(v2.1.1.9041) antibiotics update

.github/prehooks/commit-msg

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
+# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
+# Data. Journal of Statistical Software, 104(3), 1-31.                 #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+#######################################
+# This script runs on commit-msg hook #
+#######################################
+
+# Path to the commit message file
+COMMIT_MSG_FILE=$1
+
+# Read the current commit message
+COMMIT_MSG=$(cat "$COMMIT_MSG_FILE")
+# check the commit message, cancel commit if needed
+if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
+  exit 0
+fi
+
+# Path to the DESCRIPTION file
+DESCRIPTION_FILE="DESCRIPTION"
+# Read the version number from the DESCRIPTION file
+if [ -f "$DESCRIPTION_FILE" ]; then
+  currentversion=$(grep "^Version:" "$DESCRIPTION_FILE" | awk '{print $2}')
+else
+  echo "Error: DESCRIPTION file not found. Unable to prepend version number."
+  exit 1
+fi
+
+# Prepend the version number to the commit message
+echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_FILE"

.github/prehooks/pre-commit

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # ==================================================================== #
 # TITLE:                                                               #
@@ -39,7 +39,7 @@ if [ -f "$COMMIT_MSG_PATH" ]; then
   COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
 else
   echo "Commit message file not found."
-  COMMIT_MSG=""
+  exit 1
 fi
 # check the commit message, cancel commit if needed
 if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
@@ -118,15 +118,4 @@ if [ -e "NEWS.md" ]; then
 else
   echo "- no NEWS.md found!"
 fi
-
-# Prepend the version number to the commit message
-if [ -f "$COMMIT_MSG_PATH" ]; then
-  # Prepend the version number
-  echo "(v${currentversion}) ${COMMIT_MSG}" > "$COMMIT_MSG_PATH"
-  echo "- prepended version number to commit message"
-else
-  echo ""
-  echo "Commit message file not found. Unable to prepend version number."
-fi
-
 echo ""

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9038
-Date: 2024-06-04
+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

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)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9038
+# 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

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]

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)
 #'
@@ -300,7 +303,7 @@ 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,
+  expanded <- plotrange_as_table(x,
                              expand = TRUE,
                              keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
                              mic_range = mic_range)

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

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],

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,

data-raw/ab.md5

@@ -1 +1 @@
-85e31c828b6f1795c8cb18b568f15c3e
+3e7a1cbb21b49cdc7626ea3016a017cc

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"			""

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)) %>%

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

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)

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.}

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{</div>}}
 
-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)