Chlortetracyclin Χλωροτετρακυκλίνη Clorotetraciclina クロルテトラサイクリン Klortetracyklin Chlortetracyklina Chlortetracycline Clortetraciclină Хлортетрациклин Clortetraciclina Klortetracyklin Klortetrasiklin Хлортетрациклін Cinoxacin FALSE TRUE TRUE FALSE 西诺沙星 Cinoxacin Cinoxacin Cinoxacine Kinoksasiini Cinoxacine Cinoxacin Τσινοξακίνη Cinoxacina シノキサシン Cinoxacin Cinoxacin Cinoxacin Cinoxacină Циноксацин Cinoxacina Cinoxacin Cinoxacin Циноксацин Ciprofloxacin FALSE TRUE TRUE FALSE 环丙沙星 Ciprofloxacin Ciprofloxacin Ciprofloxacine Siprofloksasiini Ciprofloxacine Ciprofloxacin Σιπροφλοξασίνη Ciprofloxacina シプロフロキサシン Ciprofloxacin Ciprofloksacyna Ciprofloxacin Ciprofloxacină Ципрофлоксацин Ciprofloxacina Ciprofloxacin Siprofloksasin Ципрофлоксацин +Ciprofloxacin/metronidazole FALSE TRUE TRUE FALSE 环丙沙星/甲硝唑 Ciprofloxacin/metronidazol Ciprofloxacin/metronidazol Ciprofloxacine/metronidazol Siprofloksasiini/metronidatsoli Ciprofloxacine/métronidazole Ciprofloxacin/metronidazol Σιπροφλοξασίνη/μετρονιδαζόλη Ciprofloxacina/metronidazolo シプロフロキサシン/メトロニダゾール Ciprofloxacin/metronidazol Ciprofloksacyna/metronidazol Ciprofloxacin/metronidazol Ciprofloxacină/metronidazol Ципрофлоксацин/метронидазол Ciprofloxacina/metronidazol Ciprofloxacin/metronidazol Siprofloksasin/metronidazol Ципрофлоксацин/метронідазол +Ciprofloxacin/ornidazole FALSE TRUE TRUE FALSE 环丙沙星/奥硝唑 Ciprofloxacin/ornidazol Ciprofloxacin/ornidazol Ciprofloxacine/ornidazol Siprofloksasiini/ornidatsoli Ciprofloxacine/ornidazole Ciprofloxacin/ornidazol Σιπροφλοξασίνη/ορνιδαζόλη Ciprofloxacina/ornidazolo シプロフロキサシン/オルニダゾール Ciprofloxacin/ornidazol Ciprofloksacyna/ornidazol Ciprofloxacin/ornidazole Ciprofloxacină/ornidazol Ципрофлоксацин/орнидазол Ciprofloxacina/ornidazol Ciprofloxacin/ornidazol Siprofloksasin/ornidazol Ципрофлоксацин/орнідазол +Ciprofloxacin/tinidazole FALSE TRUE TRUE FALSE 环丙沙星/替尼唑 Ciprofloxacin/tinidazol Ciprofloxacin/tinidazol Ciprofloxacine/tinidazol Siprofloksasiini/tinidatsoli Ciprofloxacine/tinidazole Ciprofloxacin/tinidazol Σιπροφλοξασίνη/τινιδαζόλη Ciprofloxacina/tinidazolo シプロフロキサシン/チニダゾール Ciprofloxacin/tinidazol Ciprofloksacyna/tinidazol Ciprofloxacin/tinidazole Ciprofloxacină/tinidazol Ципрофлоксацин/тинидазол Ciprofloxacina/tinidazol Ciprofloxacin/tinidazol Siprofloksasin/tinidazol Ципрофлоксацин/тинідазол Clarithromycin FALSE TRUE TRUE FALSE 克拉霉素 Klaritromycin Clarithromycin Claritromycine Klaritromysiini Clarithromycine Clarithromycin Κλαριθρομυκίνη Claritromicina クラリスロマイシン Klaritromycin Klarytromycyna Claritromicina Claritromicină Кларитромицин Claritromicina Claritromycin Klaritromisin Кларитроміцин Clavulanic acid FALSE TRUE TRUE FALSE 克拉维酸 Kyselina klavulanová Clavulansyre Clavulaanzuur Klavulaanihappo Acide clavulanique Clavulansäure Κλαβουλανικό οξύ Acido clavulanico クラビュラン酸 Klavulansyre Kwas klawulanowy Ácido clavulânico Acid clavulanic Клавулановая кислота Ácido clavulánico Clavulansyra Klavulanik asit Клавуланова кислота clavulanic acid FALSE TRUE TRUE FALSE 克拉维酸 kyselina klavulanová clavulansyre clavulaanzuur klavulaanihappo acide clavulanique Clavulansäure Κλαβουλανικό οξύ acido clavulanico クラビュラン酸 klavulansyre kwas klawulanowy ácido clavulânico acid clavulanic клавулановая кислота ácido clavulánico clavulansyra klavulanik asit клавуланова кислота Clindamycin FALSE TRUE TRUE FALSE 克林霉素 Klindamycin Clindamycin Clindamycine Klindamysiini Clindamycine Clindamycin Κλινδαμυκίνη Clindamicina クリンダマイシン Klindamycin Klindamycyna Clindamicina Clindamicină Клиндамицин Clindamicina Clindamycin Klindamisin Кліндаміцин +Clindamycin inducible screening FALSE TRUE TRUE FALSE 克林霉素诱导筛选 Klindamycin induzierbares Screening Clindamycin inducible screening Clindamycine induceerbare screening Klindamysiini indusoitava seulonta Clindamycine dépistage inductible Clindamycin induzierbares Screening Κλινδαμυκίνη επαγόμενο προσυμπτωματικό έλεγχο Clindamicina inducción del cribado クリンダマイシン誘導スクリーニング Klindamycin inducible screening Klindamycyna badanie indukcyjne Clindamicina cribado inducible Clindamicină screening inductibil Клиндамицин индуцируемый скрининг Clindamicina cribado inducible Clindamycin inducible screening Klindamisin indüklenebilir tarama Кліндаміцин індукційний скринінг Clometocillin FALSE TRUE TRUE FALSE 克罗米修斯（ Clometocillin Clometocillin Clometocilline Klometosilliini Clométocilline Clometocillin Κλομετοκιλλίνη Clometocillina クロメトシリン Klometocillin Clometocillin Clometocillin Clometocilină Клометоциллин Clometocilina Klometocillin Clometocillin Клометоцилін Clotrimazole FALSE TRUE TRUE FALSE 克霉唑 Klotrimazol Clotrimazol Clotrimazol Klotrimatsoli Clotrimazole Clotrimazol Κλοτριμαζόλη Clotrimazolo クロトリマゾール Klotrimazol Klotrimazol Clotrimazole Clotrimazol Клотримазол Clotrimazol Klotrimazol Klotrimazol Клотримазол Cloxacillin FALSE TRUE TRUE FALSE 克罗西林 Kloxacilin Cloxacillin Cloxacilline Kloksasilliini Cloxacilline Cloxacillin Κλοξακιλλίνη Cloxacillina クロキサシリン Cloxacillin Cloxacillin Cloxacillin Cloxacilină Клоксациллин Cloxacilina Kloxacillin Cloxacillin Клоксацилін Colistin FALSE TRUE TRUE FALSE 唑啉酮 Kolistin Colistin Colistine Kolistiini Colistine Colistin Κολιστίνη Colistina コリスチン Kolistin Kolistyna Colistin Colistină Колистин Colistina Kolistin Kolistin Колістин +Cycloserine FALSE TRUE TRUE FALSE 环丝氨酸 Cykloserin Cykloserin Cycloserine Sykloserini Cyclosérine Cycloserin Κυκλοσερίνη Cicloserina サイクロセリン Cycloserine Cykloseryna Cicloserina Cicloserină Циклосерин Cicloserina Cycloserine Sikloserin Циклосерин Dapsone FALSE TRUE TRUE FALSE 多普生 Dapson Dapson Dapson Dapsoni Dapsone Dapson Δαψόνη Dapsone ダプソン Dapsone Dapson Dapsone Dapsone Дапсон Dapsona Dapson Dapson Дапсон Daptomycin FALSE TRUE TRUE FALSE 达托霉素 Daptomycin Daptomycin Daptomycine Daptomysiini Daptomycine Daptomycin Δαπτομυκίνη Daptomicina ダプトマイシン Daptomycin Daptomycyna Daptomicina Daptomicină Даптомицин Daptomicina Daptomycin Daptomisin Даптоміцин Dibekacin FALSE TRUE TRUE FALSE 迪贝卡星 Dibekacin Dibekacin Dibekacine Dibekasiini Dibekacine Dibekacin Διβεκακίνη Dibekacin ジベカシン Dibekacin Dibekacin Dibekacin Dibekacin Дибекацин Dibekacina Dibekacin Dibekacin Дібекацин @@ -153,6 +159,7 @@ Kanamycin FALSE TRUE TRUE FALSE 卡那霉素 Kanamycin Kanamycin Kanamycine Kana Ketoconazole FALSE TRUE TRUE FALSE 酮康唑 Ketokonazol Ketoconazol Ketoconazol Ketokonatsoli Kétoconazole Ketoconazol Κετοκοναζόλη Ketoconazolo ケトコナゾール Ketokonazol Ketokonazol Ketoconazole Ketoconazol Кетоконазол Ketoconazol Ketokonazol Ketokonazol Кетоконазол Levofloxacin FALSE TRUE TRUE FALSE 氧氟沙星 Levofloxacin Levofloxacin Levofloxacine Levofloksasiini Lévofloxacine Levofloxacin Λεβοφλοξασίνη Levofloxacina レボフロキサシン Levofloxacin Levofloxacin Levofloxacin Levofloxacină Левофлоксацин Levofloxacina Levofloxacin Levofloksasin Левофлоксацин Lincomycin FALSE TRUE TRUE FALSE 林可霉素 Linkomycin Lincomycin Lincomycine Lincomycin Lincomycine Lincomycin Λινκομυκίνη Lincomicina リンコマイシン Lincomycin Lincomycyna Lincomycin Lincomicină Линкомицин Lincomicina Lincomycin Lincomycin Лінкоміцин +Linezolid FALSE TRUE TRUE FALSE 利奈唑胺 Linezolid Linezolid Linezolid Linezolid Linezolid Linezolid Λινεζολίδη Linezolid リネゾリド Linezolid Linezolid Linezolid Linezolid Линезолид Linezolid Linezolid Linezolid Лінезолід Lomefloxacin FALSE TRUE TRUE FALSE 洛美沙星 Lomefloxacin Lomefloxacin Lomefloxacine Lomefloksasiini Loméfloxacine Lomefloxacin Λομεφλοξασίνη Lomefloxacina ロメフロキサシン Lomefloksacin Lomefloxacin Lomefloxacin Lomefloxacină Ломефлоксацин Lomefloxacina Lomefloxacin Lomefloksasin Ломефлоксацин Lysozyme FALSE TRUE TRUE FALSE 硫酸钠 Lysozym Lysozym Lysozym Lysotsyymi Lysozyme Lysozym Λυσοζύμη Lisozima リゾチーム Lysozym Lizozym Lysozyme Lizozimă Лизоцим Lisozima Lysozym Lizozim Лізоцим Mandelic acid FALSE TRUE TRUE FALSE 扁桃酸 Kyselina mandlová Mandelinsyre Amandelzuur Mandelihappo Acide mandélique Mandelsäure Μανδελικό οξύ Acido mandelico マンデル酸 Mandelsyre Kwas migdałowy Ácido mandélico Acid mandelic Мандаловая кислота Ácido mandélico Mandelsyra Mandelik asit Мигдалева кислота @@ -243,12 +250,14 @@ Sulfathiazole FALSE TRUE TRUE FALSE 磺胺噻唑 Sulfathiazol Sulfathiazol Sulfa Sulfathiourea FALSE TRUE TRUE FALSE 磺胺硫脲 Sulfathiomočovina Sulfathiourea Sulfathioureum Sulfathiourea Sulfathiourée Sulfathioharnstoff Σουλφαθειουρία Sulfathiourea スルファチオ尿素 Sulfathiourea Sulfathiourea Sulfathiourea Sulfathiourea Сульфатиомочевина Sulfathiourea Sulfatiourea Sulfathiourea Сульфатіосечовина Sultamicillin FALSE TRUE TRUE FALSE 苏打米林 Sultamicilin Sultamicillin Sultamicilline Sultamisilliini Sultamicilline Sultamicillin Σουλταμικιλλίνη Sultamicillina スルタミシリン Sultamicillin Sultamicillin Sultamicillin Sultamicilină Сультамициллин Sultamicilina Sultamicillin Sultamicillin Сультаміцилін Talampicillin FALSE TRUE TRUE FALSE 塔拉比西林 Talampicilin Talampicillin Talampicilline Talampisilliini Talampicilline Talampicillin Ταλαμπικιλλίνη Talampicillina タランピシリン Talampicillin Talampicylina Talampicilina Talampicilină Талампициллин Talampicilina Talampicillin Talampisilin Талампіцилін +Tedizolid FALSE TRUE TRUE FALSE 特地唑胺 Tedizolid Tedizolid Tedizolid Tedizolid Tedizolid Tedizolid Τεντιζολίδη Tedizolid テジゾリド Tedizolid Tedizolid Tedizolid Tedizolid Тедизолид Tedizolid Tedizolid Tedizolid Тедізолід Teicoplanin FALSE TRUE TRUE FALSE 泰科普兰素 Teicoplanin Teicoplanin Teicoplanine Teikoplaniini Teicoplanine Teicoplanin Τεϊκοπλανίνη Teicoplanina テイコプラニン Teicoplanin Teicoplanin Teicoplanin Teicoplanin Тейкопланин Teicoplanina Teicoplanin Teikoplanin Тейкопланін Telithromycin FALSE TRUE TRUE FALSE 泰利霉素 Telithromycin Telithromycin Telitromycine Telitromysiini Télithromycine Telithromycin Τελιθρομυκίνη Telitromicina テリスロマイシン Telitromycin Telitromycyna Telitromicina Telitromicină Телитромицин Telitromicina Telitromycin Telitromisin Телітроміцин Temafloxacin FALSE TRUE TRUE FALSE 氨甲环酸 Temafloxacin Temafloxacin Temafloxacine Temafloksasiini Temafloxacine Temafloxacin Τεμαφλοξασίνη Temafloxacina テマフロキサシン Temafloxacin Temafloksacyna Temafloxacin Temafloxacin Темафлоксацин Temafloxacina Temafloxacin Temafloksasin Темафлоксацин Temocillin FALSE TRUE TRUE FALSE 氨甲蝶呤 Temocillin Temocillin Temocilline Temosilliini Temocillin Temocillin Τεμοκιλλίνη Temocillina テモシリン Temocillin Temocillin Temocillin Temocilină Темоциллин Temocilina Temocillin Temocillin Темоцилін Tenofovir disoproxil FALSE TRUE TRUE FALSE 特诺福韦酯 Tenofovir disoproxil Tenofovir disoproxil Tenofovir Tenofoviiridisoproksiili Tenofovir disoproxil Tenofovir Disoproxil Τενοφοβίρη δισοπροξίλη Tenofovir disoproxil テノホビルジソプロキシル Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproxil Тенофовир дизопроксил Tenofovir disoproxil Tenofovir disoproxil Tenofovir disoproksil Тенофовір дизопроксил Terizidone FALSE TRUE TRUE FALSE 特立兹酮 Terizidon Terizidon Terizidon Teritsidoni Terizidone Terizidon Τεριζιδόνη Terizidone テリジドン Terizidon Terizidon Terizidone Terizidonă Теризидон Terizidona Terizidon Terizidon Теризидон +Thiacetazone FALSE TRUE TRUE FALSE 噻乙唑酮 Thiacetazon Thiacetazon Thiacetazone Thiacetazoni Thiacétazone Thiacetazon Θιακεταζόνη Thiacetazona チアセタゾン Thiacetazone Thiacetazon Thiacetazona Thiacetazonă Тиазетазон Thiacetazona Thiacetazone Thiasetazon Тіацетазон Thiamphenicol FALSE TRUE TRUE FALSE 硫苯尼考 Thiamfenikol Thiamphenicol Thiamfenicol Tiamfenikoli Thiamphénicol Thiamphenicol Θειαμφενικόλη Tiamfenicolo チアンフェニコール Tiamfenikol Tiamfenikol Tiamfenicol Tiamfenicol Тиамфеникол Tiamfenicol Tiamfenikol Thiamphenicol Тіамфенікол Thioacetazone/isoniazid FALSE TRUE TRUE FALSE 硫乙酰唑酮/异烟肼 Thioacetazon/isoniazid Thioacetazon/isoniazid Thioacetazon/isoniazide Tioasetatsoni/isonatsidi Thioacétazone/isoniazide Thioacetazon/Isoniazid Θειοακεταζόνη/ισονιαζίδη Tioacetazone/isoniazide チオアセタゾン／イソニアジド Thioacetazon/isoniazid Tioacetazon/izoniazyd Thioacetazone/isoniazid Tioacetazonă/isoniazidă Тиоацетазон/изониазид Tioacetazona/isoniazida Thioacetazon/isoniazid Tiyoasetazon/izoniazid Тіоацетазон/ізоніазид Ticarcillin FALSE TRUE TRUE FALSE 替卡西林 Tykarcilinu Ticarcillin Ticarcilline Ticarcillin Ticarcilline Ticarcillin Τικαρκιλλίνη Ticarcillina チカルシリン Ticarcillin Ticarcillin Ticarcilina Ticarcilină Тикарциллин Ticarcilina Ticarcillin Ticarcillin Тикарцилін diff --git a/data/antibiotics.rda b/data/antibiotics.rda index d63114c9..c3bf6e4e 100755 Binary files a/data/antibiotics.rda and b/data/antibiotics.rda differ diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 1d0eb6a7..1b5c7880 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -21,11 +21,13 @@ \alias{lincosamides} \alias{lipoglycopeptides} \alias{macrolides} +\alias{nitrofurans} \alias{oxazolidinones} \alias{penicillins} \alias{polymyxins} -\alias{streptogramins} \alias{quinolones} +\alias{rifamycins} +\alias{streptogramins} \alias{tetracyclines} \alias{trimethoprims} \alias{ureidopenicillins} @@ -66,22 +68,26 @@ fluoroquinolones(only_sir_columns = FALSE, ...) glycopeptides(only_sir_columns = FALSE, ...) -lincosamides(only_sir_columns = FALSE, ...) +lincosamides(only_sir_columns = FALSE, only_treatable = TRUE, ...) lipoglycopeptides(only_sir_columns = FALSE, ...) macrolides(only_sir_columns = FALSE, ...) +nitrofurans(only_sir_columns = FALSE, ...) + oxazolidinones(only_sir_columns = FALSE, ...) penicillins(only_sir_columns = FALSE, ...) polymyxins(only_sir_columns = FALSE, only_treatable = TRUE, ...) -streptogramins(only_sir_columns = FALSE, ...) - quinolones(only_sir_columns = FALSE, ...) +rifamycins(only_sir_columns = FALSE, ...) + +streptogramins(only_sir_columns = FALSE, ...) + tetracyclines(only_sir_columns = FALSE, ...) trimethoprims(only_sir_columns = FALSE, ...) @@ -152,13 +158,15 @@ 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), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA) \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM) -\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1) +\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), clindamycin inducible screening (CLI1), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1) \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV) \item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1) +\item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ) \item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA) \item \code{\link[=penicillins]{penicillins()}} 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), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC) \item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP) -\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA) +\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), 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), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA) +\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP) \item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA) \item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), and tigecycline (TGC) \item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT) diff --git a/man/antibiotics.Rd b/man/antibiotics.Rd index c1e15d3a..ffe2acfd 100644 --- a/man/antibiotics.Rd +++ b/man/antibiotics.Rd @@ -4,9 +4,9 @@ \name{antibiotics} \alias{antibiotics} \alias{antivirals} -\title{Data Sets with 603 Antimicrobial Drugs} +\title{Data Sets with 604 Antimicrobial Drugs} \format{ -\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 observations and 14 variables:}{ +\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 484 observations and 14 variables:}{ \itemize{ \item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{This is a unique identifier.} \item \code{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.} diff --git a/man/custom_eucast_rules.Rd b/man/custom_eucast_rules.Rd index bf61354a..7e5608db 100644 --- a/man/custom_eucast_rules.Rd +++ b/man/custom_eucast_rules.Rd @@ -86,7 +86,7 @@ x #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP) }\if{html}{\out{}} -These 28 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination: +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 aminopenicillins\cr(amoxicillin and ampicillin) @@ -104,13 +104,15 @@ These 28 antibiotic groups are allowed in the rules (case-insensitive) and can b \item fluoroquinolones\cr(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin) \item glycopeptides\cr(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod) \item glycopeptides_except_lipo\cr(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod) -\item lincosamides\cr(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin) +\item lincosamides\cr(acetylmidecamycin, acetylspiramycin, clindamycin, clindamycin inducible screening, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin) \item lipoglycopeptides\cr(dalbavancin, oritavancin, and telavancin) \item macrolides\cr(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin) +\item nitrofurans\cr(furazidin, furazolidone, nifurtoinol, nitrofurantoin, and nitrofurazone) \item oxazolidinones\cr(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone) \item penicillins\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, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, and ticarcillin/clavulanic acid) \item polymyxins\cr(colistin, polymyxin B, and polymyxin B/polysorbate 80) -\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin) +\item quinolones\cr(besifloxacin, cinoxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin) +\item rifamycins\cr(rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, and rifapentine) \item streptogramins\cr(pristinamycin and quinupristin/dalfopristin) \item tetracyclines\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tigecycline) \item tetracyclines_except_tgc\cr(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, and tetracycline)