website update

.Rbuildignore

@@ -23,14 +23,15 @@
 ^data-raw$
 ^\.lintr$
 ^tests/testthat/_snaps$
-^vignettes/AMR.Rmd$
+^vignettes/AMR\.Rmd$
-^vignettes/benchmarks.Rmd$
+^vignettes/benchmarks\.Rmd$
-^vignettes/datasets.Rmd$
+^vignettes/*\.not$
-^vignettes/EUCAST.Rmd$
+^vignettes/datasets\.Rmd$
-^vignettes/MDR.Rmd$
+^vignettes/EUCAST\.Rmd$
-^vignettes/PCA.Rmd$
+^vignettes/MDR\.Rmd$
-^vignettes/resistance_predict.Rmd$
+^vignettes/PCA\.Rmd$
-^vignettes/SPSS.Rmd$
+^vignettes/resistance_predict\.Rmd$
-^vignettes/WHONET.Rmd$
+^vignettes/SPSS\.Rmd$
+^vignettes/WHONET\.Rmd$
 ^logo.svg$
 ^CRAN-SUBMISSION$

.github/prehooks/pre-commit

@@ -0,0 +1,71 @@
+#!/bin/sh
+
+echo "Running pre-commit hook..."
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+echo ">>  Updating R documentation..."
+if command -v Rscript > /dev/null; then
+  if [ "$(Rscript -e 'cat(all(c('"'roxygen2'"', '"'pkgload'"') %in% rownames(installed.packages())))')" == "TRUE" ]; then
+    Rscript -e "suppressMessages(roxygen2::roxygenise())"
+    currentpkg=`Rscript -e "cat(pkgload::pkg_name())"`
+    git add man/*
+    echo ">>  done."
+  else
+    echo ">>  R packages 'roxygen2' and 'pkgload' are not installed!"
+    currentpkg="your"
+  fi
+else
+  echo ">>  R is not available on your system!"
+  currentpkg="your"
+fi
+echo ">>  "
+
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+echo ">>  Updating semantic versioning and date..."
+
+# get tags from remote, and remove tags not on remote:
+git fetch origin --prune --prune-tags --quiet
+currenttagfull=`git describe --tags --abbrev=0`
+currenttag=`git describe --tags --abbrev=0 | sed 's/v//'`
+if [ "$currenttag" = "" ]; then
+  # there is no tag, so set tag to 0.0.1 and commit index to current count
+  echo ">>  - no git tags found, create some using v(x).(y).(z)"
+  currenttag="0.0.1"
+  currentcommit=`git rev-list --count HEAD`
+else
+  # there is a tag, so base version number on that
+  currentcommit=`git rev-list --count ${currenttagfull}..HEAD`
+  if (( "$currentcommit" == 0 )); then
+    # tag is new, so this must become the version number
+    currentversion="$currenttag"
+  fi
+  echo ">>  - latest tag is '${currenttagfull}', with ${currentcommit} previous commits"
+fi
+if [ "$currentversion" = "" ]; then
+  # combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
+  currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
+fi
+echo ">>  - ${currentpkg} pkg version set to ${currentversion}"
+
+# set version number and date to DESCRIPTION file
+sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
+sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
+echo ">>  - updated DESCRIPTION"
+# remove leftover on macOS
+rm DESCRIPTION--
+# add to commit
+git add DESCRIPTION
+
+# set version number to NEWS file
+if [ -e "NEWS.md" ]; then
+  sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
+  echo ">>  - updated NEWS.md"
+  # remove leftover on macOS
+  rm NEWS.md--
+  # add to commit
+  git add NEWS.md
+else
+  echo ">>  - no NEWS.md found!"
+fi
+echo ">>  "

.github/workflows/check.yaml

@@ -25,12 +25,8 @@
 
 on:
   push:
-    branches:
+     # run after a git push on any branch in this repo
-      - development
+    branches: '**'
-      - main
-  pull_request:
-    branches:
-      - main
   schedule:
     # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
@@ -55,32 +51,21 @@ jobs:
           - {os: macOS-latest,   r: '4.1',     allowfail: false}
           - {os: macOS-latest,   r: '4.0',     allowfail: false}
           - {os: macOS-latest,   r: '3.6',     allowfail: false}
-          - {os: macOS-latest,   r: '3.5',     allowfail: false}
+          - {os: ubuntu-22.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: macOS-latest,   r: '3.4',     allowfail: false}
+          - {os: ubuntu-22.04,   r: '4.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          - {os: ubuntu-22.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: macOS-latest,   r: '3.2',     allowfail: false}
+          - {os: ubuntu-22.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          # - {os: macOS-latest,   r: '3.1',     allowfail: true}
+          - {os: ubuntu-22.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          # - {os: macOS-latest,   r: '3.0',     allowfail: true}
+          - {os: ubuntu-22.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-22.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: windows-latest, r: 'devel',   allowfail: true}
           - {os: windows-latest, r: '4.1',     allowfail: false}
           - {os: windows-latest, r: '4.0',     allowfail: false}
           - {os: windows-latest, r: '3.6',     allowfail: false}
-          - {os: windows-latest, r: '3.5',     allowfail: false}
-          - {os: windows-latest, r: '3.4',     allowfail: false}
-          - {os: windows-latest, r: '3.3',     allowfail: false}
-          # - {os: windows-latest, r: '3.2',     allowfail: true}
-          # - {os: windows-latest, r: '3.1',     allowfail: true}
-          # - {os: windows-latest, r: '3.0',     allowfail: true}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -99,9 +84,9 @@ jobs:
         if: runner.os == 'Linux'
         # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
         # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
-        # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
+        # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
         run: |
-          sudo apt install -y libssl-dev libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
+          sudo apt install -y libssl-dev libxml2-dev libcurl4-openssl-dev
       
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run

.github/workflows/website.yaml

@@ -0,0 +1,60 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# 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/   #
+# ==================================================================== #
+
+# Create a website from the R documentation using pkgdown
+# Git commit and push to the 'gh-pages' branch
+
+on:
+  push:
+    # only on main
+    branches: 'main'
+
+name: Update website
+
+jobs:
+  update-website:
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      # Set up R (current stable version) and developer tools
+      - uses: actions/checkout@v3
+      - uses: r-lib/actions/setup-pandoc@v2
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+            r-version: "release"
+            # use RStudio Package Manager (RSPM) to quickly install packages
+            use-public-rspm: true
+      - name: Set up R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown
+
+      # Send updates to repo using GH Actions bot
+      - name: Create website in separate branch
+        run: |
+          git config user.name "github-actions"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, clean = TRUE, install = TRUE, branch = "gh-pages")'

DESCRIPTION

@@ -1,72 +1,30 @@
 Package: AMR
-Version: 1.8.1
+Version: 1.8.1.9021
-Date: 2022-03-17
+Date: 2022-08-21
 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
     using evidence-based methods and reliable reference data such as LPSN
     <doi:10.1099/ijsem.0.004332>.
 Authors@R: c(
-  person(given = c("Matthijs", "S."),
+    person(c("Matthijs", "S."), "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.berends@certe.nl"),
-         family = "Berends", 
+    person(c("Christian", "F."), "Luz", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")),
-         email = "m.berends@certe.nl",
+    person("Dennis", "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
-         role = c("aut", "cre"),
+    person(c("Erwin", "E.", "A."), "Hassing", role = c("aut", "ctb")),
-         comment = c(ORCID = "0000-0001-7620-1800")),
+    person("Casper",  "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
-  person(given = c("Christian", "F."),
+    person("Peter",   "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
-         family = "Luz", 
+    person("Judith",  "Fonville", role = "ctb"),
-         role = c("aut", "ctb"),
+    person("Alex",    "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
-         comment = c(ORCID = "0000-0001-5809-5995")),
+    person("Corinna", "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")),
-  person(given = "Dennis",
+    person("Eric",    "Hazenberg", role = "ctb"),
-         family = "Souverein", 
+    person("Gwen",    "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
-         role = c("aut", "ctb"),
+    person("Annick",  "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
-         comment = c(ORCID = "0000-0003-0455-0336")),
+    person("Bart",    "Meijer", role = "ctb"),
-  person(given = c("Erwin", "E.", "A."),
+    person("Anton",   "Mymrikov", role = "ctb"),
-         family = "Hassing", 
+    person("Sofia",   "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
-         role = c("aut", "ctb")),
+    person("Rogier",  "Schade", role = "ctb"),
-  person(given = c("Casper", "J."),
+    person("Bhanu",   "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
-         family = "Albers", 
+    person("Anthony", "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")))
-         role = "ths",
-         comment = c(ORCID = "0000-0002-9213-6743")),
-  person(given = c("Judith", "M."),
-         family = "Fonville", 
-         role = "ctb"),
-  person(given = c("Alex", "W."),
-         family = "Friedrich", 
-         role = "ths",
-         comment = c(ORCID = "0000-0003-4881-038X")),
-  person(given = "Corinna",
-         family = "Glasner", 
-         role = "ths",
-         comment = c(ORCID = "0000-0003-1241-1328")),
-  person(given = c("Eric", "H.", "L.", "C.", "M."),
-         family = "Hazenberg", 
-         role = "ctb"),
-  person(given = "Gwen",
-         family = "Knight", 
-         role = "ctb",
-         comment = c(ORCID = "0000-0002-7263-9896")),
-  person(given = "Annick",
-         family = "Lenglet", 
-         role = "ctb",
-         comment = c(ORCID = "0000-0003-2013-8405")),
-  person(given = c("Bart", "C."),
-         family = "Meijer", 
-         role = "ctb"),
-  person(given = "Sofia",
-         family = "Ny",
-         role = "ctb",
-         comment = c(ORCID = "0000-0002-2017-1363")),
-  person(given = c("Rogier", "P."),
-         family = "Schade", 
-         role = "ctb"),
-  person(given = c("Bhanu", "N.", "M."),
-         family = "Sinha", 
-         role = "ths",
-         comment = c(ORCID = "0000-0003-1634-0010")),
-  person(given = "Anthony", 
-         family = "Underwood", 
-         role = "ctb",
-         comment = c(ORCID = "0000-0002-8547-4277")))
 Depends: R (>= 3.0.0)
 Enhances:
   cleaner,
@@ -76,7 +34,6 @@ Enhances:
 Suggests: 
   curl,
   dplyr,
-  ggtext,
   knitr,
   progress,
   readxl,
@@ -90,5 +47,5 @@ BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -50,7 +50,6 @@ S3method(any,mic)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)
-S3method(as.integer,mic)
 S3method(as.list,custom_eucast_rules)
 S3method(as.list,custom_mdro_guideline)
 S3method(as.matrix,mic)
@@ -310,6 +309,7 @@ export(quinolones)
 export(random_disk)
 export(random_mic)
 export(random_rsi)
+export(reset_AMR_locale)
 export(resistance)
 export(resistance_predict)
 export(right_join_microorganisms)
@@ -318,6 +318,7 @@ export(rsi_predict)
 export(scale_rsi_colours)
 export(scale_y_percent)
 export(semi_join_microorganisms)
+export(set_AMR_locale)
 export(set_ab_names)
 export(set_mo_source)
 export(skewness)
@@ -325,6 +326,7 @@ export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
 export(theme_rsi)
+export(translate_AMR)
 export(trimethoprims)
 export(ureidopenicillins)
 importFrom(graphics,arrows)

NEWS.md

@@ -1,8 +1,27 @@
+# AMR 1.8.1.9021
+
+### New
+* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
+* Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. The `AMR` package is now available in 16 languages.
+
+### Changed
+* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
+* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values  consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
+* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
+* Small fix for using `ab_from_text()`
+* Fixes for reading in text files using `set_mo_source()`, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package
+* Using any `random_*()` function (such as `random_mic()`) is now possible by directly calling the package without loading it first: `AMR::random_mic(10)`
+* Added *Toxoplasma gondii* (`P_TXPL_GOND`) to the `microorganisms` data set, together with its genus, family, and order
+* Changed value in column `prevalence` of the `microorganisms` data set from 3 to 2 for these genera: *Acholeplasma*, *Alistipes*, *Alloprevotella*, *Bergeyella*, *Borrelia*, *Brachyspira*, *Butyricimonas*, *Cetobacterium*, *Chlamydia*, *Chlamydophila*, *Deinococcus*, *Dysgonomonas*, *Elizabethkingia*, *Empedobacter*, *Haloarcula*, *Halobacterium*, *Halococcus*, *Myroides*, *Odoribacter*, *Ornithobacterium*, *Parabacteroides*, *Pedobacter*, *Phocaeicola*, *Porphyromonas*, *Riemerella*, *Sphingobacterium*, *Streptobacillus*, *Tenacibaculum*, *Terrimonas*, *Victivallis*, *Wautersiella*, *Weeksella*
+* Fix for using the form `df[carbapenems() == "R", ]` using the latest `vctrs` package
+* Fix for using `info = FALSE` in `mdro()`
+
+### Other
+* New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
+* Added Peter Dutey-Magni and Anton Mymrikov as contributors, to thank them for their valuable input
+
 # `AMR` 1.8.1
 
-
-All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
-
 ### Changed
 * Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
 * Support for antibiotic interpretations of the MIPS laboratory system: `"U"` for S ('susceptible urine'), `"D"` for I ('susceptible dose-dependent')

R/aa_helper_functions.R

@@ -638,7 +638,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
   if (isTRUE(initial_captital)) {
     v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
   }
-  if (length(v) == 1) {
+  if (length(v) <= 1) {
     return(paste0(quotes, v, quotes))
   }
   if (identical(v, c("I", "R", "S"))) {

R/ab.R

@@ -26,7 +26,6 @@
 #' Transform Input to an Antibiotic ID
 #'
 #' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [character] vector to determine to antibiotic ID
 #' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
 #' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
@@ -55,7 +54,6 @@
 #' * [antibiotics] for the [data.frame] that is being used to determine ATCs
 #' * [ab_from_text()] for a function to retrieve antimicrobial drugs from clinical text (from health care records)
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
 #' # these examples all return "ERY", the ID of erythromycin:
@@ -282,9 +280,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       x_new[i] <- note_if_more_than_one_found(found, i, from_text)
       next
     }
-
+    
     # INITIAL SEARCH - More uncertain results ----
-
+    
     if (initial_search == TRUE && fast_mode == FALSE) {
       # only run on first try
       
@@ -313,7 +311,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
                                        for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
                                          y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
                                                         TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
-                                                                                  !isFALSE(TRANSLATIONS$fixed)), "pattern"],
+                                                                             !isFALSE(TRANSLATIONS$fixed)), "pattern"],
                                                         y[i])
                                        }
                                      }
@@ -463,7 +461,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     warning_("in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
              vector_and(x_unknown), ".")
   }
-
+  
   x_result <- x_new[match(x_bak_clean, x)]
   if (length(x_result) == 0) {
     x_result <- NA_character_

R/ab_from_text.R

@@ -26,7 +26,6 @@
 #' Retrieve Antimicrobial Drug Names and Doses from Clinical Text
 #' 
 #' Use this function on e.g. clinical texts from health care records. It returns a [list] with all antimicrobial drugs, doses and forms of administration found in the texts.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param text text to analyse
 #' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
 #' @param collapse a [character] to pass on to `paste(, collapse = ...)` to only return one [character] per element of `text`, see *Examples*
@@ -53,7 +52,6 @@
 #' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))` 
 #' @export
 #' @return A [list], or a  [character] if `collapse` is not `NULL`
-#' @inheritSection AMR Read more on Our Website!
 #' @examples 
 #' # mind the bad spelling of amoxicillin in this line, 
 #' # straight from a true health care record:

R/ab_property.R

@@ -26,7 +26,6 @@
 #' Get Properties of an Antibiotic
 #'
 #' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
 #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
 #' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
@@ -54,7 +53,6 @@
 #' @export
 #' @seealso [antibiotics]
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # all properties:
 #' ab_name("AMX")       # "Amoxicillin"
@@ -101,15 +99,18 @@
 #' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
-#'     set_ab_names()
+#'     set_ab_names() %>%
+#'     head()
 #'     
 #'   # this does the same:
 #'   example_isolates %>%
-#'     rename_with(set_ab_names)
+#'     rename_with(set_ab_names)%>%
+#'     head()
 #'   
 #'   # set_ab_names() works with any AB property:
 #'   example_isolates %>%
-#'     set_ab_names(property = "atc")
+#'     set_ab_names(property = "atc")%>%
+#'     head()
 #'     
 #'  example_isolates %>%
 #'    set_ab_names(where(is.rsi)) %>%
@@ -125,7 +126,7 @@ ab_name <- function(x, language = get_AMR_locale(), tolower = FALSE, ...) {
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   meet_criteria(tolower, allow_class = "logical", has_length = 1)
   
-  x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE)
+  x <- translate_into_language(ab_validate(x = x, property = "name", ...), language = language, only_affect_ab_names = TRUE)
   if (tolower == TRUE) {
     # use perl to only transform the first character
     # as we want "polymyxin B", not "polymyxin b"
@@ -166,7 +167,7 @@ ab_tradenames <- function(x, ...) {
 ab_group <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-  translate_AMR(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
+  translate_into_language(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
 }
 
 #' @rdname ab_property
@@ -204,7 +205,7 @@ ab_atc <- function(x, only_first = FALSE, ...) {
 ab_atc_group1 <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-  translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language, only_affect_ab_names = TRUE)
+  translate_into_language(ab_validate(x = x, property = "atc_group1", ...), language = language, only_affect_ab_names = TRUE)
 }
 
 #' @rdname ab_property
@@ -212,7 +213,7 @@ ab_atc_group1 <- function(x, language = get_AMR_locale(), ...) {
 ab_atc_group2 <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-  translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language, only_affect_ab_names = TRUE)
+  translate_into_language(ab_validate(x = x, property = "atc_group2", ...), language = language, only_affect_ab_names = TRUE)
 }
 
 #' @rdname ab_property
@@ -331,7 +332,7 @@ ab_property <- function(x, property = "name", language = get_AMR_locale(), ...)
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(property, is_in = colnames(antibiotics), has_length = 1)
   meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
-  translate_AMR(ab_validate(x = x, property = property, ...), language = language)
+  translate_into_language(ab_validate(x = x, property = property, ...), language = language)
 }
 
 #' @rdname ab_property
@@ -430,7 +431,7 @@ ab_validate <- function(x, property, ...) {
     # so the 'call.' can be set to FALSE
     tryCatch(x[1L] %in% antibiotics[1, property],
              error = function(e) stop(e$message, call. = FALSE))
-
+    
     if (!all(x %in% AB_lookup[, property])) {
       x <- as.ab(x, ...)
       x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]

R/ab_selectors.R

@@ -26,7 +26,6 @@
 #' Antibiotic Selectors
 #' 
 #' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
 #' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
 #' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
@@ -46,103 +45,105 @@
 #' @return (internally) a [character] vector of column names, with additional class `"ab_selector"`
 #' @export
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+
 #' @examples 
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
+#' df <- example_isolates[ , c("hospital_id", "mo",
+#'                             "AMP", "AMC", "TZP", "CXM", "CRO", "GEN",
+#'                             "TOB", "COL", "IPM", "MEM", "TEC", "VAN")]
 #' 
 #' # base R ------------------------------------------------------------------
 #' 
 #' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
-#' example_isolates[, carbapenems()]
+#' df[, carbapenems()]
 #' 
 #' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-#' example_isolates[, c("mo", aminoglycosides())]
+#' df[, c("mo", aminoglycosides())]
 #' 
 #' # select only antibiotic columns with DDDs for oral treatment
-#' example_isolates[, administrable_per_os()]
+#' df[, administrable_per_os()]
 #' 
 #' # filter using any() or all()
-#' example_isolates[any(carbapenems() == "R"), ]
+#' df[any(carbapenems() == "R"), ]
-#' subset(example_isolates, any(carbapenems() == "R"))
+#' subset(df, any(carbapenems() == "R"))
 #' 
 #' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
-#' example_isolates[any(carbapenems()), ]
+#' df[any(carbapenems()), ]
-#' example_isolates[all(carbapenems()), ]
+#' df[all(carbapenems()), ]
 #' 
 #' # filter with multiple antibiotic selectors using c()
-#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
+#' df[all(c(carbapenems(), aminoglycosides()) == "R"), ]
 #' 
 #' # filter + select in one go: get penicillins in carbapenems-resistant strains
-#' example_isolates[any(carbapenems() == "R"), penicillins()]
+#' df[any(carbapenems() == "R"), penicillins()]
 #' 
 #' # You can combine selectors with '&' to be more specific. For example,
 #' # penicillins() would select benzylpenicillin ('peni G') and
 #' # administrable_per_os() would select erythromycin. Yet, when combined these
 #' # drugs are both omitted since benzylpenicillin is not administrable per os
 #' # and erythromycin is not a penicillin:
-#' example_isolates[, penicillins() & administrable_per_os()]
+#' df[, penicillins() & administrable_per_os()]
 #' 
 #' # ab_selector() applies a filter in the `antibiotics` data set and is thus very
 #' # flexible. For instance, to select antibiotic columns with an oral DDD of at
 #' # least 1 gram:
-#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
+#' df[, ab_selector(oral_ddd > 1 & oral_units == "g")]
 #' 
 #' # dplyr -------------------------------------------------------------------
 #' \donttest{
 #' if (require("dplyr")) {
 #' 
 #'   # get AMR for all aminoglycosides e.g., per hospital:
-#'   example_isolates %>%
+#'   df %>%
 #'     group_by(hospital_id) %>% 
 #'     summarise(across(aminoglycosides(), resistance))
 #'     
 #'   # You can combine selectors with '&' to be more specific:
-#'   example_isolates %>%
+#'   df %>%
 #'     select(penicillins() & administrable_per_os())
 #'   
 #'   # get AMR for only drugs that matter - no intrinsic resistance:
-#'   example_isolates %>%
+#'   df %>%
 #'     filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>% 
 #'     group_by(hospital_id) %>% 
 #'     summarise(across(not_intrinsic_resistant(), resistance))
 #'     
 #'   # get susceptibility for antibiotics whose name contains "trim":
-#'   example_isolates %>%
+#'   df %>%
 #'     filter(first_isolate()) %>% 
 #'     group_by(hospital_id) %>% 
 #'     summarise(across(ab_selector(name %like% "trim"), susceptibility))
 #' 
 #'   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
-#'   example_isolates %>% 
+#'   df %>% 
 #'     select(carbapenems())
 #'     
 #'   # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
-#'   example_isolates %>% 
+#'   df %>% 
 #'     select(mo, aminoglycosides())
 #'     
 #'  # any() and all() work in dplyr's filter() too:
-#'  example_isolates %>% 
+#'  df %>% 
 #'     filter(any(aminoglycosides() == "R"),
 #'            all(cephalosporins_2nd() == "R"))
 #'     
 #'  # also works with c():
-#'  example_isolates %>% 
+#'  df %>% 
 #'     filter(any(c(carbapenems(), aminoglycosides()) == "R"))
 #'     
 #'  # not setting any/all will automatically apply all():
-#'  example_isolates %>% 
+#'  df %>% 
 #'     filter(aminoglycosides() == "R")
-#'  #> i Assuming a filter on all 4 aminoglycosides.
 #'     
 #'   # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
-#'   example_isolates %>% 
+#'   df %>% 
 #'     select(mo, ab_class("mycobact"))
 #'     
-#'   # get bug/drug combinations for only macrolides in Gram-positives:
+#'   # get bug/drug combinations for only glycopeptides in Gram-positives:
-#'   example_isolates %>% 
+#'   df %>% 
 #'     filter(mo_is_gram_positive()) %>% 
-#'     select(mo, macrolides()) %>% 
+#'     select(mo, glycopeptides()) %>% 
 #'     bug_drug_combinations() %>%
 #'     format()
 #'     
@@ -151,10 +152,12 @@
 #'     select(penicillins())         # only the 'J01CA01' column will be selected
 #'     
 #'     
-#'   # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
+#'   # with recent versions of dplyr this is all equal:
-#'   example_isolates[carbapenems() == "R", ]
+#'   x <- df[carbapenems() == "R", ]
-#'   example_isolates %>% filter(carbapenems() == "R")
+#'   y <- df %>% filter(carbapenems() == "R")
-#'   example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
+#'   z <- df %>% filter(if_all(carbapenems(), ~.x == "R"))
+#'   identical(x, y)
+#'   identical(y, z)
 #' }
 #' }
 ab_class <- function(ab_class, 

R/age.R

@@ -25,8 +25,7 @@
 
 #' Age in Years of Individuals
 #'
-#' Calculates age in years based on a reference date, which is the sytem date at default.
+#' Calculates age in years based on a reference date, which is the system date at default.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x date(s), [character] (vectors) will be coerced with [as.POSIXlt()]
 #' @param reference reference date(s) (defaults to today), [character] (vectors) will be coerced with [as.POSIXlt()]
 #' @param exact a [logical] to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
@@ -37,15 +36,19 @@
 #' This function vectorises over both `x` and `reference`, meaning that either can have a length of 1 while the other argument has a larger length.
 #' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
 #' @seealso To split ages into groups, use the [age_groups()] function.
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
-#' # 10 random birth dates
+#' # 10 random pre-Y2K birth dates
-#' df <- data.frame(birth_date = Sys.Date() - runif(10) * 25000)
+#' df <- data.frame(birth_date = as.Date("2000-01-01") - runif(10) * 25000)
+#' 
 #' # add ages
 #' df$age <- age(df$birth_date)
+#' 
 #' # add exact ages
 #' df$age_exact <- age(df$birth_date, exact = TRUE)
+#' 
+#' # add age at millenium switch
+#' df$age_at_y2k <- age(df$birth_date, "2000-01-01")
 #'
 #' df
 age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
@@ -115,7 +118,6 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
 #' Split Ages into Age Groups
 #'
 #' Split ages into age groups defined by the `split` argument. This allows for easier demographic (antimicrobial resistance) analysis.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x age, e.g. calculated with [age()]
 #' @param split_at values to split `x` at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See *Details*.
 #' @param na.rm a [logical] to indicate whether missing values should be removed
@@ -131,7 +133,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
 #' @return Ordered [factor]
 #' @seealso To determine ages, based on one or more reference dates, use the [age()] function.
 #' @export
-#' @inheritSection AMR Read more on Our Website!
+
 #' @examples
 #' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
 #'
@@ -150,7 +152,7 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
 #' age_groups(ages, split_at = "fives")
 #'
 #' # split specifically for children
-#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
+#' age_groups(ages, c(1, 2, 4, 6, 13, 18))
 #' age_groups(ages, "children")
 #'
 #' \donttest{
@@ -161,7 +163,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
 #'     filter(mo == as.mo("E. coli")) %>%
 #'     group_by(age_group = age_groups(age)) %>%
 #'     select(age_group, CIP) %>%
-#'     ggplot_rsi(x = "age_group", minimum = 0)
+#'     ggplot_rsi(x = "age_group",
+#'                minimum = 0,
+#'                x.title = "Age Group",
+#'                title = "Ciprofloxacin resistance per age group")
 #' }
 #' }
 age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {

R/atc_online.R

@@ -26,7 +26,6 @@
 #' Get ATC Properties from WHOCC Website
 #'
 #' Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param atc_code a [character] (vector) with ATC code(s) of antibiotics, will be coerced with [as.ab()] and [ab_atc()] internally if not a valid ATC code
 #' @param property property of an ATC code. Valid values are `"ATC"`, `"Name"`, `"DDD"`, `"U"` (`"unit"`), `"Adm.R"`, `"Note"` and `groups`. For this last option, all hierarchical groups of an ATC code will be returned, see *Examples*.
 #' @param administration type of administration when using `property = "Adm.R"`, see *Details*
@@ -51,7 +50,7 @@
 #' 
 #' - `"g"` = gram
 #' - `"mg"` = milligram
-#' - `"mcg"`` = microgram
+#' - `"mcg"` = microgram
 #' - `"U"` = unit
 #' - `"TU"` = thousand units
 #' - `"MU"` = million units
@@ -61,7 +60,6 @@
 #' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
 #' @export
 #' @rdname atc_online
-#' @inheritSection AMR Read more on Our Website!
 #' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
 #' @examples
 #' \donttest{

R/availability.R

@@ -26,12 +26,10 @@
 #' Check Availability of Columns
 #'
 #' Easy check for data availability of all columns in a data set. This makes it easy to get an idea of which antimicrobial combinations can be used for calculation with e.g. [susceptibility()] and [resistance()].
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param tbl a [data.frame] or [list]
 #' @param width number of characters to present the visual availability, defaults to filling the width of the console
 #' @details The function returns a [data.frame] with columns `"resistant"` and `"visual_resistance"`. The values in that columns are calculated with [resistance()].
 #' @return [data.frame] with column names of `tbl` as row names
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
 #' availability(example_isolates)

R/bug_drug_combinations.R

@@ -26,7 +26,6 @@
 #' Determine Bug-Drug Combinations
 #' 
 #' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @inheritParams eucast_rules
 #' @param combine_IR a [logical] to indicate whether values R and I should be summed
 #' @param add_ab_group a [logical] to indicate where the group of the antimicrobials must be included as a first column
@@ -41,11 +40,10 @@
 #' @rdname bug_drug_combinations
 #' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
 #' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
-#' @inheritSection AMR Read more on Our Website!
 #' @examples 
 #' \donttest{
 #' x <- bug_drug_combinations(example_isolates)
-#' x
+#' head(x)
 #' format(x, translate_ab = "name (atc)")
 #' 
 #' # Use FUN to change to transformation of microorganism codes
@@ -285,7 +283,7 @@ format.bug_drug_combinations <- function(x,
     y <- y %pm>% 
       pm_select(-ab_group) %pm>%
       pm_rename("Drug" = ab_txt)
-    colnames(y)[1] <- translate_AMR(colnames(y)[1], language, only_unknown = FALSE)
+    colnames(y)[1] <- translate_into_language(colnames(y)[1], language, only_unknown = FALSE)
   } else {
     y <- y %pm>% 
       pm_rename("Group" = ab_group,
@@ -293,7 +291,7 @@ format.bug_drug_combinations <- function(x,
   }
   
   if (!is.null(language)) {
-    colnames(y) <- translate_AMR(colnames(y), language, only_unknown = FALSE)
+    colnames(y) <- translate_into_language(colnames(y), language, only_unknown = FALSE)
   }
   
   if (remove_intrinsic_resistant == TRUE) {

R/catalogue_of_life.R

@@ -59,7 +59,6 @@ format_included_data_number <- function(data) {
 #' The Catalogue of Life (<http://www.catalogueoflife.org>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
 #'
 #' The syntax used to transform the original data to a cleansed \R format, can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R>.
-#' @inheritSection AMR Read more on Our Website!
 #' @name catalogue_of_life
 #' @rdname catalogue_of_life
 #' @seealso Data set [microorganisms] for the actual data. \cr
@@ -71,28 +70,19 @@ format_included_data_number <- function(data) {
 #'
 #' # Get a note when a species was renamed
 #' mo_shortname("Chlamydophila psittaci")
-#' # Note: 'Chlamydophila psittaci' (Everett et al., 1999) was renamed back to
-#' #       'Chlamydia psittaci' (Page, 1968)
-#' #> [1] "C. psittaci"
 #'
 #' # Get any property from the entire taxonomic tree for all included species
 #' mo_class("E. coli")
-#' #> [1] "Gammaproteobacteria"
 #'
 #' mo_family("E. coli")
-#' #> [1] "Enterobacteriaceae"
 #'
 #' mo_gramstain("E. coli") # based on kingdom and phylum, see ?mo_gramstain
-#' #> [1] "Gram-negative"
 #'
 #' mo_ref("E. coli")
-#' #> [1] "Castellani et al., 1919"
 #'
 #' # Do not get mistaken - this package is about microorganisms
 #' mo_kingdom("C. elegans")
-#' #> [1] "Fungi"                 # Fungi?!
 #' mo_name("C. elegans")
-#' #> [1] "Cladosporium elegans"  # Because a microorganism was found
 NULL
 
 #' Version info of included Catalogue of Life
@@ -102,7 +92,6 @@ NULL
 #' @details For LPSN, see [microorganisms].
 #' @return a [list], which prints in pretty format
 #' @inheritSection catalogue_of_life Catalogue of Life
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 catalogue_of_life_version <- function() {
   

R/count.R

@@ -28,7 +28,6 @@
 #' @description These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in `summarise()` from the `dplyr` package and also support grouped variables, see *Examples*.
 #'
 #' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed.
 #' @inheritParams proportion
 #' @inheritSection as.rsi Interpretation of R and S/I
@@ -45,11 +44,11 @@
 #' @rdname count
 #' @name count
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # example_isolates is a data set available in the AMR package.
-#' ?example_isolates
+#' # run ?example_isolates for more info.
 #' 
+#' # base R ------------------------------------------------------------
 #' count_resistant(example_isolates$AMX)   # counts "R"
 #' count_susceptible(example_isolates$AMX) # counts "S" and "I"
 #' count_all(example_isolates$AMX)         # counts "S", "I" and "R"
@@ -72,6 +71,7 @@
 #' count_susceptible(example_isolates$AMX)
 #' susceptibility(example_isolates$AMX) * n_rsi(example_isolates$AMX)
 #'
+#' # dplyr -------------------------------------------------------------
 #' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%

R/custom_eucast_rules.R

@@ -26,82 +26,67 @@
 #' Define Custom EUCAST Rules
 #' 
 #' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
-#' @inheritSection lifecycle Stable Lifecycle
+#' @param ... rules in [formula][`~`()] notation, see *Examples*
-#' @param ... rules in formula notation, see *Examples*
 #' @details
 #' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
-#' 
 #' @section How it works:
 #' 
 #' ### Basics
 #' 
 #' If you are familiar with the [`case_when()`][dplyr::case_when()] function of the `dplyr` package, you will recognise the input method to set your own rules. Rules must be set using what \R considers to be the 'formula notation'. The rule itself is written *before* the tilde (`~`) and the consequence of the rule is written *after* the tilde:
 #' 
-#' ```
+#' ```{r}
 #' x <- custom_eucast_rules(TZP == "S" ~ aminopenicillins == "S",
 #'                          TZP == "R" ~ aminopenicillins == "R")
 #' ```
 #' 
 #' These are two custom EUCAST rules: if TZP (piperacillin/tazobactam) is "S", all aminopenicillins (ampicillin and amoxicillin) must be made "S", and if TZP is "R", aminopenicillins must be made "R". These rules can also be printed to the console, so it is immediately clear how they work:
 #' 
-#' ```
+#' ```{r}
 #' x
-#' #> A set of custom EUCAST rules:
-#' #> 
-#' #>   1. If TZP is S then set to S:
-#' #>      amoxicillin (AMX), ampicillin (AMP)
-#' #> 
-#' #>   2. If TZP is R then set to R:
-#' #>      amoxicillin (AMX), ampicillin (AMP)
 #' ```
 #' 
 #' The rules (the part *before* the tilde, in above example `TZP == "S"` and `TZP == "R"`) must be evaluable in your data set: it should be able to run as a filter in your data set without errors. This means for the above example that the column `TZP` must exist. We will create a sample data set and test the rules set:
 #' 
-#' ```
+#' ```{r}
-#' df <- data.frame(mo = c("E. coli", "K. pneumoniae"),
+#' df <- data.frame(mo = c("Escherichia coli", "Klebsiella pneumoniae"),
-#'                  TZP = "R",
+#'                  TZP = as.rsi("R"),
-#'                  amox = "",
+#'                  ampi = as.rsi("S"),
-#'                  AMP = "")
+#'                  cipro = as.rsi("S"))
 #' df
-#' #>              mo TZP amox AMP
+#' 
-#' #> 1       E. coli   R         
+#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
-#' #> 2 K. pneumoniae   R         
-#'                  
-#' eucast_rules(df, rules = "custom", custom_rules = x)
-#' #>              mo TZP amox AMP
-#' #> 1       E. coli   R    R   R     
-#' #> 2 K. pneumoniae   R    R   R  
 #' ```
 #' 
 #' ### Using taxonomic properties in rules
 #' 
-#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), quote = "``", sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
+#' There is one exception in variables used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
 #' 
-#' ```
+#' ```{r}
 #' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
 #'                          TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
 #'
-#' eucast_rules(df, rules = "custom", custom_rules = y)
+#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
-#' #>              mo TZP amox AMP
-#' #> 1       E. coli   R         
-#' #> 2 K. pneumoniae   R    R   R
 #' ```
 #' 
 #' ### Usage of antibiotic group names
 #' 
 #' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
 #' 
-#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("``", tolower(gsub("^AB_", "", x)), "``\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
+#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
 #' @returns A [list] containing the custom rules
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
 #' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
 #'                          AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
+#' x
+#' 
+#' # run the custom rule set (verbose = TRUE will return a logbook instead of the data set):
 #' eucast_rules(example_isolates,
 #'              rules = "custom",
 #'              custom_rules = x,
-#'              info = FALSE)
+#'              info = FALSE,
+#'              verbose = TRUE)
 #'              
 #' # combine rule sets
 #' x2 <- c(x,

R/data.R

@@ -72,8 +72,10 @@
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection WHOCC WHOCC
-#' @inheritSection AMR Read more on Our Website!
 #' @seealso [microorganisms], [intrinsic_resistant]
+#' @examples
+#' head(antibiotics)
+#' head(antivirals)
 "antibiotics"
 
 #' @rdname antibiotics
@@ -104,6 +106,7 @@
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 #' - 3 entries of *Trichomonas* (*T. vaginalis*, and its family and genus)
+#' - 4 entries of *Toxoplasma* (*T. gondii*, and its order, family and genus)
 #' - 1 entry of *Candida* (*C.  krusei*), that is not (yet) in the Catalogue of Life
 #' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
 #' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
@@ -111,13 +114,10 @@
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
 #' 
 #' ## Direct download
-#' This data set is available as 'flat file' for use even without \R - you can find the file here:
+#' This data set is available as 'flat file' for use even without \R - you can find the file here: <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>. 
 #' 
-#' * <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>
+#' The file in \R format (with preserved data structure) can be found here: <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>.
 #' 
-#' The file in \R format (with preserved data structure) can be found here:
-#' 
-#' * <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>
 #' @section About the Records from LPSN (see *Source*):
 #' The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.
 #' 
@@ -138,8 +138,9 @@
 #' 
 #' * Retrieved from the `r SNOMED_VERSION$title`, OID `r SNOMED_VERSION$current_oid`, version `r SNOMED_VERSION$current_version`; url: <`r SNOMED_VERSION$url`>
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant]
+#' @examples
+#' head(microorganisms)
 "microorganisms"
 
 #' Data Set with Previously Accepted Taxonomic Names
@@ -155,8 +156,9 @@
 #' 
 #' Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @seealso [as.mo()] [mo_property()] [microorganisms]
+#' @examples
+#' head(microorganisms.old)
 "microorganisms.old"
 
 #' Data Set with `r format(nrow(microorganisms.codes), big.mark = ",")` Common Microorganism Codes
@@ -167,8 +169,9 @@
 #' - `mo`\cr ID of the microorganism in the [microorganisms] data set
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection catalogue_of_life Catalogue of Life
-#' @inheritSection AMR Read more on Our Website!
 #' @seealso [as.mo()] [microorganisms]
+#' @examples
+#' head(microorganisms.codes)
 "microorganisms.codes"
 
 #' Data Set with `r format(nrow(example_isolates), big.mark = ",")` Example Isolates
@@ -186,7 +189,8 @@
 #' - `mo`\cr ID of microorganism created with [as.mo()], see also [microorganisms]
 #' - `PEN:RIF`\cr `r sum(vapply(FUN.VALUE = logical(1), example_isolates, is.rsi))` different antibiotics with class [`rsi`] (see [as.rsi()]); these column names occur in the [antibiotics] data set and can be translated with [ab_name()]
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+#' @examples
+#' head(example_isolates)
 "example_isolates"
 
 #' Data Set with Unclean Data
@@ -199,7 +203,8 @@
 #' - `bacteria`\cr info about microorganism that can be transformed with [as.mo()], see also [microorganisms]
 #' - `AMX:GEN`\cr 4 different antibiotics that have to be transformed with [as.rsi()]
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+#' @examples
+#' head(example_isolates_unclean)
 "example_isolates_unclean"
 
 #' Data Set with `r format(nrow(WHONET), big.mark = ",")` Isolates - WHONET Example
@@ -233,7 +238,8 @@
 #' - `Date of data entry`\cr [Date] this data was entered in WHONET
 #' - `AMP_ND10:CIP_EE`\cr `r sum(vapply(FUN.VALUE = logical(1), WHONET, is.rsi))` different antibiotics. You can lookup the abbreviations in the [antibiotics] data set, or use e.g. [`ab_name("AMP")`][ab_name()] to get the official name immediately. Before analysis, you should transform this to a valid antibiotic class, using [as.rsi()].
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+#' @examples
+#' head(WHONET)
 "WHONET"
 
 #' Data Set for R/SI Interpretation
@@ -251,10 +257,12 @@
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
 #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
 #' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
+#' @details 
+#' The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @seealso [intrinsic_resistant]
+#' @examples
+#' head(rsi_translation)
 "rsi_translation"
 
 #' Data Set with Bacterial Intrinsic Resistance
@@ -267,18 +275,8 @@
 #' 
 #' This data set is based on `r format_eucast_version_nr(3.3)`.
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
-#' \donttest{
+#' head(intrinsic_resistant)
-#' if (require("dplyr")) {
-#'   intrinsic_resistant %>%
-#'     mutate(mo = mo_name(mo),
-#'            ab = ab_name(mo))
-#'     filter(ab == "Vancomycin" & mo %like% "Enterococcus") %>% 
-#'     pull(mo)
-#'   #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
-#' }
-#' }
 "intrinsic_resistant"
 
 #' Data Set with Treatment Dosages as Defined by EUCAST
@@ -296,5 +294,6 @@
 #' - `eucast_version`\cr Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply
 #' @details `r format_eucast_version_nr(11.0)` are based on the dosages in this data set.
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+#' @examples
+#' head(dosage)
 "dosage"

R/deprecated.R

@@ -26,8 +26,6 @@
 #' Deprecated Functions
 #'
 #' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
-#' @inheritSection lifecycle Retired Lifecycle
-#' @inheritSection AMR Read more on Our Website!
 #' @keywords internal
 #' @name AMR-deprecated
 # @export

R/disk.R

@@ -26,7 +26,6 @@
 #' Transform Input to Disk Diffusion Diameters
 #'
 #' This transforms a vector to a new class [`disk`], which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @rdname as.disk
 #' @param x vector
 #' @param na.rm a [logical] indicating whether missing values should be removed
@@ -35,27 +34,31 @@
 #' @aliases disk
 #' @export
 #' @seealso [as.rsi()]
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
-#' \donttest{
+#' # transform existing disk zones to the `disk` class (using base R)
-#' # transform existing disk zones to the `disk` class
+#' df <- data.frame(microorganism = "Escherichia coli",
-#' df <- data.frame(microorganism = "E. coli",
 #'                  AMP = 20,
 #'                  CIP = 14,
 #'                  GEN = 18,
 #'                  TOB = 16)
 #' df[, 2:5] <- lapply(df[, 2:5], as.disk)
-#' # same with dplyr:
+#' str(df)
-#' # df %>% mutate(across(AMP:TOB, as.disk))
+#' 
+#' \donttest{
+#' # transforming is easier with dplyr:
+#' if (require("dplyr")) {
+#'   df %>% mutate(across(AMP:TOB, as.disk))
+#' }
+#' }
 #' 
 #' # interpret disk values, see ?as.rsi
 #' as.rsi(x = as.disk(18),
 #'        mo = "Strep pneu",  # `mo` will be coerced with as.mo()
 #'        ab = "ampicillin",  # and `ab` with as.ab()
 #'        guideline = "EUCAST")
-#'        
+#'
-#' as.rsi(df)
+#' # interpret whole data set, pretend to be all from urinary tract infections:
-#' }
+#' as.rsi(df, uti = TRUE)
 as.disk <- function(x, na.rm = FALSE) {
   meet_criteria(x, allow_class = c("disk", "character", "numeric", "integer"), allow_NA = TRUE)
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
@@ -65,6 +68,7 @@ as.disk <- function(x, na.rm = FALSE) {
     if (na.rm == TRUE) {
       x <- x[!is.na(x)]
     }
+    x[trimws(x) == ""] <- NA
     x.bak <- x
     
     na_before <- length(x[is.na(x)])

R/episode.R

@@ -26,7 +26,6 @@
 #' Determine (New) Episodes for Patients
 #' 
 #' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
 #' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
 #' @param ... ignored, only in place to allow future extensions
@@ -42,16 +41,16 @@
 #' @seealso [first_isolate()]
 #' @rdname get_episode
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # `example_isolates` is a data set available in the AMR package.
-#' # See ?example_isolates.
+#' # See ?example_isolates
+#' df <- example_isolates[sample(seq_len(2000), size = 200), ]
 #' 
-#' get_episode(example_isolates$date, episode_days = 60)    # indices
+#' get_episode(df$date, episode_days = 60)    # indices
-#' is_new_episode(example_isolates$date, episode_days = 60) # TRUE/FALSE
+#' is_new_episode(df$date, episode_days = 60) # TRUE/FALSE
 #' 
 #' # filter on results from the third 60-day episode only, using base R
-#' example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
+#' df[which(get_episode(df$date, 60) == 3), ]
 #' 
 #' # the functions also work for less than a day, e.g. to include one per hour:
 #' get_episode(c(Sys.time(),
@@ -62,24 +61,24 @@
 #' if (require("dplyr")) {
 #'   # is_new_episode() can also be used in dplyr verbs to determine patient
 #'   # episodes based on any (combination of) grouping variables:
-#'   example_isolates %>%
+#'   df %>%
 #'     mutate(condition = sample(x = c("A", "B", "C"), 
 #'                               size = 2000,
 #'                               replace = TRUE)) %>% 
 #'     group_by(condition) %>%
-#'     mutate(new_episode = is_new_episode(date, 365))
+#'     mutate(new_episode = is_new_episode(date, 365)) %>%
+#'     select(patient_id, date, condition, new_episode)
 #'     
-#'   example_isolates %>%
+#'   df %>%
 #'     group_by(hospital_id, patient_id) %>%
 #'     transmute(date, 
 #'               patient_id,
 #'               new_index = get_episode(date, 60),
 #'               new_logical = is_new_episode(date, 60))
 #'   
-#'   
+#'   df %>%
-#'   example_isolates %>%
 #'     group_by(hospital_id) %>% 
-#'     summarise(patients = n_distinct(patient_id),
+#'     summarise(n_patients = n_distinct(patient_id),
 #'               n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),
 #'               n_episodes_60  = sum(is_new_episode(date, episode_days = 60)),
 #'               n_episodes_30  = sum(is_new_episode(date, episode_days = 30)))
@@ -87,21 +86,23 @@
 #'     
 #'   # grouping on patients and microorganisms leads to the same
 #'   # results as first_isolate() when using 'episode-based':
-#'   x <- example_isolates %>%
+#'   x <- df %>%
 #'     filter_first_isolate(include_unknown = TRUE,
 #'                          method = "episode-based")
 #'     
-#'   y <- example_isolates %>%
+#'   y <- df %>%
 #'     group_by(patient_id, mo) %>%
-#'     filter(is_new_episode(date, 365))
+#'     filter(is_new_episode(date, 365)) %>%
+#'     ungroup()
 #'
-#'   identical(x$patient_id, y$patient_id)
+#'   identical(x, y)
 #'   
 #'   # but is_new_episode() has a lot more flexibility than first_isolate(),
 #'   # since you can now group on anything that seems relevant:
-#'   example_isolates %>%
+#'   df %>%
 #'     group_by(patient_id, mo, hospital_id, ward_icu) %>%
-#'     mutate(flag_episode = is_new_episode(date, 365))
+#'     mutate(flag_episode = is_new_episode(date, 365)) %>%
+#'     select(group_vars(.), flag_episode)
 #' }
 #' }
 get_episode <- function(x, episode_days, ...) {

R/eucast_rules.R

@@ -52,7 +52,6 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
 #' 
 #' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC`
 #' @param info a [logical] to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
 #' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
@@ -76,11 +75,11 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' 
 #' Custom rules can be created using [custom_eucast_rules()], e.g.:
 #' 
-#' ```
+#' ```{r}
 #' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
 #'                          AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
 #'
-#' eucast_rules(example_isolates, rules = "custom", custom_rules = x)
+#' eucast_rules(example_isolates, rules = "custom", custom_rules = x, info = FALSE)
 #' ```
 #' 
 #' 
@@ -113,8 +112,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
+#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
+
 #' @examples
 #' \donttest{
 #' a <- data.frame(mo = c("Staphylococcus aureus",
@@ -131,33 +131,26 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #'                 FOX = "S",       # Cefoxitin
 #'                 stringsAsFactors = FALSE)
 #'
-#' a
+#' head(a)
-#' #                       mo  VAN  AMX  COL  CAZ  CXM  PEN  FOX
-#' # 1  Staphylococcus aureus    -    -    -    -    -    S    S
-#' # 2  Enterococcus faecalis    -    -    -    -    -    S    S
-#' # 3       Escherichia coli    -    -    -    -    -    S    S
-#' # 4  Klebsiella pneumoniae    -    -    -    -    -    S    S
-#' # 5 Pseudomonas aeruginosa    -    -    -    -    -    S    S
 #'
 #'
 #' # apply EUCAST rules: some results wil be changed
 #' b <- eucast_rules(a)
 #'
-#' b
+#' head(b)
-#' #                       mo  VAN  AMX  COL  CAZ  CXM  PEN  FOX
-#' # 1  Staphylococcus aureus    -    S    R    R    S    S    S
-#' # 2  Enterococcus faecalis    -    -    R    R    R    S    R
-#' # 3       Escherichia coli    R    -    -    -    -    R    S
-#' # 4  Klebsiella pneumoniae    R    R    -    -    -    R    S
-#' # 5 Pseudomonas aeruginosa    R    R    -    -    R    R    R
 #'
 #'
 #' # do not apply EUCAST rules, but rather get a data.frame
 #' # containing all details about the transformations:
 #' c <- eucast_rules(a, verbose = TRUE)
+#' head(c)
 #' }
 #' 
+#' # Dosage guidelines:
+#' 
 #' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
+#' 
+#' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
 eucast_rules <- function(x,
                          col_mo = NULL,
                          info = interactive(),

R/first_isolate.R

@@ -26,7 +26,6 @@
 #' Determine First Isolates
 #'
 #' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
 #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
 #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
@@ -126,7 +125,6 @@
 #' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
 #' 
 #' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
@@ -134,7 +132,7 @@
 #' example_isolates[first_isolate(), ]
 #' \donttest{
 #' # get all first Gram-negatives
-#' example_isolates[which(first_isolate() & mo_is_gram_negative()), ]
+#' example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ]
 #'
 #' if (require("dplyr")) {
 #'   # filter on first isolates using dplyr:
@@ -143,12 +141,13 @@
 #'  
 #'   # short-hand version:
 #'   example_isolates %>%
-#'     filter_first_isolate()
+#'     filter_first_isolate(info = FALSE)
 #'     
-#'  # grouped determination of first isolates (also prints group names):
+#'  # flag the first isolates per group:
 #'  example_isolates %>%
 #'    group_by(hospital_id) %>%
-#'    mutate(first = first_isolate())
+#'    mutate(first = first_isolate()) %>%
+#'    select(hospital_id, date, patient_id, mo, first)
 #'   
 #'   # now let's see if first isolates matter:
 #'   A <- example_isolates %>%
@@ -163,6 +162,9 @@
 #'               resistance = resistance(GEN))  # gentamicin resistance
 #'  
 #'   # Have a look at A and B.
+#'   A
+#'   B
+#'   
 #'   # B is more reliable because every isolate is counted only once.
 #'   # Gentamicin resistance in hospital D appears to be 4.2% higher than
 #'   # when you (erroneously) would have used all isolates for analysis.

R/g.test.R

@@ -26,7 +26,6 @@
 #' *G*-test for Count Data
 #'
 #' [g.test()] performs chi-squared contingency table tests and goodness-of-fit tests, just like [chisq.test()] but is more reliable (1). A *G*-test can be used to see whether the number of observations in each category fits a theoretical expectation (called a ***G*-test of goodness-of-fit**), or to see whether the proportions of one variable are different for different values of the other variable (called a ***G*-test of independence**).
-#' @inheritSection lifecycle Questioning Lifecycle
 #' @inherit stats::chisq.test params return
 #' @details If `x` is a [matrix] with one row or column, or if `x` is a vector and `y` is not given, then a *goodness-of-fit test* is performed (`x` is treated as a one-dimensional contingency table). The entries of `x` must be non-negative integers. In this case, the hypothesis tested is whether the population probabilities equal those in `p`, or are all equal if `p` is not given.
 #'
@@ -76,7 +75,6 @@
 #' - The possibility to simulate p values with `simulate.p.value` was removed
 #' @export
 #' @importFrom stats pchisq complete.cases
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # = EXAMPLE 1 =
 #' # Shivrain et al. (2006) crossed clearfield rice (which are resistant
@@ -88,8 +86,7 @@
 #' # ratio.
 #'
 #' x <- c(772, 1611, 737)
-#' G <- g.test(x, p = c(1, 2, 1) / 4)
+#' g.test(x, p = c(1, 2, 1) / 4)
-#' # G$p.value = 0.12574.
 #'
 #' # There is no significant difference from a 1:2:1 ratio.
 #' # Meaning: resistance controlled by a single gene with two co-dominant
@@ -105,11 +102,9 @@
 #'
 #' x <- c(1752, 1895)
 #' g.test(x)
-#' # p = 0.01787343
 #'
 #' # There is a significant difference from a 1:1 ratio.
 #' # Meaning: there are significantly more left-billed birds.
-#'
 g.test <- function(x,
                    y = NULL,
                    # correct = TRUE,

R/ggplot_pca.R

@@ -26,7 +26,6 @@
 #' PCA Biplot with `ggplot2`
 #'
 #' Produces a `ggplot2` variant of a so-called [biplot](https://en.wikipedia.org/wiki/Biplot) for PCA (principal component analysis), but is more flexible and more appealing than the base \R [biplot()] function.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x an object returned by [pca()], [prcomp()] or [princomp()]
 #' @inheritParams stats::biplot.prcomp
 #' @param labels an optional vector of labels for the observations. If set, the labels will be placed below their respective points. When using the [pca()] function as input for `x`, this will be determined automatically based on the attribute `non_numeric_cols`, see [pca()].
@@ -64,23 +63,28 @@
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
 #'
-#' # See ?pca for more info about Principal Component Analysis (PCA).
 #' \donttest{
 #' if (require("dplyr")) {
-#'   pca_model <- example_isolates %>% 
+#'   # calculate the resistance per group first 
-#'     filter(mo_genus(mo) == "Staphylococcus") %>% 
+#'   resistance_data <- example_isolates %>% 
-#'     group_by(species = mo_shortname(mo)) %>%
+#'     group_by(order = mo_order(mo),       # group on anything, like order
-#'     summarise_if (is.rsi, resistance) %>%
+#'              genus = mo_genus(mo)) %>%   #   and genus as we do here;
-#'     pca(FLC, AMC, CXM, GEN, TOB, TMP, SXT, CIP, TEC, TCY, ERY)
+#'     filter(n() >= 30) %>%                # filter on only 30 results per group
+#'     summarise_if(is.rsi, resistance)     # then get resistance of all drugs
 #'     
-#'   # old (base R)
+#'   # now conduct PCA for certain antimicrobial agents
-#'   biplot(pca_model)
+#'   pca_result <- resistance_data %>%         
+#'     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) 
+#'     
+#'   summary(pca_result)
 #'   
-#'   # new 
+#'   # old base R plotting method:
-#'   ggplot_pca(pca_model)
+#'   biplot(pca_result)
+#'   # new ggplot2 plotting method using this package:
+#'   ggplot_pca(pca_result)
 #'   
 #'   if (require("ggplot2")) {
-#'     ggplot_pca(pca_model) +
+#'     ggplot_pca(pca_result) +
 #'       scale_colour_viridis_d() +
 #'       labs(title = "Title here")
 #'   }

R/ggplot_rsi.R

@@ -26,7 +26,6 @@
 #' AMR Plots with `ggplot2`
 #'
 #' Use these functions to create bar plots for AMR data analysis. All functions rely on [ggplot2][ggplot2::ggplot()] functions.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param data a [data.frame] with column(s) of class [`rsi`] (see [as.rsi()])
 #' @param position position adjustment of bars, either `"fill"`, `"stack"` or `"dodge"`
 #' @param x variable to show on x axis, either `"antibiotic"` (default) or `"interpretation"` or a grouping variable
@@ -65,7 +64,6 @@
 #' [ggplot_rsi()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See *Examples*.
 #' @rdname ggplot_rsi
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' \donttest{
 #' if (require("ggplot2") & require("dplyr")) {

R/guess_ab_col.R

@@ -26,7 +26,6 @@
 #' Guess Antibiotic Column
 #'
 #' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame]
 #' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
 #' @param verbose a [logical] to indicate whether additional info should be printed
@@ -34,7 +33,6 @@
 #' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precedence over shorter column names.**
 #' @return A column name of `x`, or `NULL` when no result is found.
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' df <- data.frame(amox = "S",
 #'                  tetr = "R")

R/italicise_taxonomy.R

@@ -25,8 +25,7 @@
 
 #' Italicise Taxonomic Families, Genera, Species, Subspecies
 #' 
-#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
+#' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param string a [character] (vector)
 #' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
 #' @details 
@@ -35,23 +34,12 @@
 #' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
 #' 
 #' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
-#' @inheritSection AMR Read more on Our Website!
 #' @export
 #' @examples
 #' italicise_taxonomy("An overview of Staphylococcus aureus isolates")
 #' italicise_taxonomy("An overview of S. aureus isolates")
 #' 
 #' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
-#' 
-#' # since ggplot2 supports no markdown (yet), use
-#' # italicise_taxonomy() and the `ggtext` package for titles:
-#' \donttest{
-#' if (require("ggplot2") && require("ggtext")) {
-#'   autoplot(example_isolates$AMC,
-#'            title = italicise_taxonomy("Amoxi/clav in E. coli")) +
-#'     theme(plot.title = ggtext::element_markdown())
-#' }
-#' }
 italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
   if (missing(type)) {
     type <- "markdown"

R/join_microorganisms.R

@@ -26,7 +26,6 @@
 #' Join [microorganisms] to a Data Set
 #'
 #' Join the data set [microorganisms] easily to an existing data set or to a [character] vector.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @rdname join
 #' @name join
 #' @aliases join inner_join
@@ -37,7 +36,6 @@
 #' @details **Note:** As opposed to the `join()` functions of `dplyr`, [character] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. 
 #' 
 #' If the `dplyr` package is installed, their join functions will be used. Otherwise, the much slower [merge()] and [interaction()] functions from base \R will be used.
-#' @inheritSection AMR Read more on Our Website!
 #' @return a [data.frame]
 #' @export
 #' @examples

R/key_antimicrobials.R

@@ -26,7 +26,6 @@
 #' (Key) Antimicrobials for First Weighted Isolates
 #'
 #' These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see [first_isolate()]). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically
 #' @param y,z [character] vectors to compare
 #' @inheritParams first_isolate
@@ -82,7 +81,6 @@
 #' @rdname key_antimicrobials
 #' @export
 #' @seealso [first_isolate()]
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
@@ -110,7 +108,7 @@
 #'       first_weighted = first_isolate(col_keyantimicrobials = "keyab")
 #'     )
 #'  
-#'   # Check the difference, in this data set it results in more isolates:
+#'   # Check the difference in this data set, 'weighted' results in more isolates:
 #'   sum(my_patients$first_regular, na.rm = TRUE)
 #'   sum(my_patients$first_weighted, na.rm = TRUE)
 #' }

R/kurtosis.R

@@ -26,14 +26,15 @@
 #' Kurtosis of the Sample
 #'
 #' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a vector of values, a [matrix] or a [data.frame]
 #' @param na.rm a [logical] to indicate whether `NA` values should be stripped before the computation proceeds
 #' @param excess a [logical] to indicate whether the *excess kurtosis* should be returned, defined as the kurtosis minus 3.
 #' @seealso [skewness()]
 #' @rdname kurtosis
-#' @inheritSection AMR Read more on Our Website!
 #' @export
+#' @examples 
+#' kurtosis(rnorm(10000))
+#' kurtosis(rnorm(10000), excess = TRUE)
 kurtosis <- function(x, na.rm = FALSE, excess = FALSE) {
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
   meet_criteria(excess, allow_class = "logical", has_length = 1)

R/lifecycle.R

@@ -1,54 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Data Analysis for R                   #
-#                                                                      #
-# SOURCE                                                               #
-# https://github.com/msberends/AMR                                     #
-#                                                                      #
-# LICENCE                                                              #
-# (c) 2018-2022 Berends MS, Luz CF et al.                              #
-# Developed at the University of Groningen, the Netherlands, in        #
-# collaboration with non-profit organisations Certe Medical            #
-# Diagnostics & Advice, and University Medical Center Groningen.       # 
-#                                                                      #
-# 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/   #
-# ==================================================================== #
-
-###############
-# NOTE TO SELF: could also have done this with the 'lifecycle' package, but why add a package dependency for such an easy job??
-###############
-
-#' Lifecycles of Functions in the `AMR` Package
-#' @name lifecycle
-#' @rdname lifecycle
-#' @description Functions in this `AMR` package are categorised using [the lifecycle circle of the Tidyverse as found on www.tidyverse.org/lifecycle](https://lifecycle.r-lib.org/articles/stages.html).
-#' 
-#' \if{html}{\figure{lifecycle_tidyverse.svg}{options: height="200" style=margin-bottom:"5"} \cr}
-#' This page contains a section for every lifecycle (with text borrowed from the aforementioned Tidyverse website), so they can be used in the manual pages of the functions. 
-#' @section Experimental Lifecycle:
-#' \if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:"5"} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **experimental**. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this `AMR` package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
-#' @section Maturing Lifecycle:
-#' \if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:"5"} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **maturing**. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome [to suggest changes at our repository](https://github.com/msberends/AMR/issues) or [write us an email (see section 'Contact Us')][AMR::AMR].
-#' @section Stable Lifecycle:
-#' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
-#' 
-#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
-#' @section Retired Lifecycle:
-#' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:"5"} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.
-#' @section Questioning Lifecycle:
-#' \if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:"5"} \cr}
-#' The [lifecycle][AMR::lifecycle] of this function is **questioning**. This function might be no longer be optimal approach, or is it questionable whether this function should be in this `AMR` package at all.
-NULL

R/like.R

@@ -26,7 +26,6 @@
 #' Vectorised Pattern Matching with Keyboard Shortcut
 #'
 #' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [character] vector where matches are sought, or an object which can be coerced by [as.character()] to a [character] vector.
 #' @param pattern a [character] vector containing regular expressions (or a [character] string for `fixed = TRUE`) to be matched in the given [character] vector. Coerced by [as.character()] to a [character] string if possible.
 #' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
@@ -44,27 +43,21 @@
 #' Using RStudio? The `%like%`/`%unlike%` functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like `Shift+Ctrl+L` or `Shift+Cmd+L` (see menu `Tools` > `Modify Keyboard Shortcuts...`). If you keep pressing your shortcut, the inserted text will be iterated over `%like%` -> `%unlike%` -> `%like_case%` -> `%unlike_case%`.
 #' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R), although altered as explained in *Details*.
 #' @seealso [grepl()]
-#' @inheritSection AMR Read more on Our Website!
+
 #' @examples
 #' a <- "This is a test"
 #' b <- "TEST"
 #' a %like% b
-#' #> TRUE
 #' b %like% a
-#' #> FALSE
 #' 
 #' # also supports multiple patterns
 #' a <- c("Test case", "Something different", "Yet another thing")
 #' b <- c(     "case",           "diff",      "yet")
 #' a %like% b
-#' #> TRUE TRUE TRUE
 #' a %unlike% b
-#' #> FALSE FALSE FALSE
 #' 
 #' a[1] %like% b
-#' #> TRUE FALSE FALSE
 #' a %like% b[1]
-#' #> TRUE FALSE FALSE
 #' 
 #' # get isolates whose name start with 'Ent' or 'ent'
 #' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ]

R/mdro.R

@@ -26,7 +26,6 @@
 #' Determine Multidrug-Resistant Organisms (MDRO)
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national and custom guidelines.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank for automatic determination.
 #' @param guideline a specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
 #' @param ... in case of [custom_mdro_guideline()]: a set of rules, see section *Using Custom Guidelines* below. Otherwise: column name of an antibiotic, see section *Antibiotics* below.
@@ -137,15 +136,17 @@
 #' @rdname mdro
 #' @aliases MDR XDR PDR BRMO 3MRGN 4MRGN
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @source
 #' See the supported guidelines above for the [list] of publications used for this function.
 #' @examples
-#' mdro(example_isolates, guideline = "EUCAST")
+#' out <- mdro(example_isolates, guideline = "EUCAST")
+#' str(out)
+#' table(out)
 #' 
-#' mdro(example_isolates,
+#' out <- mdro(example_isolates,
-#'      guideline = custom_mdro_guideline(AMX == "R" ~ "Custom MDRO 1",
+#'             guideline = custom_mdro_guideline(AMX == "R" ~ "Custom MDRO 1",
-#'                                        VAN == "R" ~ "Custom MDRO 2"))
+#'                                               VAN == "R" ~ "Custom MDRO 2"))
+#' table(out)
 #' 
 #' \donttest{
 #' if (require("dplyr")) {
@@ -155,10 +156,10 @@
 #'   
 #'   # no need to define `x` when used inside dplyr verbs:
 #'   example_isolates %>%
-#'     mutate(MDRO = mdro(),
+#'     mutate(MDRO = mdro()) %>%
-#'            EUCAST = eucast_exceptional_phenotypes(),
+#'     pull(MDRO) %>%
-#'            BRMO = brmo(),
+#'     table()
-#'            MRGN = mrgn())
+#'            
 #' }
 #' }
 mdro <- function(x = NULL,
@@ -191,8 +192,10 @@ mdro <- function(x = NULL,
   
   info.bak <- info
   # don't thrown info's more than once per call
-  info <- message_not_thrown_before("mdro")
+  if (isTRUE(info)) {
-
+    info <- message_not_thrown_before("mdro")
+  }
+  
   if (interactive() & verbose == TRUE & info == TRUE) {
     txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
                   "\n\nThis may overwrite your existing data if you use e.g.:",

R/mic.R

@@ -43,11 +43,11 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' Transform Input to Minimum Inhibitory Concentrations (MIC)
 #'
 #' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @rdname as.mic
 #' @param x a [character] or [numeric] vector
 #' @param na.rm a [logical] indicating whether missing values should be removed
-#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
+#' @param ... arguments passed on to methods
+#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
 #' 
 #' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
 #' 
@@ -86,36 +86,43 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
 #' ```
 #' 
 #' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
+#' 
+#' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
+#' 
+#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `<mic>` class.
 #' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
 #' @aliases mic
 #' @export
 #' @seealso [as.rsi()]
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
+#' mic_data
 #' is.mic(mic_data)
 #'
 #' # this can also coerce combined MIC/RSI values:
-#' as.mic("<=0.002; S") # will return <=0.002
+#' as.mic("<=0.002; S")
 #' 
-#' # mathematical processing treats MICs as [numeric] values
+#' # mathematical processing treats MICs as numeric values
 #' fivenum(mic_data)
 #' quantile(mic_data)
 #' all(mic_data < 512)
 #'
 #' # interpret MIC values
 #' as.rsi(x = as.mic(2),
-#'        mo = as.mo("S. pneumoniae"),
+#'        mo = as.mo("Streptococcus pneumoniae"),
 #'        ab = "AMX",
 #'        guideline = "EUCAST")
-#' as.rsi(x = as.mic(4),
+#' as.rsi(x = as.mic(c(0.01, 2, 4, 8)),
-#'        mo = as.mo("S. pneumoniae"),
+#'        mo = as.mo("Streptococcus pneumoniae"),
 #'        ab = "AMX",
 #'        guideline = "EUCAST")
 #'
 #' # plot MIC values, see ?plot
 #' plot(mic_data)
 #' plot(mic_data, mo = "E. coli", ab = "cipro")
+#' autoplot(mic_data, mo = "E. coli", ab = "cipro")
+#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
+#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk") # Ukrainian
 as.mic <- function(x, na.rm = FALSE) {
   meet_criteria(x, allow_class = c("mic", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
@@ -127,6 +134,7 @@ as.mic <- function(x, na.rm = FALSE) {
     if (na.rm == TRUE) {
       x <- x[!is.na(x)]
     }
+    x[trimws(x) == ""] <- NA
     x.bak <- x
     
     # comma to period
@@ -196,7 +204,8 @@ all_valid_mics <- function(x) {
 }
 
 #' @rdname as.mic
-#' @details `NA_mic_` is a missing value of the new `<mic>` class.
+#' @details `NA_mic_` is a missing value of the new `<mic>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
 #' @export
 NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
                            new_class =  c("mic", "ordered", "factor"))
@@ -214,13 +223,6 @@ as.double.mic <- function(x, ...) {
   as.double(gsub("[<=>]+", "", as.character(x), perl = TRUE))
 }
 
-#' @method as.integer mic
-#' @export
-#' @noRd
-as.integer.mic <- function(x, ...) {
-  as.integer(gsub("[<=>]+", "", as.character(x), perl = TRUE))
-}
-
 #' @method as.numeric mic
 #' @export
 #' @noRd
@@ -228,11 +230,12 @@ as.numeric.mic <- function(x, ...) {
   as.numeric(gsub("[<=>]+", "", as.character(x), perl = TRUE))
 }
 
+#' @rdname as.mic
 #' @method droplevels mic
+#' @param as.mic a [logical] to indicate whether the `<mic>` class should be kept, defaults to `FALSE`
 #' @export
-#' @noRd
+droplevels.mic <- function(x, as.mic = FALSE, ...) {
-droplevels.mic <- function(x, exclude = if (any(is.na(levels(x)))) NULL else NA, as.mic = TRUE, ...) {
+  x <- droplevels.factor(x, ...)
-  x <- droplevels.factor(x, exclude = exclude, ...)
   if (as.mic == TRUE) {
     class(x) <- c("mic", "ordered", "factor")
   }
@@ -260,7 +263,9 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat("Class <mic>\n")
+  cat("Class <mic>",
+      ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
+      "\n", sep = "")
   print(as.character(x), quote = FALSE)
   att <- attributes(x)
   if ("na.action" %in% names(att)) {

R/mo.R

@@ -26,7 +26,6 @@
 #' Transform Input to a Microorganism Code
 #'
 #' Use this function to determine a valid microorganism code ([`mo`]). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see *Source*). The input can be almost anything: a full name (like `"Staphylococcus aureus"`), an abbreviated name (such as `"S. aureus"`), an abbreviation known in the field (such as `"MRSA"`), or just a genus. See *Examples*.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [character] vector or a [data.frame] with one or two columns
 #' @param Becker a [logical] to indicate whether staphylococci should be categorised into coagulase-negative staphylococci ("CoNS") and coagulase-positive staphylococci ("CoPS") instead of their own species, according to Karsten Becker *et al.* (1,2,3).
 #'
@@ -116,7 +115,6 @@
 #'
 #' The [`mo_*`][mo_property()] functions (such as [mo_genus()], [mo_gramstain()]) to get properties based on the returned code.
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' \donttest{
 #' # These examples all return "B_STPHY_AURS", the ID of S. aureus:
@@ -174,7 +172,7 @@ as.mo <- function(x,
   meet_criteria(info, allow_class = "logical", has_length = 1)
   
   check_dataset_integrity()
-
+  
   if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo)
                & isFALSE(Becker)
                & isFALSE(Lancefield), error = function(e) FALSE)) {
@@ -182,19 +180,19 @@ as.mo <- function(x,
     # is.mo() won't work - MO codes might change between package versions
     return(set_clean_class(x, new_class = c("mo", "character")))
   }
-
+  
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
   # replace mo codes used in older package versions
   x <- replace_old_mo_codes(x, property = "mo")
   # ignore cases that match the ignore pattern
   x <- replace_ignore_pattern(x, ignore_pattern)
-
+  
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
   # Laboratory systems: remove (translated) entries like "no growth", etc.
-  x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
+  x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
-  x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
+  x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
   uncertainty_level <- translate_allow_uncertain(allow_uncertain)
   
   if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
@@ -204,25 +202,25 @@ as.mo <- function(x,
     return(set_clean_class(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE],
                            new_class = c("mo", "character")))
   }
-
+  
   if (!is.null(reference_df)
       && check_validity_mo_source(reference_df)
       && isFALSE(Becker)
       && isFALSE(Lancefield)
       && all(x %in% unlist(reference_df), na.rm = TRUE)) {
-
+    
     reference_df <- repair_reference_df(reference_df)
     suppressWarnings(
       y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
         pm_left_join(reference_df, by = "x") %pm>%
         pm_pull(mo) 
     )
-
+    
   } else if (all(x[!is.na(x)] %in% MO_lookup$mo)
              & isFALSE(Becker)
              & isFALSE(Lancefield)) {
     y <- x
-
+    
   } else {
     # will be checked for mo class in validation and uses exec_as.mo internally if necessary
     y <- mo_validate(x = x, property = "mo",
@@ -282,7 +280,7 @@ exec_as.mo <- function(x,
   meet_criteria(actual_uncertainty, allow_class = "numeric", has_length = 1)
   meet_criteria(actual_input, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
-
+  
   check_dataset_integrity()
   
   if (isTRUE(debug) && initial_search == TRUE) {
@@ -297,13 +295,13 @@ exec_as.mo <- function(x,
                      initial = initial_search,
                      uncertainty = actual_uncertainty,
                      input_actual = actual_input) {
-
+    
     if (!is.null(input_actual)) {
       input <- input_actual
     } else {
       input <- tryCatch(x_backup[i], error = function(e) "")
     }
-
+    
     # `column` can be NULL for all columns, or a selection
     # returns a [character] (vector) - if `column` > length 1 then with columns as names
     if (isTRUE(debug_mode)) {
@@ -360,19 +358,19 @@ exec_as.mo <- function(x,
       res
     }
   }
-
+  
   # start off with replaced language-specific non-ASCII characters with ASCII characters
   x <- parse_and_convert(x)
   # replace mo codes used in older package versions
   x <- replace_old_mo_codes(x, property)
   # ignore cases that match the ignore pattern
   x <- replace_ignore_pattern(x, ignore_pattern)
-
+  
   # WHONET: xxx = no growth
   x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
   # Laboratory systems: remove (translated) entries like "no growth", etc.
-  x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
+  x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
-  x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
+  x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
   
   if (initial_search == TRUE) {
     # keep track of time - give some hints to improve speed if it takes a long time
@@ -383,7 +381,7 @@ exec_as.mo <- function(x,
     pkg_env$mo_renamed <- NULL
   }
   pkg_env$mo_renamed_last_run <- NULL
-
+  
   failures <- character(0)
   uncertainty_level <- translate_allow_uncertain(allow_uncertain)
   uncertainties <- data.frame(uncertainty = integer(0),
@@ -393,7 +391,7 @@ exec_as.mo <- function(x,
                               mo = character(0),
                               candidates = character(0),
                               stringsAsFactors = FALSE)
-
+  
   x_input <- x
   # already strip leading and trailing spaces
   x <- trimws(x)
@@ -405,7 +403,7 @@ exec_as.mo <- function(x,
          & !is.null(x)
          & !identical(x, "")
          & !identical(x, "xxx")]
-
+  
   # defined df to check for
   if (!is.null(reference_df)) {
     check_validity_mo_source(reference_df)
@@ -420,27 +418,27 @@ exec_as.mo <- function(x,
     } else {
       return(rep(NA_character_, length(x_input)))
     }
-
+    
   } else if (all(x %in% reference_df[, 1][[1]])) {
     # all in reference df
     colnames(reference_df)[1] <- "x"
     suppressWarnings(
       x <- MO_lookup[match(reference_df[match(x, reference_df$x), "mo", drop = TRUE], MO_lookup$mo), property, drop = TRUE]
     )
-
+    
   } else if (all(x %in% reference_data_to_use$mo)) {
     x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
-
+    
   } else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
     # we need special treatment for very prevalent full names, they are likely!
     # e.g. as.mo("Staphylococcus aureus")
     x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE]
-
+    
   } else if (all(x %in% reference_data_to_use$fullname)) {
     # we need special treatment for very prevalent full names, they are likely!
     # e.g. as.mo("Staphylococcus aureus")
     x <- MO_lookup[match(x, MO_lookup$fullname), property, drop = TRUE]
-
+    
   } else if (all(toupper(x) %in% microorganisms.codes$code)) {
     # commonly used MO codes
     x <- MO_lookup[match(microorganisms.codes[match(toupper(x),
@@ -450,9 +448,9 @@ exec_as.mo <- function(x,
                          MO_lookup$mo),
                    property,
                    drop = TRUE]
-
+    
   } else if (!all(x %in% microorganisms[, property])) {
-
+    
     strip_whitespace <- function(x, dyslexia_mode) {
       # all whitespaces (tab, new lines, etc.) should be one space
       # and spaces before and after should be left blank
@@ -465,7 +463,7 @@ exec_as.mo <- function(x,
       }
       trimmed
     }
-
+    
     x_backup_untouched <- x
     x <- strip_whitespace(x, dyslexia_mode)
     # translate 'unknown' names back to English
@@ -514,7 +512,7 @@ exec_as.mo <- function(x,
       
       # when ending in SPE instead of SPP and preceded by 2-4 characters
       x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE)
-
+      
       x_backup_without_spp <- x
       # translate to English for supported languages of mo_property
       x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, perl = TRUE)
@@ -1222,7 +1220,7 @@ exec_as.mo <- function(x,
                 cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (6) remove non-taxonomic prefix and suffix\n"))
               }
               x_without_nontax <- gsub("(^[a-zA-Z]+[./-]+[a-zA-Z]+[^a-zA-Z]* )([a-zA-Z.]+ [a-zA-Z]+.*)",
-                                              "\\2", a.x_backup, perl = TRUE)
+                                       "\\2", a.x_backup, perl = TRUE)
               x_without_nontax <- gsub("( *[(].*[)] *)[^a-zA-Z]*$", "", x_without_nontax, perl = TRUE)
               if (isTRUE(debug)) {
                 message("Running '", x_without_nontax, "'")
@@ -1572,15 +1570,15 @@ exec_as.mo <- function(x,
     # 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
     CoNS <- MO_lookup[which(MO_lookup$mo %in% MO_CONS), property, drop = TRUE]
     x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1)
-
+    
     CoPS <- MO_lookup[which(MO_lookup$mo %in% MO_COPS), property, drop = TRUE]
     x[x %in% CoPS] <- lookup(mo == "B_STPHY_COPS", uncertainty = -1)
-
+    
     if (Becker == "all") {
       x[x %in% lookup(fullname %like_case% "^Staphylococcus aureus", n = Inf)] <- lookup(mo == "B_STPHY_COPS", uncertainty = -1)
     }
   }
-
+  
   # Lancefield ----
   if (Lancefield == TRUE | Lancefield == "all") {
     # group A - S. pyogenes
@@ -1602,15 +1600,15 @@ exec_as.mo <- function(x,
     # group K - S. salivarius
     x[x %in% lookup(genus == "Streptococcus" & species == "salivarius", n = Inf)] <- lookup(fullname == "Streptococcus group K", uncertainty = -1)
   }
-
+  
   # Wrap up ----------------------------------------------------------------
-
+  
   # comply to x, which is also unique and without empty values
   x_input_unique_nonempty <- unique(x_input[!is.na(x_input)
                                             & !is.null(x_input)
                                             & !identical(x_input, "")
                                             & !identical(x_input, "xxx")])
-
+  
   x <- x[match(x_input, x_input_unique_nonempty)]
   if (property == "mo") {
     x <- set_clean_class(x, new_class = c("mo", "character"))
@@ -1618,11 +1616,11 @@ exec_as.mo <- function(x,
   
   # keep track of time
   end_time <- Sys.time()
-
+  
   if (length(mo_renamed()) > 0) {
     print(mo_renamed())
   }
-
+  
   if (initial_search == FALSE) {
     # we got here from uncertain_fn().
     if (NROW(uncertainties) == 0) {
@@ -1656,7 +1654,7 @@ exec_as.mo <- function(x,
   if (isTRUE(debug) && initial_search == TRUE) {
     cat("Finished function", time_track(), "\n")
   }
-
+  
   x
 }
 
@@ -2208,3 +2206,282 @@ strip_words <- function(text, n, side = "right") {
   })
   vapply(FUN.VALUE = character(1), out, paste, collapse = " ")
 }
+
+
+as.mo2 <- function(x,
+                   Becker = FALSE,
+                   Lancefield = FALSE,
+                   allow_uncertain = TRUE,
+                   reference_df = get_mo_source(),
+                   info = interactive(),
+                   property = "mo",
+                   initial_search = TRUE,
+                   dyslexia_mode = FALSE,
+                   debug = FALSE,
+                   ignore_pattern = getOption("AMR_ignore_pattern"),
+                   reference_data_to_use = MO_lookup,
+                   actual_uncertainty = 1,
+                   actual_input = NULL,
+                   language = get_AMR_locale()) {
+  meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
+  meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
+  meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
+  meet_criteria(allow_uncertain, allow_class = c("logical", "numeric", "integer"), has_length = 1)
+  meet_criteria(reference_df, allow_class = "data.frame", allow_NULL = TRUE)
+  meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
+  meet_criteria(initial_search, allow_class = "logical", has_length = 1)
+  meet_criteria(dyslexia_mode, allow_class = "logical", has_length = 1)
+  meet_criteria(debug, allow_class = "logical", has_length = 1)
+  meet_criteria(ignore_pattern, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(reference_data_to_use, allow_class = "data.frame")
+  meet_criteria(actual_uncertainty, allow_class = "numeric", has_length = 1)
+  meet_criteria(actual_input, allow_class = "character", allow_NULL = TRUE)
+  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
+  
+  check_dataset_integrity()
+  
+  if (isTRUE(debug) && initial_search == TRUE) {
+    time_start_tracking()
+  }
+  
+  lookup <- function(needle,
+                     column = property,
+                     haystack = reference_data_to_use,
+                     n = 1,
+                     debug_mode = debug,
+                     initial = initial_search,
+                     uncertainty = actual_uncertainty,
+                     input_actual = actual_input) {
+    
+    if (!is.null(input_actual)) {
+      input <- input_actual
+    } else {
+      input <- tryCatch(x_backup[i], error = function(e) "")
+    }
+    
+    # `column` can be NULL for all columns, or a selection
+    # returns a [character] (vector) - if `column` > length 1 then with columns as names
+    if (isTRUE(debug_mode)) {
+      cat(font_silver("Looking up: ", substitute(needle), collapse = ""), 
+          "\n           ", time_track())
+    }
+    if (length(column) == 1) {
+      res_df <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      if (NROW(res_df) > 1 & uncertainty != -1) {
+        # sort the findings on matching score
+        scores <- mo_matching_score(x = input,
+                                    n = res_df[, "fullname", drop = TRUE])
+        res_df <- res_df[order(scores, decreasing = TRUE), , drop = FALSE]
+      }
+      res <- as.character(res_df[, column, drop = TRUE])
+      if (length(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no match)\n"))
+        }
+        NA_character_
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res_df), " results)\n")))
+        }
+        if ((length(res) > n | uncertainty > 1) & uncertainty != -1) {
+          # save the other possible results as well, but not for forced certain results (then uncertainty == -1)
+          uncertainties <<- rbind(uncertainties,
+                                  format_uncertainty_as_df(uncertainty_level = uncertainty,
+                                                           input = input,
+                                                           result_mo = res_df[1, "mo", drop = TRUE],
+                                                           candidates = as.character(res_df[, "fullname", drop = TRUE])),
+                                  stringsAsFactors = FALSE)
+        }
+        res[seq_len(min(n, length(res)))]
+      }
+    } else {
+      if (is.null(column)) {
+        column <- names(haystack)
+      }
+      res <- haystack[which(eval(substitute(needle), envir = haystack, enclos = parent.frame())), , drop = FALSE]
+      res <- res[seq_len(min(n, nrow(res))), column, drop = TRUE]
+      if (NROW(res) == 0) {
+        if (isTRUE(debug_mode)) {
+          cat(font_red(" (no rows)\n"))
+        }
+        res <- rep(NA_character_, length(column))
+      } else {
+        if (isTRUE(debug_mode)) {
+          cat(font_green(paste0(" MATCH (", NROW(res), " rows)\n")))
+        }
+      }
+      res <- as.character(res)
+      names(res) <- column
+      res
+    }
+  }
+  
+  # start off with replaced language-specific non-ASCII characters with ASCII characters
+  x <- parse_and_convert(x)
+  # replace mo codes used in older package versions
+  x <- replace_old_mo_codes(x, property)
+  # ignore cases that match the ignore pattern
+  x <- replace_ignore_pattern(x, ignore_pattern)
+  
+  # WHONET: xxx = no growth
+  x[tolower(as.character(paste0(x, ""))) %in% c("", "xxx", "na", "nan")] <- NA_character_
+  # Laboratory systems: remove (translated) entries like "no growth", etc.
+  x[trimws2(x) %like% translate_into_language("no .*growth", language = language)] <- NA_character_
+  x[trimws2(x) %like% paste0("^(", translate_into_language("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
+  
+  if (initial_search == TRUE) {
+    # keep track of time - give some hints to improve speed if it takes a long time
+    start_time <- Sys.time()
+    
+    pkg_env$mo_failures <- NULL
+    pkg_env$mo_uncertainties <- NULL
+    pkg_env$mo_renamed <- NULL
+  }
+  pkg_env$mo_renamed_last_run <- NULL
+  
+  failures <- character(0)
+  uncertainty_level <- translate_allow_uncertain(allow_uncertain)
+  uncertainties <- data.frame(uncertainty = integer(0),
+                              input = character(0),
+                              fullname = character(0),
+                              renamed_to = character(0),
+                              mo = character(0),
+                              candidates = character(0),
+                              stringsAsFactors = FALSE)
+  
+  x_input <- x
+  # already strip leading and trailing spaces
+  x <- trimws(x)
+  # only check the uniques, which is way faster
+  x <- unique(x)
+  # remove empty values (to later fill them in again with NAs)
+  # ("xxx" is WHONET code for 'no growth')
+  x <- x[!is.na(x)
+         & !is.null(x)
+         & !identical(x, "")
+         & !identical(x, "xxx")]
+  
+  # defined df to check for
+  if (!is.null(reference_df)) {
+    check_validity_mo_source(reference_df)
+    reference_df <- repair_reference_df(reference_df)
+  }
+  
+  # all empty
+  if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
+    if (property == "mo") {
+      return(set_clean_class(rep(NA_character_, length(x_input)),
+                             new_class = c("mo", "character")))
+    } else {
+      return(rep(NA_character_, length(x_input)))
+    }
+    
+  } else if (all(x %in% reference_df[, 1][[1]])) {
+    # all in reference df
+    colnames(reference_df)[1] <- "x"
+    suppressWarnings(
+      x <- MO_lookup[match(reference_df[match(x, reference_df$x), "mo", drop = TRUE], MO_lookup$mo), property, drop = TRUE]
+    )
+    
+  } else if (all(x %in% reference_data_to_use$mo)) {
+    x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
+    
+  } else if (all(tolower(x) %in% reference_data_to_use$fullname_lower)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(tolower(x), MO_lookup$fullname_lower), property, drop = TRUE]
+    
+  } else if (all(x %in% reference_data_to_use$fullname)) {
+    # we need special treatment for very prevalent full names, they are likely!
+    # e.g. as.mo("Staphylococcus aureus")
+    x <- MO_lookup[match(x, MO_lookup$fullname), property, drop = TRUE]
+    
+  } else if (all(toupper(x) %in% microorganisms.codes$code)) {
+    # commonly used MO codes
+    x <- MO_lookup[match(microorganisms.codes[match(toupper(x),
+                                                    microorganisms.codes$code),
+                                              "mo",
+                                              drop = TRUE],
+                         MO_lookup$mo),
+                   property,
+                   drop = TRUE]
+    
+  } else if (!all(x %in% microorganisms[, property])) {
+    
+    strip_whitespace <- function(x, dyslexia_mode) {
+      # all whitespaces (tab, new lines, etc.) should be one space
+      # and spaces before and after should be left blank
+      trimmed <- trimws2(x)
+      # also, make sure the trailing and leading characters are a-z or 0-9
+      # in case of non-regex
+      if (dyslexia_mode == FALSE) {
+        trimmed <- gsub("^[^a-zA-Z0-9)(]+", "", trimmed, perl = TRUE)
+        trimmed <- gsub("[^a-zA-Z0-9)(]+$", "", trimmed, perl = TRUE)
+      }
+      trimmed
+    }
+    
+    x_backup_untouched <- x
+    x <- strip_whitespace(x, dyslexia_mode)
+    # translate 'unknown' names back to English
+    if (any(tolower(x) %like_case% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
+      trns <- subset(TRANSLATIONS, pattern %like% "unknown")
+      langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
+      for (l in langs) {
+        for (i in seq_len(nrow(trns))) {
+          if (!is.na(trns[i, l, drop = TRUE])) {
+            x <- gsub(pattern = trns[i, l, drop = TRUE],
+                      replacement = trns$pattern[i],
+                      x = x,
+                      ignore.case = TRUE,
+                      perl = TRUE)
+          }
+        }
+      }
+    }
+    
+    # remove spp and species
+    x <- gsub("(^| )[ .]*(spp|ssp|ss|sp|subsp|subspecies|biovar|biotype|serovar|species)[ .]*( |$)", "", x, ignore.case = TRUE, perl = TRUE)
+    x <- strip_whitespace(x, dyslexia_mode)
+    
+    x_backup <- x
+    
+    # from here on case-insensitive
+    x <- tolower(x)
+    
+    x_backup[x %like_case% "^(fungus|fungi)$"] <- "(unknown fungus)" # will otherwise become the kingdom
+    x_backup[x_backup_untouched == "Fungi"] <- "Fungi" # is literally the kingdom
+    
+    # Fill in fullnames and MO codes directly
+    known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
+    x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
+    known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
+    x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
+    known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
+    x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
+                                                                     microorganisms.codes$code), "mo", drop = TRUE],
+                                          MO_lookup$mo), property, drop = TRUE]
+    already_known <- known_names | known_codes_mo | known_codes_lis
+    
+    # now only continue where the right taxonomic output is not already known
+    if (any(!already_known)) {
+      x_unknown <- x[!already_known]
+      x_unknown <- gsub(" ?[(].*[)] ?", "", x_unknown, perl = TRUE)
+      x_unknown <- gsub("[^a-z ]", " ", x_unknown, perl = TRUE)
+      x_unknown <- gsub(" +", " ", x_unknown, perl = TRUE)
+      print(x_unknown)
+      x_search <- gsub("([a-z])[a-z]*( ([a-z])[a-z]*)?( ([a-z])[a-z]*)?", "^\\1.* \\3.* \\5.*", x_unknown, perl = TRUE)
+      x_search <- gsub("( [.][*])+$", "", x_search, perl = TRUE)
+      print(x_search)
+      for (i in seq_len(length(x_unknown))) {
+        # search first, second and third part
+        mos_to_search <- MO_lookup[which(MO_lookup$fullname_lower %like_case% x_search[i]), "fullname", drop = TRUE]
+        score <- mo_matching_score(x_unknown[i], mos_to_search)
+        out <- mos_to_search[order(score, decreasing = TRUE)][1:25] # keep first 25
+        print(score[order(score, decreasing = TRUE)][1])
+        x[!already_known][i] <- MO_lookup$mo[match(out[1], MO_lookup$fullname)]
+      }
+    }
+  }
+  x
+}

R/mo_matching_score.R

@@ -26,7 +26,6 @@
 #' Calculate the Matching Score for Microorganisms
 #' 
 #' This algorithm is used by [as.mo()] and all the [`mo_*`][mo_property()] functions to determine the most probable match of taxonomic records based on user input. 
-#' @inheritSection lifecycle Stable Lifecycle
 #' @author Dr Matthijs Berends
 #' @param x Any user input value(s)
 #' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
@@ -53,7 +52,6 @@
 #' Since `AMR` version 1.8.1, common microorganism abbreviations are ignored in determining the matching score. These abbreviations are currently: `r vector_and(pkg_env$mo_field_abbreviations, quotes = FALSE)`.
 #' @export
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples 
 #' as.mo("E. coli")
 #' mo_uncertainties()

R/mo_property.R

@@ -26,7 +26,6 @@
 #' Get Properties of a Microorganism
 #'
 #' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. See *Examples*.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
 #' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
 #' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
@@ -67,93 +66,91 @@
 #' @export
 #' @seealso Data set [microorganisms]
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # taxonomic tree -----------------------------------------------------------
-#' mo_kingdom("E. coli")         # "Bacteria"
+#' mo_kingdom("Klebsiella pneumoniae")
-#' mo_phylum("E. coli")          # "Proteobacteria"
+#' mo_phylum("Klebsiella pneumoniae")
-#' mo_class("E. coli")           # "Gammaproteobacteria"
+#' mo_class("Klebsiella pneumoniae")
-#' mo_order("E. coli")           # "Enterobacterales"
+#' mo_order("Klebsiella pneumoniae")
-#' mo_family("E. coli")          # "Enterobacteriaceae"
+#' mo_family("Klebsiella pneumoniae")
-#' mo_genus("E. coli")           # "Escherichia"
+#' mo_genus("Klebsiella pneumoniae")
-#' mo_species("E. coli")         # "coli"
+#' mo_species("Klebsiella pneumoniae")
-#' mo_subspecies("E. coli")      # ""
+#' mo_subspecies("Klebsiella pneumoniae")
 #'
 #' # colloquial properties ----------------------------------------------------
-#' mo_name("E. coli")            # "Escherichia coli"
+#' mo_name("Klebsiella pneumoniae")
-#' mo_fullname("E. coli")        # "Escherichia coli" - same as mo_name()
+#' mo_fullname("Klebsiella pneumoniae")
-#' mo_shortname("E. coli")       # "E. coli"
+#' mo_shortname("Klebsiella pneumoniae")
 #'
 #' # other properties ---------------------------------------------------------
-#' mo_gramstain("E. coli")       # "Gram-negative"
+#' mo_gramstain("Klebsiella pneumoniae")
-#' mo_snomed("E. coli")          # 112283007, 116395006, ... (SNOMED codes)
+#' mo_snomed("Klebsiella pneumoniae")
-#' mo_type("E. coli")            # "Bacteria" (equal to kingdom, but may be translated)
+#' mo_type("Klebsiella pneumoniae")
-#' mo_rank("E. coli")            # "species"
+#' mo_rank("Klebsiella pneumoniae")
-#' mo_url("E. coli")             # get the direct url to the online database entry
+#' mo_url("Klebsiella pneumoniae")
-#' mo_synonyms("E. coli")        # get previously accepted taxonomic names
+#' mo_synonyms("Klebsiella pneumoniae")
 #'
 #' # scientific reference -----------------------------------------------------
-#' mo_ref("E. coli")             # "Castellani et al., 1919"
+#' mo_ref("Klebsiella pneumoniae")
-#' mo_authors("E. coli")         # "Castellani et al."
+#' mo_authors("Klebsiella pneumoniae")
-#' mo_year("E. coli")            # 1919
+#' mo_year("Klebsiella pneumoniae")
-#' mo_lpsn("E. coli")            # 776057 (LPSN record ID)
+#' mo_lpsn("Klebsiella pneumoniae")
 #'
 #' # abbreviations known in the field -----------------------------------------
-#' mo_genus("MRSA")              # "Staphylococcus"
+#' mo_genus("MRSA")
-#' mo_species("MRSA")            # "aureus"
+#' mo_species("MRSA")
-#' mo_shortname("VISA")          # "S. aureus"
+#' mo_shortname("VISA")
-#' mo_gramstain("VISA")          # "Gram-positive"
+#' mo_gramstain("VISA")
 #'
-#' mo_genus("EHEC")              # "Escherichia"
+#' mo_genus("EHEC")
-#' mo_species("EHEC")            # "coli"
+#' mo_species("EHEC")
 #'
 #' # known subspecies ---------------------------------------------------------
-#' mo_name("doylei")             # "Campylobacter jejuni doylei"
+#' mo_name("doylei")
-#' mo_genus("doylei")            # "Campylobacter"
+#' mo_genus("doylei")
-#' mo_species("doylei")          # "jejuni"
+#' mo_species("doylei")
-#' mo_subspecies("doylei")       # "doylei"
+#' mo_subspecies("doylei")
 #'
-#' mo_fullname("K. pneu rh")     # "Klebsiella pneumoniae rhinoscleromatis"
+#' mo_fullname("K. pneu rh")
-#' mo_shortname("K. pneu rh")    # "K. pneumoniae"
+#' mo_shortname("K. pneu rh")
 #'
 #' \donttest{
 #' # Becker classification, see ?as.mo ----------------------------------------
-#' mo_fullname("S. epi")                     # "Staphylococcus epidermidis"
+#' mo_fullname("S. epi")
-#' mo_fullname("S. epi", Becker = TRUE)      # "Coagulase-negative Staphylococcus (CoNS)"
+#' mo_fullname("S. epi", Becker = TRUE)
-#' mo_shortname("S. epi")                    # "S. epidermidis"
+#' mo_shortname("S. epi")
-#' mo_shortname("S. epi", Becker = TRUE)     # "CoNS"
+#' mo_shortname("S. epi", Becker = TRUE)
 #'
 #' # Lancefield classification, see ?as.mo ------------------------------------
-#' mo_fullname("S. pyo")                     # "Streptococcus pyogenes"
+#' mo_fullname("S. pyo")
-#' mo_fullname("S. pyo", Lancefield = TRUE)  # "Streptococcus group A"
+#' mo_fullname("S. pyo", Lancefield = TRUE)
-#' mo_shortname("S. pyo")                    # "S. pyogenes"
+#' mo_shortname("S. pyo")
-#' mo_shortname("S. pyo", Lancefield = TRUE) # "GAS" (='Group A Streptococci')
+#' mo_shortname("S. pyo", Lancefield = TRUE)
 #'
 #'
 #' # language support  --------------------------------------------------------
-#' mo_gramstain("E. coli", language = "de")  # "Gramnegativ"
+#' mo_gramstain("Klebsiella pneumoniae", language = "de")
-#' mo_gramstain("E. coli", language = "nl")  # "Gram-negatief"
+#' mo_gramstain("Klebsiella pneumoniae", language = "nl")
-#' mo_gramstain("E. coli", language = "es")  # "Gram negativo"
+#' mo_gramstain("Klebsiella pneumoniae", language = "es")
 #'
 #' # mo_type is equal to mo_kingdom, but mo_kingdom will remain official
-#' mo_kingdom("E. coli")                     # "Bacteria" on a German system
+#' mo_kingdom("Klebsiella pneumoniae")
-#' mo_type("E. coli")                        # "Bakterien" on a German system
+#' mo_type("Klebsiella pneumoniae")
-#' mo_type("E. coli")                        # "Bacteria" on an English system
+#' mo_type("Klebsiella pneumoniae")
 #'
 #' mo_fullname("S. pyogenes",
 #'             Lancefield = TRUE,
-#'             language = "de")              # "Streptococcus Gruppe A"
+#'             language = "de")
 #' mo_fullname("S. pyogenes",
 #'             Lancefield = TRUE,
-#'             language = "nl")              # "Streptococcus groep A"
+#'             language = "nl")
 #'
 #'
 #' # other --------------------------------------------------------------------
 #' 
-#' mo_is_yeast(c("Candida", "E. coli"))      # TRUE, FALSE
+#' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
 #' 
-#' # gram stains and intrinsic resistance can also be used as a filter in dplyr verbs
+#' # gram stains and intrinsic resistance can be used as a filter in dplyr verbs
-#' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
 #'     filter(mo_is_gram_positive())
@@ -164,11 +161,11 @@
 #' 
 #' 
 #' # get a list with the complete taxonomy (from kingdom to subspecies)
-#' mo_taxonomy("E. coli")
+#' mo_taxonomy("Klebsiella pneumoniae")
+#' 
 #' # get a list with the taxonomy, the authors, Gram-stain,
-#' #   SNOMED codes, and URL to the online database
+#' # SNOMED codes, and URL to the online database
-#' mo_info("E. coli")
+#' mo_info("Klebsiella pneumoniae")
-#' }
 #' }
 mo_name <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
@@ -178,10 +175,10 @@ mo_name <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...),
+  translate_into_language(mo_validate(x = x, property = "fullname", language = language, ...),
-                language = language,
+                          language = language,
-                only_unknown = FALSE,
+                          only_unknown = FALSE,
-                only_affect_mo_names = TRUE)
+                          only_affect_mo_names = TRUE)
 }
 
 #' @rdname mo_property
@@ -223,7 +220,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), ...) {
   
   shortnames[is.na(x.mo)] <- NA_character_
   load_mo_failures_uncertainties_renamed(metadata)
-  translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
+  translate_into_language(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
 }
 
 
@@ -238,7 +235,7 @@ mo_subspecies <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -251,7 +248,7 @@ mo_species <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -264,7 +261,7 @@ mo_genus <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -277,7 +274,7 @@ mo_family <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -290,7 +287,7 @@ mo_order <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -303,7 +300,7 @@ mo_class <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -316,7 +313,7 @@ mo_phylum <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -329,7 +326,7 @@ mo_kingdom <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
 }
 
 #' @rdname mo_property
@@ -349,7 +346,7 @@ mo_type <- function(x, language = get_AMR_locale(), ...) {
   x.mo <- as.mo(x, language = language, ...)
   out <- mo_kingdom(x.mo, language = NULL)
   out[which(mo_is_yeast(x.mo))] <- "Yeasts"
-  translate_AMR(out, language = language, only_unknown = FALSE)
+  translate_into_language(out, language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
@@ -380,7 +377,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), ...) {
     | x.mo == "B_GRAMP"] <- "Gram-positive"
   
   load_mo_failures_uncertainties_renamed(metadata)
-  translate_AMR(x, language = language, only_unknown = FALSE)
+  translate_into_language(x, language = language, only_unknown = FALSE)
 }
 
 #' @rdname mo_property
@@ -435,9 +432,7 @@ mo_is_yeast <- function(x, language = get_AMR_locale(), ...) {
   metadata <- get_mo_failures_uncertainties_renamed()
   
   x.kingdom <- mo_kingdom(x.mo, language = NULL)
-  x.phylum <- mo_phylum(x.mo, language = NULL)
   x.class <- mo_class(x.mo, language = NULL)
-  x.order <- mo_order(x.mo, language = NULL)
   
   load_mo_failures_uncertainties_renamed(metadata)
   
@@ -705,7 +700,7 @@ mo_property <- function(x, property = "fullname", language = get_AMR_locale(), .
   meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
+  translate_into_language(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
 }
 
 mo_validate <- function(x, property, language, ...) {
@@ -724,7 +719,7 @@ mo_validate <- function(x, property, language, ...) {
   if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
     # special case for mo_* functions where class is already <mo>
     x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
-
+    
   } else {
     # try to catch an error when inputting an invalid argument
     # so the 'call.' can be set to FALSE

R/mo_source.R

@@ -28,17 +28,16 @@
 #' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all [`mo_*`][mo_property()] functions (such as [mo_genus()] and [mo_gramstain()]).
 #'
 #' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
-#' @inheritSection lifecycle Stable Lifecycle
+#' @param path location of your reference file, this can be any text file (comma-, tab- or pipe-separated) or an Excel file (see *Details*). Can also be `""`, `NULL` or `FALSE` to delete the reference file.
-#' @param path location of your reference file, see *Details*. Can be `""`, `NULL` or `FALSE` to delete the reference file.
 #' @param destination destination of the compressed data file, default to the user's home directory.
 #' @rdname mo_source
 #' @name mo_source
 #' @aliases set_mo_source get_mo_source
 #' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
 #'
-#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
+#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
 #' 
-#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an attribute to the compressed data file. 
+#' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an [attribute][base::attributes()] to the compressed data file. 
 #' 
 #' The function [get_mo_source()] will return the data set by reading `"mo_source.rds"` with [readRDS()]. If the original file has changed (by checking the location and timestamp of the original file), it will call [set_mo_source()] to update the data file automatically if used in an interactive session.
 #'
@@ -46,15 +45,15 @@
 #' 
 #' @section How to Setup:
 #' 
-#' Imagine this data on a sheet of an Excel file (mo codes were looked up in the [microorganisms] data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
+#' Imagine this data on a sheet of an Excel file. The first column contains the organisation specific codes, the second column contains valid taxonomic names:
 #' 
 #' ```
-#'   |         A          |       B      |
+#'   |         A          |            B          |
-#' --|--------------------|--------------|
+#' --|--------------------|-----------------------|
-#' 1 | Organisation XYZ   | mo           |
+#' 1 | Organisation XYZ   | mo                    |
-#' 2 | lab_mo_ecoli       | B_ESCHR_COLI |
+#' 2 | lab_mo_ecoli       | Escherichia coli      |
-#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
+#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
-#' 4 |                    |              |
+#' 4 |                    |                       |
 #' ```
 #'
 #' We save it as `"home/me/ourcodes.xlsx"`. Now we have to set it as a source:
@@ -89,13 +88,13 @@
 #' If we edit the Excel file by, let's say, adding row 4 like this:
 #' 
 #' ```
-#'   |         A          |       B      |
+#'   |         A          |            B          |
-#' --|--------------------|--------------|
+#' --|--------------------|-----------------------|
-#' 1 | Organisation XYZ   | mo           |
+#' 1 | Organisation XYZ   | mo                    |
-#' 2 | lab_mo_ecoli       | B_ESCHR_COLI |
+#' 2 | lab_mo_ecoli       | Escherichia coli      |
-#' 3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
+#' 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae |
-#' 4 | lab_Staph_aureus   | B_STPHY_AURS |
+#' 4 | lab_Staph_aureus   | Staphylococcus aureus |
-#' 5 |                    |              |
+#' 5 |                    |                       |
 #' ```
 #'
 #' ...any new usage of an MO function in this package will update your data file:
@@ -121,7 +120,6 @@
 #' 
 #' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
   meet_criteria(path, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(destination, allow_class = "character", has_length = 1)
@@ -144,6 +142,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   
   stop_ifnot(file.exists(path), "file not found: ", path)
   
+  df <- NULL
   if (path %like% "[.]rds$") {
     df <- readRDS(path)
     
@@ -153,28 +152,34 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
     df <- readxl::read_excel(path)
     
   } else if (path %like% "[.]tsv$") {
-    df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+    df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
+    
+  } else if (path %like% "[.]csv$") {
+    df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE)
     
   } else {
     # try comma first
     try(
-      df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
+      df <- utils::read.table(file = path, header = TRUE, sep = ",", stringsAsFactors = FALSE),
       silent = TRUE)
     if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
       # try tab
       try(
-        df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
+        df <- utils::read.table(file = path, header = TRUE, sep = "\t", stringsAsFactors = FALSE),
         silent = TRUE)
     }
     if (!check_validity_mo_source(df, stop_on_error = FALSE)) {
       # try pipe
       try(
-        df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
+        df <- utils::read.table(file = path, header = TRUE, sep = "|", stringsAsFactors = FALSE),
         silent = TRUE)
     }
   }
   
   # check integrity
+  if (is.null(df)) {
+    stop_("the path '", path, "' could not be imported as a dataset.")
+  }
   check_validity_mo_source(df)
   
   df <- subset(df, !is.na(mo))
@@ -187,7 +192,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
   }
   
   df <- as.data.frame(df, stringAsFactors = FALSE)
-  df[, "mo"] <- set_clean_class(df[, "mo", drop = TRUE], c("mo", "character"))
+  df[, "mo"] <- as.mo(df[, "mo", drop = TRUE])
   
   # success
   if (file.exists(mo_source_destination)) {
@@ -275,9 +280,9 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
       return(FALSE)
     }
   }
-  if (!all(x$mo %in% c("", microorganisms$mo), na.rm = TRUE)) {
+  if (!all(x$mo %in% c("", microorganisms$mo, microorganisms$fullname), na.rm = TRUE)) {
     if (stop_on_error == TRUE) {
-      invalid <- x[which(!x$mo %in% c("", microorganisms$mo)), , drop = FALSE]
+      invalid <- x[which(!x$mo %in% c("", microorganisms$mo, microorganisms$fullname)), , drop = FALSE]
       if (nrow(invalid) > 1) {
         plural <- "s"
       } else {

R/pca.R

@@ -26,7 +26,6 @@
 #' Principal Component Analysis (for AMR)
 #' 
 #' Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a [data.frame] containing [numeric] columns
 #' @param ... columns of `x` to be selected for PCA, can be unquoted since it supports quasiquotation.
 #' @inheritParams stats::prcomp
@@ -36,7 +35,6 @@
 #' @return An object of classes [pca] and [prcomp]
 #' @importFrom stats prcomp
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples 
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
@@ -47,6 +45,7 @@
 #'   resistance_data <- example_isolates %>% 
 #'     group_by(order = mo_order(mo),       # group on anything, like order
 #'              genus = mo_genus(mo)) %>%   #   and genus as we do here;
+#'     filter(n() >= 30) %>%                # filter on only 30 results per group
 #'     summarise_if(is.rsi, resistance)     # then get resistance of all drugs
 #'     
 #'   # now conduct PCA for certain antimicrobial agents
@@ -55,8 +54,17 @@
 #'     
 #'   pca_result
 #'   summary(pca_result)
+#'   
+#'   # old base R plotting method:
 #'   biplot(pca_result)
-#'   ggplot_pca(pca_result) # a new and convenient plot function
+#'   # new ggplot2 plotting method using this package:
+#'   ggplot_pca(pca_result)
+#'   
+#'   if (require("ggplot2")) {
+#'     ggplot_pca(pca_result) +
+#'       scale_colour_viridis_d() +
+#'       labs(title = "Title here")
+#'   }
 #' }
 #' }
 pca <- function(x,

R/plot.R

@@ -26,8 +26,7 @@
 #' Plotting for Classes `rsi`, `mic` and `disk`
 #' 
 #' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
-#' @inheritSection lifecycle Stable Lifecycle
+
-#' @inheritSection AMR Read more on Our Website!
 #' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
 #' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
 #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
@@ -61,6 +60,7 @@
 #' # when providing the microorganism and antibiotic, colours will show interpretations:
 #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
 #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
+#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
 #' 
 #' \donttest{
 #' if (require("ggplot2")) {
@@ -79,7 +79,7 @@ plot.mic <- function(x,
                      mo = NULL,
                      ab = NULL,
                      guideline = "EUCAST",
-                     main = paste("MIC values of", deparse(substitute(x))),
+                     main = deparse(substitute(x)),
                      ylab = "Frequency",
                      xlab = "Minimum Inhibitory Concentration (mg/L)",
                      colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -98,10 +98,10 @@ plot.mic <- function(x,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if (length(colours_RSI) == 1) {
@@ -149,7 +149,7 @@ plot.mic <- function(x,
     
     legend("top",
            x.intersp = 0.5,
-           legend = translate_AMR(legend_txt, language = language),
+           legend = translate_into_language(legend_txt, language = language),
            fill = legend_col,
            horiz = TRUE,
            cex = 0.75,
@@ -166,7 +166,7 @@ barplot.mic <- function(height,
                         mo = NULL,
                         ab = NULL,
                         guideline = "EUCAST",
-                        main = paste("MIC values of", deparse(substitute(height))),
+                        main = deparse(substitute(height)),
                         ylab = "Frequency",
                         xlab = "Minimum Inhibitory Concentration (mg/L)",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -185,10 +185,10 @@ barplot.mic <- function(height,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   main <- gsub(" +", " ", paste0(main, collapse = " "))
@@ -211,7 +211,7 @@ autoplot.mic <- function(object,
                          mo = NULL,
                          ab = NULL,
                          guideline = "EUCAST",
-                         title = paste("MIC values of", deparse(substitute(object))),
+                         title = deparse(substitute(object)),
                          ylab = "Frequency",
                          xlab = "Minimum Inhibitory Concentration (mg/L)",
                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -231,10 +231,10 @@ autoplot.mic <- function(object,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if ("main" %in% names(list(...))) {
@@ -259,8 +259,8 @@ autoplot.mic <- function(object,
   df$cols[df$cols == colours_RSI[1]] <- "Resistant"
   df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
   df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
-  df$cols <- factor(translate_AMR(df$cols, language = language),
+  df$cols <- factor(translate_into_language(df$cols, language = language),
-                    levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
+                    levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
                                            language = language),
                     ordered = TRUE)
   p <- ggplot2::ggplot(df)
@@ -270,7 +270,7 @@ autoplot.mic <- function(object,
               "Susceptible" = colours_RSI[2],
               "Susceptible, incr. exp." = colours_RSI[3],
               "Intermediate" = colours_RSI[3])
-    names(vals) <- translate_AMR(names(vals), language = language)
+    names(vals) <- translate_into_language(names(vals), language = language)
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) + 
       # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@@ -299,7 +299,7 @@ fortify.mic <- function(object, ...) {
 #' @importFrom graphics barplot axis mtext legend
 #' @rdname plot
 plot.disk <- function(x,
-                      main = paste("Disk zones of", deparse(substitute(x))),
+                      main = deparse(substitute(x)),
                       ylab = "Frequency",
                       xlab = "Disk diffusion diameter (mm)",
                       mo = NULL,
@@ -321,10 +321,10 @@ plot.disk <- function(x,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if (length(colours_RSI) == 1) {
@@ -372,7 +372,7 @@ plot.disk <- function(x,
     }
     legend("top", 
            x.intersp = 0.5,
-           legend = translate_AMR(legend_txt, language = language),
+           legend = translate_into_language(legend_txt, language = language),
            fill = legend_col,
            horiz = TRUE,
            cex = 0.75,
@@ -386,7 +386,7 @@ plot.disk <- function(x,
 #' @export
 #' @noRd
 barplot.disk <- function(height,
-                         main = paste("Disk zones of", deparse(substitute(height))),
+                         main = deparse(substitute(height)),
                          ylab = "Frequency",
                          xlab = "Disk diffusion diameter (mm)",
                          mo = NULL,
@@ -408,10 +408,10 @@ barplot.disk <- function(height,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   main <- gsub(" +", " ", paste0(main, collapse = " "))
@@ -433,7 +433,7 @@ barplot.disk <- function(height,
 autoplot.disk <- function(object,
                           mo = NULL,
                           ab = NULL,
-                          title = paste("Disk zones of", deparse(substitute(object))),
+                          title = deparse(substitute(object)),
                           ylab = "Frequency",
                           xlab = "Disk diffusion diameter (mm)",
                           guideline = "EUCAST",
@@ -454,10 +454,10 @@ autoplot.disk <- function(object,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if ("main" %in% names(list(...))) {
@@ -483,8 +483,8 @@ autoplot.disk <- function(object,
   df$cols[df$cols == colours_RSI[1]] <- "Resistant"
   df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
   df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
-  df$cols <- factor(translate_AMR(df$cols, language = language),
+  df$cols <- factor(translate_into_language(df$cols, language = language),
-                    levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
+                    levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
                                            language = language),
                     ordered = TRUE)
   p <- ggplot2::ggplot(df)
@@ -494,7 +494,7 @@ autoplot.disk <- function(object,
               "Susceptible" = colours_RSI[2],
               "Susceptible, incr. exp." = colours_RSI[3],
               "Intermediate" = colours_RSI[3])
-    names(vals) <- translate_AMR(names(vals), language = language)
+    names(vals) <- translate_into_language(names(vals), language = language)
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) + 
       # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@@ -525,12 +525,21 @@ fortify.disk <- function(object, ...) {
 plot.rsi <- function(x,
                      ylab = "Percentage",
                      xlab = "Antimicrobial Interpretation",
-                     main = paste("Resistance Overview of", deparse(substitute(x))),
+                     main = deparse(substitute(x)),
+                     language = get_AMR_locale(),
                      ...) {
   meet_criteria(ylab, allow_class = "character", has_length = 1)
   meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   
+  # translate if not specifically set
+  if (missing(ylab)) {
+    ylab <- translate_into_language(ylab, language = language)
+  }
+  if (missing(xlab)) {
+    xlab <- translate_into_language(xlab, language = language)
+  }
+  
   data <- as.data.frame(table(x), stringsAsFactors = FALSE)
   colnames(data) <- c("x", "n")
   data$s <- round((data$n / sum(data$n)) * 100, 1)
@@ -576,7 +585,7 @@ plot.rsi <- function(x,
 #' @export
 #' @noRd
 barplot.rsi <- function(height,
-                        main = paste("Resistance Overview of", deparse(substitute(height))),
+                        main = deparse(substitute(height)),
                         xlab = "Antimicrobial Interpretation",
                         ylab = "Frequency",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -592,10 +601,10 @@ barplot.rsi <- function(height,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if (length(colours_RSI) == 1) {
@@ -620,7 +629,7 @@ barplot.rsi <- function(height,
 #' @rdname plot
 # will be exported using s3_register() in R/zzz.R
 autoplot.rsi <- function(object,
-                         title = paste("Resistance Overview of", deparse(substitute(object))),
+                         title = deparse(substitute(object)),
                          xlab = "Antimicrobial Interpretation",
                          ylab = "Frequency",
                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@@ -634,10 +643,10 @@ autoplot.rsi <- function(object,
   
   # translate if not specifically set
   if (missing(ylab)) {
-    ylab <- translate_AMR(ylab, language = language)
+    ylab <- translate_into_language(ylab, language = language)
   }
   if (missing(xlab)) {
-    xlab <- translate_AMR(xlab, language = language)
+    xlab <- translate_into_language(xlab, language = language)
   }
   
   if ("main" %in% names(list(...))) {
@@ -738,7 +747,11 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
                ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
       guideline_txt <- ""
     } else {
-      guideline_txt <- paste0("(", guideline, ")")
+      guideline_txt <- guideline
+      if (isTRUE(list(...)$uti)) {
+        guideline_txt <- paste("UTIs,", guideline_txt)
+      }
+      guideline_txt <- paste0("(", guideline_txt, ")")
     }
     sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
   } else {

R/proportion.R

@@ -28,7 +28,6 @@
 #' @description These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in `summarise()` from the `dplyr` package and also support grouped variables, see *Examples*.
 #'
 #' [resistance()] should be used to calculate resistance, [susceptibility()] should be used to calculate susceptibility.\cr
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See *Examples*.
 #' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
 #' @param as_percent a [logical] to indicate whether the output must be returned as a hundred fold with % sign (a character). A value of `0.123456` will then be returned as `"12.3%"`.
@@ -88,11 +87,11 @@
 #' @aliases portion
 #' @name proportion
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # example_isolates is a data set available in the AMR package.
-#' ?example_isolates
+#' # run ?example_isolates for more info.
 #' 
+#' # base R ------------------------------------------------------------
 #' resistance(example_isolates$AMX)     # determines %R
 #' susceptibility(example_isolates$AMX) # determines %S+I
 #'
@@ -103,6 +102,7 @@
 #' proportion_IR(example_isolates$AMX)
 #' proportion_R(example_isolates$AMX)
 #'
+#' # dplyr -------------------------------------------------------------
 #' \donttest{
 #' if (require("dplyr")) {
 #'   example_isolates %>%
@@ -157,10 +157,11 @@
 #'     proportion_df(translate = FALSE)
 #'  
 #'   # It also supports grouping variables
+#'   # (use rsi_df to also include the count)
 #'   example_isolates %>%
 #'     select(hospital_id, AMX, CIP) %>%
 #'     group_by(hospital_id) %>%
-#'     proportion_df(translate = FALSE)
+#'     rsi_df(translate = FALSE)
 #' }
 #' }
 resistance <- function(...,

R/random.R

@@ -25,8 +25,7 @@
 
 #' Random MIC Values/Disk Zones/RSI Generation
 #'
-#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
+#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible. 
-#' @inheritSection lifecycle Stable Lifecycle 
 #' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
 #' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()]
 #' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()]
@@ -34,26 +33,25 @@
 #' @param ... ignored, only in place to allow future extensions
 #' @details The base \R function [sample()] is used for generating values.
 #' 
-#' Generated values are based on the latest EUCAST guideline implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
+#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
 #' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
 #' @name random
 #' @rdname random
 #' @export
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
-#' random_mic(100)
+#' random_mic(25)
-#' random_disk(100)
+#' random_disk(25)
-#' random_rsi(100)
+#' random_rsi(25)
 #' 
 #' \donttest{
 #' # make the random generation more realistic by setting a bug and/or drug:
-#' random_mic(100, "Klebsiella pneumoniae")                 # range 0.0625-64
+#' random_mic(25, "Klebsiella pneumoniae")                 # range 0.0625-64
-#' random_mic(100, "Klebsiella pneumoniae", "meropenem")    # range 0.0625-16
+#' random_mic(25, "Klebsiella pneumoniae", "meropenem")    # range 0.0625-16
-#' random_mic(100, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
+#' random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
 #' 
-#' random_disk(100, "Klebsiella pneumoniae")                  # range 8-50
+#' random_disk(25, "Klebsiella pneumoniae")                  # range 8-50
-#' random_disk(100, "Klebsiella pneumoniae", "ampicillin")    # range 11-17
+#' random_disk(25, "Klebsiella pneumoniae", "ampicillin")    # range 11-17
-#' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
+#' random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
 #' }
 random_mic <- function(size = NULL, mo = NULL, ab = NULL, ...) {
   meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
@@ -89,6 +87,7 @@ random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
 }
 
 random_exec <- function(type, size, mo = NULL, ab = NULL) {
+  check_dataset_integrity()
   df <- rsi_translation %pm>%
     pm_filter(guideline %like% "EUCAST") %pm>%
     pm_arrange(pm_desc(guideline)) %pm>%

R/resistance_predict.R

@@ -26,7 +26,6 @@
 #' Predict Antimicrobial Resistance
 #'
 #' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param object model data to be plotted
 #' @param col_ab column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`)
 #' @param col_date column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class
@@ -34,7 +33,7 @@
 #' @param year_max highest year to use in the prediction model, defaults to 10 years after today
 #' @param year_every unit of sequence between lowest year found in the data and `year_max`
 #' @param minimum minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.
-#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)``, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
+#' @param model the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using `glm(..., family = binomial)`, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See *Details* for all valid options.
 #' @param I_as_S a [logical] to indicate whether values `"I"` should be treated as `"S"` (will otherwise be treated as `"R"`). The default, `TRUE`, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section *Interpretation of S, I and R* below. 
 #' @param preserve_measurements a [logical] to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be `NA`.
 #' @param info a [logical] to indicate whether textual analysis should be printed with the name and [summary()] of the statistical model.
@@ -64,7 +63,6 @@
 #' @rdname resistance_predict
 #' @export
 #' @importFrom stats predict glm lm
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' x <- resistance_predict(example_isolates, 
 #'                         col_ab = "AMX",
@@ -99,24 +97,8 @@
 #'                        model = "binomial",
 #'                        info = FALSE,
 #'                        minimum = 15)
-#'                        
+#'   head(data)
 #'   autoplot(data)
-#'
-#'   ggplot(data,
-#'          aes(x = year)) +
-#'     geom_col(aes(y = value),
-#'              fill = "grey75") +
-#'     geom_errorbar(aes(ymin = se_min,
-#'                       ymax = se_max),
-#'                   colour = "grey50") +
-#'     scale_y_continuous(limits = c(0, 1),
-#'                        breaks = seq(0, 1, 0.1),
-#'                        labels = paste0(seq(0, 100, 10), "%")) +
-#'     labs(title = expression(paste("Forecast of Amoxicillin Resistance in ",
-#'                                   italic("E. coli"))),
-#'          y = "%R",
-#'          x = "Year") +
-#'     theme_minimal(base_size = 13)
 #' }
 #' }
 resistance_predict <- function(x,

R/rsi.R

@@ -26,14 +26,13 @@
 #' Interpret MIC and Disk Values, or Clean Raw R/SI Data
 #'
 #' Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered [factor] with levels `S < I < R`.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @rdname as.rsi
 #' @param x vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
 #' @param mo any (vector of) text that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically
 #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
 #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
 #' @inheritParams first_isolate
-#' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
+#' @param guideline defaults to EUCAST `r  max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
@@ -98,15 +97,10 @@
 #' @export
 #' @seealso [as.mic()], [as.disk()], [as.mo()]
 #' @inheritSection AMR Reference Data Publicly Available
-#' @inheritSection AMR Read more on Our Website!
 #' @examples
+#' example_isolates
 #' summary(example_isolates) # see all R/SI results at a glance
-#' \donttest{
+#' 
-#' if (require("skimr")) {
-#'   # class <rsi> supported in skim() too:
-#'   skim(example_isolates)
-#' }
-#' }
 #' # For INTERPRETING disk diffusion and MIC values -----------------------
 #'        
 #' # a whole data set, even with combined MIC values and disk zones
@@ -179,7 +173,7 @@
 #'   example_isolates %>%
 #'     mutate_if(is.rsi.eligible, as.rsi)
 #'     
-#'   # note: from dplyr 1.0.0 on, this will be: 
+#'   # since dplyr 1.0.0, this can also be: 
 #'   # example_isolates %>%
 #'   #   mutate(across(where(is.rsi.eligible), as.rsi))
 #' }
@@ -189,7 +183,7 @@ as.rsi <- function(x, ...) {
 }
 
 #' @rdname as.rsi
-#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
+#' @details `NA_rsi_` is a missing value of the new `<rsi>` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
 #' @export
 NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
                            new_class =  c("rsi", "ordered", "factor"))
@@ -796,7 +790,7 @@ exec_as.rsi <- function(method,
                            lookup_lancefield[i],
                            lookup_other[i]))
     
-    if (any(get_record$uti == TRUE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "msg3", ab)) {
+    if (any(get_record$uti == TRUE, na.rm = TRUE) && !any(uti == TRUE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "msg3", ab)) {
       warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use argument `uti` to set which isolates are from urine. See ?as.rsi.")
       rise_warning <- TRUE
     }
@@ -818,18 +812,20 @@ exec_as.rsi <- function(method,
       if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
         new_rsi[i] <- NA_character_
       } else if (method == "mic") {
-        new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
+        new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
-                                      isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
+                                      isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
                                       # these basically call `<=.mic()` and `>=.mic()`:
-                                      x[i] <= get_record$breakpoint_S ~ "S",
+                                      isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
-                                      x[i] >= get_record$breakpoint_R ~ "R",
+                                      guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
+                                      guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise
                                       TRUE ~ NA_character_)
       } else if (method == "disk") {
         new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
-                                      isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
+                                      guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
+                                      guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise

R/skewness.R

@@ -28,13 +28,13 @@
 #' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
 #'
 #' When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.
-#' @inheritSection lifecycle Stable Lifecycle
 #' @param x a vector of values, a [matrix] or a [data.frame]
 #' @param na.rm a [logical] value indicating whether `NA` values should be stripped before the computation proceeds
 #' @seealso [kurtosis()]
 #' @rdname skewness
-#' @inheritSection AMR Read more on Our Website!
 #' @export
+#' @examples 
+#' skewness(runif(1000))
 skewness <- function(x, na.rm = FALSE) {
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
   UseMethod("skewness")

R/translate.R

@@ -23,132 +23,133 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Translate Strings from AMR Package
+#' Translate Strings from the AMR Package
 #'
 #' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
-#' @inheritSection lifecycle Stable Lifecycle
+#' @param x text to translate
-#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.). 
+#' @param lang language to choose. Use one of these supported language names or ISO-639-1 codes: `r paste0('"', sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), '" ("' , LANGUAGES_SUPPORTED, '")', collapse = ", ")`.
+#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_and(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
 #'
-#' Currently supported languages are: `r vector_and(names(LANGUAGES_SUPPORTED), quotes = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
+#' Please read about adding or updating a language in [our Wiki](https://github.com/msberends/AMR/wiki/).
-#'
-#' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
 #'
 #' ## Changing the Default Language
-#' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
+#' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [Sys.getlocale("LC_COLLATE")]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
 #' 
-#'   1. Setting the R option `AMR_locale`, e.g. by running `options(AMR_locale = "de")`
+#'   1. Setting the R option `AMR_locale`, either by using `set_AMR_locale()` or by running e.g. `options(AMR_locale = "de")`.
-#'   2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory
+#'   
+#'      Note that setting an \R option only works in the same session. Save the command `options(AMR_locale = "(your language)")` to your `.Rprofile` file to apply it for every session.
+#'   2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory.
 #' 
 #' Thus, if the R option `AMR_locale` is set, the system variables `LANGUAGE` and `LANG` will be ignored.
-#' @inheritSection AMR Read more on Our Website!
 #' @rdname translate
 #' @name translate
 #' @export
 #' @examples
-#' # The 'language' argument of below functions
+#' # Current settings (based on system language)
-#' # will be set automatically to your system language
+#' ab_name("Ciprofloxacin")
-#' # with get_AMR_locale()
+#' mo_name("Coagulase-negative Staphylococcus")
 #'
-#' # English
+#' # setting another language
-#' mo_name("CoNS", language = "en")
+#' set_AMR_locale("Greek")
-#' #> "Coagulase-negative Staphylococcus (CoNS)"
+#' ab_name("Ciprofloxacin")
-#'
+#' mo_name("Coagulase-negative Staphylococcus")
-#' # Danish
-#' mo_name("CoNS", language = "da")
-#' #> "Koagulase-negative stafylokokker (KNS)"
 #' 
-#' # Dutch
+#' set_AMR_locale("Spanish")
-#' mo_name("CoNS", language = "nl")
+#' ab_name("Ciprofloxacin")
-#' #> "Coagulase-negatieve Staphylococcus (CNS)"
+#' mo_name("Coagulase-negative Staphylococcus")
+#' 
+#' # set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1:
+#' set_AMR_locale("Deutsch")
+#' set_AMR_locale("German")
+#' set_AMR_locale("de")
 #'
-#' # German
+#' # reset to system default
-#' mo_name("CoNS", language = "de")
+#' reset_AMR_locale()
-#' #> "Koagulase-negative Staphylococcus (KNS)"
-#'
-#' # Italian
-#' mo_name("CoNS", language = "it")
-#' #> "Staphylococcus negativo coagulasi (CoNS)"
-#'
-#' # Portuguese
-#' mo_name("CoNS", language = "pt")
-#' #> "Staphylococcus coagulase negativo (CoNS)"
-#'
-#' # Spanish
-#' mo_name("CoNS", language = "es")
-#' #> "Staphylococcus coagulasa negativo (SCN)"
 get_AMR_locale <- function() {
-  # AMR versions 1.3.0 and prior used the environmental variable:
-  if (!identical("", Sys.getenv("AMR_locale"))) {
-    options(AMR_locale = Sys.getenv("AMR_locale"))
-  }
-  
   if (!is.null(getOption("AMR_locale", default = NULL))) {
-    lang <- getOption("AMR_locale")
+    return(validate_language(getOption("AMR_locale"), extra_txt = "set with `options(AMR_locale = ...)`"))
-    if (lang %in% LANGUAGES_SUPPORTED) {
-      return(lang)
-    } else {
-      stop_("unsupported language set as option 'AMR_locale': \"", lang, "\" - use either ",
-            vector_or(paste0('"', LANGUAGES_SUPPORTED, '" (', names(LANGUAGES_SUPPORTED), ")"), quotes = FALSE))
-    }
-  } else {
-    # now check the LANGUAGE system variable - return it if set
-    if (!identical("", Sys.getenv("LANGUAGE"))) {
-      return(coerce_language_setting(Sys.getenv("LANGUAGE")))
-    }
-    if (!identical("", Sys.getenv("LANG"))) {
-      return(coerce_language_setting(Sys.getenv("LANG")))
-    }
   }
   
-  # fallback - automatic determination based on LC_COLLATE
+  lang <- ""
-  if (interactive() && message_not_thrown_before("get_AMR_locale", entire_session = TRUE)) {
+  # now check the LANGUAGE system variable - return it if set
-    lang <- coerce_language_setting(Sys.getlocale("LC_COLLATE"))
+  if (!identical("", Sys.getenv("LANGUAGE"))) {
-    if (lang != "en") {
+    lang <- Sys.getenv("LANGUAGE")
-      message_("Assuming the ", names(LANGUAGES_SUPPORTED)[LANGUAGES_SUPPORTED == lang], 
-               " language for the AMR package. Change this with `options(AMR_locale = \"...\")` or see `?get_AMR_locale()`. ",
-               "Supported languages are ", vector_and(names(LANGUAGES_SUPPORTED), quotes = FALSE),
-               ". This note will be shown once per session.")
-    }
-    return(lang)
   }
-  coerce_language_setting(Sys.getlocale("LC_COLLATE"))
+  if (!identical("", Sys.getenv("LANG"))) {
+    lang <- Sys.getenv("LANG")
+  }
+  if (lang == "") {
+    lang <- Sys.getlocale("LC_COLLATE")
+  }
+  
+  lang <- find_language(lang)
+  if (lang != "en" && interactive() && message_not_thrown_before("get_AMR_locale", entire_session = TRUE)) {
+    message_("Assuming the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym,  " language (",
+             LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package. Change this with `set_AMR_locale()`. ",
+             "This note will be shown once per session.")
+  }
+  lang
 }
 
-coerce_language_setting <- function(lang) {
+#' @rdname translate
-  # grepl() with ignore.case = FALSE is 8x faster than %like_case%
+#' @export
-  if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE, perl = TRUE)) {
+set_AMR_locale <- function(lang) {
-    # as first option to optimise speed
+  lang <- validate_language(lang)
-    "en"
+  options(AMR_locale = lang)
-  } else if (grepl("^(German|Deutsch|de_|DE_)", lang, ignore.case = FALSE, perl = TRUE)) {
+  message_("Using the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym,  " language (", LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package for this session.")
-    "de"
+}
-  } else if (grepl("^(Dutch|Nederlands|nl_|NL_)", lang, ignore.case = FALSE, perl = TRUE)) {
+
-    "nl"
+#' @rdname translate
-  } else if (grepl("^(Danish|Dansk|da_|DA_)", lang, ignore.case = FALSE, perl = TRUE)) {
+#' @export
-    "da"
+reset_AMR_locale <- function() {
-  } else if (grepl("^(Spanish|Espa.+ol|es_|ES_)", lang, ignore.case = FALSE, perl = TRUE)) {
+  options(AMR_locale = NULL)
-    "es"
+}
-  } else if (grepl("^(Italian|Italiano|it_|IT_)", lang, ignore.case = FALSE, perl = TRUE)) {
+
-    "it"
+#' @rdname translate
-  } else if (grepl("^(French|Fran.+ais|fr_|FR_)", lang, ignore.case = FALSE, perl = TRUE)) {
+#' @export
-    "fr"
+translate_AMR <- function(x, language = get_AMR_locale()) {
-  } else if (grepl("^(Portuguese|Portugu.+s|pt_|PT_)", lang, ignore.case = FALSE, perl = TRUE)) {
+  translate_into_language(x, language = language)
-    "pt"
+}
-  } else if (grepl("^(Russian|pycc|ru_|RU_)", lang, ignore.case = FALSE, perl = TRUE)) {
+
-    "ru"
+validate_language <- function(language, extra_txt = character(0)) {
-  } else if (grepl("^(Swedish|Svenskt|sv_|SV_)", lang, ignore.case = FALSE, perl = TRUE)) {
+  if (trimws(tolower(language)) %in% c("en", "english", "", "false", NA)) {
-    "sv"
+    return("en")
-  } else {
-    # other language -> set to English
-    "en"
   }
+  lang <- find_language(language, fallback = FALSE)
+  stop_ifnot(length(lang) > 0 && lang %in% LANGUAGES_SUPPORTED,
+             "unsupported language for AMR package", extra_txt, ": \"", language, "\". Use one of these language names or ISO-639-1 codes: ",
+             paste0('"', vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]),
+                    '" ("' , LANGUAGES_SUPPORTED, '")', collapse = ", "),
+             call = FALSE)
+  lang
+}
+
+find_language <- function(lang, fallback = TRUE) {
+  lang <- Map(function(l, n, check = lang) {
+    grepl(paste0("^(", l[1], "|", l[2], "|",
+                 n, "(_|$)|", toupper(n), "(_|$))"),
+          check,
+          ignore.case = FALSE,
+          perl = TRUE,
+          useBytes = FALSE)
+  },
+  LANGUAGES_SUPPORTED_NAMES,
+  LANGUAGES_SUPPORTED,
+  USE.NAMES = TRUE)
+  lang <- names(which(lang == TRUE))
+  if (isTRUE(fallback) && length(lang) == 0) {
+    # other language -> set to English
+    lang <- "en"
+  }
+  lang
 }
 
 # translate strings based on inst/translations.tsv
-translate_AMR <- function(from,
+translate_into_language <- function(from,
-                          language = get_AMR_locale(), 
+                                    language = get_AMR_locale(), 
-                          only_unknown = FALSE,
+                                    only_unknown = FALSE,
-                          only_affect_ab_names = FALSE,
+                                    only_affect_ab_names = FALSE,
-                          only_affect_mo_names = FALSE) {
+                                    only_affect_mo_names = FALSE) {
   
   if (is.null(language)) {
     return(from)
@@ -162,15 +163,12 @@ translate_AMR <- function(from,
   from_unique <- unique(from)
   from_unique_translated <- from_unique
   
-  stop_ifnot(language %in% LANGUAGES_SUPPORTED,
+  # get ISO-639-1 of language
-             "unsupported language: \"", language, "\" - use either ",
+  lang <- validate_language(language)
-             vector_or(LANGUAGES_SUPPORTED, quotes = TRUE),
-             call = FALSE)
-  
   # only keep lines where translation is available for this language
-  df_trans <- df_trans[which(!is.na(df_trans[, language, drop = TRUE])), , drop = FALSE]
+  df_trans <- df_trans[which(!is.na(df_trans[, lang, drop = TRUE])), , drop = FALSE]
   # and where the original string is not equal to the string in the target language
-  df_trans <- df_trans[which(df_trans[, "pattern", drop = TRUE] != df_trans[, language, drop = TRUE]), , drop = FALSE]
+  df_trans <- df_trans[which(df_trans[, "pattern", drop = TRUE] != df_trans[, lang, drop = TRUE]), , drop = FALSE]
   if (only_unknown == TRUE) {
     df_trans <- subset(df_trans, pattern %like% "unknown")
   }
@@ -203,7 +201,7 @@ translate_AMR <- function(from,
   
   lapply(seq_len(nrow(df_trans)), 
          function(i) from_unique_translated <<- gsub(pattern = df_trans$pattern[i],
-                                                     replacement = df_trans[i, language, drop = TRUE],
+                                                     replacement = df_trans[i, lang, drop = TRUE],
                                                      x = from_unique_translated,
                                                      ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i], 
                                                      fixed = !df_trans$regular_expr[i],
@@ -211,7 +209,7 @@ translate_AMR <- function(from,
   
   # force UTF-8 for diacritics
   from_unique_translated <- enc2utf8(from_unique_translated)
-
+  
   # a kind of left join to get all results back
   from_unique_translated[match(from.bak, from_unique)]
 }

R/vctrs.R

@@ -28,8 +28,9 @@
 # They are to convert AMR-specific classes to bare characters and integers.
 # All of them will be exported using s3_register() in R/zzz.R when loading the package.
 
-# S3: ab_selector
 # see https://github.com/tidyverse/dplyr/issues/5955 why this is required
+
+# S3: ab_selector
 vec_ptype2.character.ab_selector <- function(x, y, ...) {
   x
 }
@@ -40,6 +41,17 @@ vec_cast.character.ab_selector <- function(x, to, ...) {
   unclass(x)
 }
 
+# S3: ab_selector_any_all
+vec_ptype2.logical.ab_selector_any_all <- function(x, y, ...) {
+  x
+}
+vec_ptype2.ab_selector_any_all.logical <- function(x, y, ...) {
+  y
+}
+vec_cast.logical.ab_selector_any_all <- function(x, to, ...) {
+  unclass(x)
+}
+
 # S3: ab
 vec_ptype2.character.ab <- function(x, y, ...) {
   x

R/whocc.R

@@ -35,7 +35,7 @@
 #' The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
 #' 
 #' **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.** See <https://www.whocc.no/copyright_disclaimer/.>
-#' @inheritSection AMR Read more on Our Website!
+
 #' @name WHOCC
 #' @rdname WHOCC
 #' @examples

R/zzz.R

@@ -87,6 +87,9 @@ if (utf8_supported && !is_latex) {
   s3_register("vctrs::vec_ptype2", "ab_selector.character")
   s3_register("vctrs::vec_ptype2", "character.ab_selector")
   s3_register("vctrs::vec_cast", "character.ab_selector")
+  s3_register("vctrs::vec_ptype2", "ab_selector_any_all.logical")
+  s3_register("vctrs::vec_ptype2", "logical.ab_selector_any_all")
+  s3_register("vctrs::vec_cast", "logical.ab_selector_any_all")
   s3_register("vctrs::vec_ptype2", "disk.integer")
   s3_register("vctrs::vec_ptype2", "integer.disk")
   s3_register("vctrs::vec_cast", "integer.disk")
@@ -106,11 +109,6 @@ if (utf8_supported && !is_latex) {
   assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
   # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
   assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
-  
-  # for building the website, only print first 5 rows of a data set
-  # if (Sys.getenv("IN_PKGDOWN") != "" && !interactive()) {
-  #   ...
-  # }
 }
 
 # Helper functions --------------------------------------------------------
@@ -131,7 +129,12 @@ create_MO_lookup <- function() {
   MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
   
   # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
-  MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
+    MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
+  } else {
+    MO_lookup$fullname_lower <- ""
+    warning("MO table updated - Run: source(\"data-raw/_internals.R\")", call. = FALSE)
+  }
   
   # add a column with only "e coli" like combinations
   MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)

README.md

@@ -8,9 +8,7 @@
 
 <img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" />
 
-The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/main/data-raw).
+`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 175 countries.
-
-`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 150 countries.
  
 After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
 

_pkgdown.yml

@@ -26,13 +26,39 @@
 title: "AMR (for R)"
 url: "https://msberends.github.io/AMR/"
 
-development:
+template:
-  mode: "release" # improves indexing by search engines
+  bootstrap: 5
-  version_tooltip: "Latest development version"
+  bootswatch: "flatly"
+  assets: "pkgdown/logos" # use logos in this folder
+  bslib:
+    code_font: {google: "Fira Code"}
+    body-text-align: "justify"
+    line-height-base: 1.75
+    # the green "success" colour of this bootstrap theme should be the same as the green in our logo
+    success: "#128f76"
+    link-color: "#128f76"
+    navbar-padding-y: "0.5rem"
+  opengraph:
+    twitter:
+      creator: "@msberends"
+      site: "@univgroningen"
+      card: summary_large_image
 
 news:
   one_page: true
   cran_dates: true
+  
+footer:
+  structure: 
+    left: [devtext]
+    right: [logo]
+  components:
+    devtext: '<code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl">University Medical Center Groningen</a>.'
+    logo: '<a target="_blank" href="https://www.rug.nl"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.png" style="max-width: 200px;"></a>'
+
+home:
+  sidebar:
+    structure: [toc, links, authors, citation]
 
 navbar:
   title: "AMR (for R)"
@@ -161,7 +187,6 @@ reference:
     - "`catalogue_of_life`"
     - "`catalogue_of_life_version`"
     - "`WHOCC`"
-    - "`lifecycle`"
     - "`example_isolates_unclean`"
     - "`rsi_translation`"
     - "`WHONET`"
@@ -200,14 +225,3 @@ reference:
     contents:
     - "`AMR-deprecated`"
 
-template:
-  bootstrap: 3
-  opengraph:
-    twitter:
-      creator: "@msberends"
-      site: "@univgroningen"
-      card: summary_large_image
-  assets: "pkgdown/logos" # use logos in this folder
-  params:
-    noindex: false
-    bootswatch: "flatly"

data-raw/_install_deps.R

@@ -25,7 +25,8 @@
 
 # some old R instances have trouble installing tinytest, so we ship it too
 install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
-install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
+install.packages(getwd(), repos = NULL, type = "source")
+# install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
                      unlist(strsplit(unlist(packageDescription("AMR",

data-raw/_internals.R

@@ -29,18 +29,20 @@
 library(dplyr, warn.conflicts = FALSE)
 devtools::load_all(quiet = TRUE)
 
+set_AMR_locale("en")
+
 old_globalenv <- ls(envir = globalenv())
 
 # Save internal data to R/sysdata.rda -------------------------------------
 
 # See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
 EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
-                                       skip = 10,
+                                     skip = 10,
-                                       sep = "\t",
+                                     sep = "\t",
-                                       stringsAsFactors = FALSE,
+                                     stringsAsFactors = FALSE,
-                                       header = TRUE,
+                                     header = TRUE,
-                                       strip.white = TRUE,
+                                     strip.white = TRUE,
-                                       na = c(NA, "", NULL)) %>% 
+                                     na = c(NA, "", NULL)) %>% 
   # take the order of the reference.rule_group column in the original data file
   mutate(reference.rule_group = factor(reference.rule_group,
                                        levels = unique(reference.rule_group),
@@ -53,34 +55,6 @@ EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
   mutate(reference.rule_group = as.character(reference.rule_group)) %>% 
   select(-sorting_rule)
 
-# Translations
-TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
-                                       sep = "\t",
-                                       stringsAsFactors = FALSE,
-                                       header = TRUE,
-                                       blank.lines.skip = TRUE,
-                                       fill = TRUE,
-                                       strip.white = TRUE,
-                                       encoding = "UTF-8",
-                                       fileEncoding = "UTF-8",
-                                       na.strings = c(NA, "", NULL),
-                                       allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
-                                       quote = "")
-
-# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
-LANGUAGES_SUPPORTED <- c(Danish = "da",
-                         German = "de",
-                         English = "en",
-                         Spanish = "es",
-                         French = "fr",
-                         Italian = "it",
-                         Dutch = "nl",
-                         Portuguese = "pt",
-                         Russian = "ru",
-                         Swedish = "sv")
-
-# EXAMPLE_ISOLATES <- readRDS("data-raw/example_isolates.rds")
-
 # vectors of CoNS and CoPS, improves speed in as.mo()
 create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
   # Determination of which staphylococcal species are CoNS/CoPS according to:
@@ -137,6 +111,29 @@ MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
 MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
 MO_FULLNAME_LOWER <- create_MO_fullname_lower()
+MO_PREVALENT_GENERA <- c("Absidia", "Acholeplasma", "Acremonium", "Actinotignum", "Aedes", "Alistipes", "Alloprevotella",
+                         "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles",
+                         "Apophysomyces", "Arachnia", "Aspergillus", "Aureobasidium", "Bacteroides", "Basidiobolus",
+                         "Beauveria", "Bergeyella", "Blastocystis", "Blastomyces", "Borrelia", "Brachyspira", "Branhamella",
+                         "Butyricimonas", "Candida", "Capillaria", "Capnocytophaga", "Catabacter", "Cetobacterium", "Chaetomium",
+                         "Chlamydia", "Chlamydophila", "Chryseobacterium", "Chrysonilia", "Cladophialophora", "Cladosporium",
+                         "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Deinococcus", "Demodex",
+                         "Dermatobia", "Diphyllobothrium", "Dirofilaria", "Dysgonomonas", "Echinostoma", "Elizabethkingia",
+                         "Empedobacter", "Enterobius", "Exophiala", "Exserohilum", "Fasciola", "Flavobacterium", "Fonsecaea",
+                         "Fusarium", "Fusobacterium", "Giardia", "Haloarcula", "Halobacterium", "Halococcus", "Hendersonula",
+                         "Heterophyes", "Histoplasma", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Lelliottia",
+                         "Leptosphaeria", "Leptotrichia", "Lucilia", "Lumbricus", "Malassezia", "Malbranchea", "Metagonimus",
+                         "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Myroides", "Necator",
+                         "Nectria", "Ochroconis", "Odoribacter", "Oesophagostomum", "Oidiodendron", "Opisthorchis",
+                         "Ornithobacterium", "Parabacteroides", "Pediculus", "Pedobacter", "Phlebotomus", "Phocaeicola",
+                         "Phocanema", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Porphyromonas", "Prevotella",
+                         "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus", "Rhodotorula", "Riemerella",
+                         "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Sphingobacterium",
+                         "Spirometra", "Spiroplasma", "Sporobolomyces", "Stachybotrys", "Streptobacillus", "Strongyloides",
+                         "Syngamus", "Taenia", "Tannerella", "Tenacibaculum", "Terrimonas", "Toxocara", "Treponema", "Trichinella",
+                         "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus",
+                         "Trichuris", "Tritirachium", "Trombicula", "Tunga", "Ureaplasma", "Victivallis", "Wautersiella",
+                         "Weeksella", "Wuchereria")
 
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -193,13 +190,11 @@ AB_LOOKUP <- create_AB_lookup()
 
 # Export to package as internal data ----
 usethis::use_data(EUCAST_RULES_DF, 
-                  TRANSLATIONS,
-                  LANGUAGES_SUPPORTED,
-                  # EXAMPLE_ISOLATES,
                   MO_CONS,
                   MO_COPS,
                   MO_STREP_ABCG,
                   MO_FULLNAME_LOWER,
+                  MO_PREVALENT_GENERA,
                   AB_LOOKUP,
                   AB_AMINOGLYCOSIDES,
                   AB_AMINOPENICILLINS,
@@ -252,7 +247,9 @@ changed_md5 <- function(object) {
 }
 
 # give official names to ABs and MOs
-rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
+rsi <- AMR::rsi_translation %>% 
+  mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>% 
+  mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
 if (changed_md5(rsi)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('rsi_translation')} to {usethis::ui_value('/data-raw/')}"))
   write_md5(rsi)
@@ -273,7 +270,7 @@ if (changed_md5(mo)) {
   try(haven::write_sas(dplyr::select(mo, -snomed), "data-raw/microorganisms.sas"), silent = TRUE)
   try(haven::write_sav(dplyr::select(mo, -snomed), "data-raw/microorganisms.sav"), silent = TRUE)
   try(haven::write_dta(dplyr::select(mo, -snomed), "data-raw/microorganisms.dta"), silent = TRUE)
-  try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), silent = TRUE)
+  try(openxlsx::write.xlsx(dplyr::select(mo, -snomed), "data-raw/microorganisms.xlsx"), silent = TRUE)
 }
 
 if (changed_md5(microorganisms.old)) {
@@ -312,8 +309,8 @@ if (changed_md5(av)) {
 }
 
 # give official names to ABs and MOs
-intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo),
+intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo, language = NULL),
-                         antibiotic = ab_name(intrinsic_resistant$ab),
+                         antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
                          stringsAsFactors = FALSE)
 if (changed_md5(intrinsicR)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))
@@ -337,6 +334,8 @@ if (changed_md5(dosage)) {
   try(openxlsx::write.xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
 }
 
+reset_AMR_locale()
+
 # remove leftovers from global env
 current_globalenv <- ls(envir = globalenv())
 rm(list = current_globalenv[!current_globalenv %in% old_globalenv])

data-raw/_language_update.R

@@ -0,0 +1,82 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# 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/   #
+# ==================================================================== #
+
+# Run this file to update the languages used in the packages:
+# source("data-raw/_language_update.R")
+
+if (!file.exists("DESCRIPTION") || !"Package: AMR" %in% readLines("DESCRIPTION")) {
+  stop("Be sure to run this script in the root location of the AMR package folder.\n",
+       "Working directory expected to contain the DESCRIPTION file of the AMR package.\n",
+       "Current working directory: ", getwd(),
+       call. = FALSE)
+}
+
+# save old global env to restore later
+lang_env <- new.env(hash = FALSE)
+
+# load current internal data into new env
+load("R/sysdata.rda", envir = lang_env)
+
+# replace language objects with updates
+message("Reading translation file...")
+lang_env$TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
+                                           sep = "\t",
+                                           stringsAsFactors = FALSE,
+                                           header = TRUE,
+                                           blank.lines.skip = TRUE,
+                                           fill = TRUE,
+                                           strip.white = TRUE,
+                                           encoding = "UTF-8",
+                                           fileEncoding = "UTF-8",
+                                           na.strings = c(NA, "", NULL),
+                                           allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
+                                           quote = "")
+
+lang_env$LANGUAGES_SUPPORTED_NAMES <- c(list(en = list(exonym = "English", endonym = "English")),
+                                        lapply(lang_env$TRANSLATIONS[, which(nchar(colnames(lang_env$TRANSLATIONS)) == 2)],
+                                               function(x) list(exonym = x[1], endonym = x[2])))
+
+lang_env$LANGUAGES_SUPPORTED <- names(lang_env$LANGUAGES_SUPPORTED_NAMES)
+
+# save env to internal package data
+# usethis::use_data() does not allow to save a list :(
+message("Saving to internal data...")
+save(list = names(lang_env),
+     file = "R/sysdata.rda",
+     ascii = FALSE,
+     version = 2,
+     compress = "xz",
+     envir = lang_env)
+
+rm(lang_env)
+
+if ("roxygen2" %in% utils::installed.packages()) {
+  message("Updating package documentation...")
+  suppressMessages(roxygen2::roxygenise(package.dir = "."))
+} else {
+  message("NOTE: please install the roxygen2 package to update package documentation, and run this script again.")
+}
+
+message("Done!")

data-raw/microorganisms.old.md5

@@ -1 +1 @@
-ee4434541c7b6529b391d2684748e28b
+19af89838b60bc8549d4474609629e8d

data-raw/microorganisms.old.txt

@@ -278,9 +278,9 @@
 "Adelosina duthiersi"	"Quinqueloculina duthiersi"	"Schlumberger, 1886"	3
 "Adelosina linneiana"	"Pseudotriloculina linneiana"	"DOrbigny, 1839"	3
 "Aecidium ipomoeae-panduratae"	"Albugo ipomoeae-panduratae"	"Schwein, 1822"	3
-"Aedimorphus alboannulatus"	"Aedes alboannulatus"	"Theobald, 1905"	3
+"Aedimorphus alboannulatus"	"Aedes alboannulatus"	"Theobald, 1905"	2
-"Aedimorphus albotaeniatus"	"Aedes albotaeniatus"	"Theobald, 1903"	3
+"Aedimorphus albotaeniatus"	"Aedes albotaeniatus"	"Theobald, 1903"	2
-"Aedimorphus australis"	"Aedes australis"	"Taylor, 1914"	3
+"Aedimorphus australis"	"Aedes australis"	"Taylor, 1914"	2
 "Aegyria angustata"	"Dysteria angustata"	"Claparede et al., 1859"	3
 "Aegyria astyla"	"Dysteria astyla"	"Maskell, 1887"	3
 "Aegyria distyla"	"Dysteria distyla"	"Maskell, 1887"	3
@@ -880,7 +880,7 @@
 "Astacolus subaculeata"	"Vaginulinopsis subaculeata"	"Cushman, 1923"	3
 "Astacolus sublegumen"	"Vaginulinopsis sublegumen"	"Parr, 1950"	3
 "Asterellina pulchella"	"Eoeponidella pulchella"	"Parker, 1952"	3
-"Asterias ocellifera"	"Nectria ocellifera"	"Lamarck, 1816"	3
+"Asterias ocellifera"	"Nectria ocellifera"	"Lamarck, 1816"	2
 "Asterigerinata pulchella"	"Eoeponidella pulchella"	"Parker, 1952"	3
 "Asteromella anthemidis"	"Phoma anthemidis"	"Ruppr, 1958"	2
 "Asteromella longissima"	"Phoma longissima"	"Petr"	2
@@ -1324,8 +1324,8 @@
 "Bacteriovorax marinus"	"Halobacteriovorax marinus"	"Baer et al., 2004"	2
 "Bacteriovorax starrii"	"Peredibacter starrii"	"Baer et al., 2000"	2
 "Bacteroides amylophilus"	"Ruminobacter amylophilus"	"Hamlin et al., 1956"	1
-"Bacteroides asaccharolyticus"	"Porphyromonas asaccharolytica"	"Finegold et al., 1977"	3
+"Bacteroides asaccharolyticus"	"Porphyromonas asaccharolytica"	"Finegold et al., 1977"	2
-"Bacteroides barnesiae"	"Phocaeicola barnesiae"	"Lan et al., 2006"	3
+"Bacteroides barnesiae"	"Phocaeicola barnesiae"	"Lan et al., 2006"	2
 "Bacteroides bivius"	"Prevotella bivia"	"Holdeman et al., 1977"	2
 "Bacteroides buccae"	"Prevotella buccae"	"Holdeman et al., 1982"	2
 "Bacteroides buccalis"	"Prevotella buccalis"	"Shah et al., 1982"	2
@@ -1333,32 +1333,32 @@
 "Bacteroides capillus"	"Prevotella buccae"	"Kornman et al., 1982"	2
 "Bacteroides cellulosolvens"	"Pseudobacteroides cellulosolvens"	"Murray et al., 1984"	2
 "Bacteroides chinchillae"	"Bacteroides sartorii"	"Kitahara et al., 2011"	
-"Bacteroides chinchillae"	"Phocaeicola sartorii"	"Kitahara et al., 2011"	3
+"Bacteroides chinchillae"	"Phocaeicola sartorii"	"Kitahara et al., 2011"	2
 "Bacteroides coagulans"	"Ezakiella coagulans"	"Eggerth et al., 1933"	2
-"Bacteroides coprocola"	"Phocaeicola coprocola"	"Kitahara et al., 2005"	3
+"Bacteroides coprocola"	"Phocaeicola coprocola"	"Kitahara et al., 2005"	2
-"Bacteroides coprophilus"	"Phocaeicola coprophilus"	"Hayashi et al., 2016"	3
+"Bacteroides coprophilus"	"Phocaeicola coprophilus"	"Hayashi et al., 2016"	2
 "Bacteroides corporis"	"Prevotella corporis"	"Johnson et al., 1983"	2
 "Bacteroides denticola"	"Prevotella denticola"	"Shah et al., 1982"	2
 "Bacteroides disiens"	"Prevotella disiens"	"Holdeman et al., 1977"	2
-"Bacteroides distasonis"	"Parabacteroides distasonis"	"Eggerth et al., 1933"	3
+"Bacteroides distasonis"	"Parabacteroides distasonis"	"Eggerth et al., 1933"	2
-"Bacteroides dorei"	"Phocaeicola dorei"	"Bakir et al., 2016"	3
+"Bacteroides dorei"	"Phocaeicola dorei"	"Bakir et al., 2016"	2
-"Bacteroides endodontalis"	"Porphyromonas endodontalis"	"Van Steenbergen et al., 1984"	3
+"Bacteroides endodontalis"	"Porphyromonas endodontalis"	"Van Steenbergen et al., 1984"	2
 "Bacteroides forsythus"	"Tannerella forsythia"	"Tanner et al., 1986"	3
 "Bacteroides furcosus"	"Anaerorhabdus furcosa"	"Hauduroy et al., 1937"	2
-"Bacteroides gingivalis"	"Porphyromonas gingivalis"	"Coykendall et al., 1980"	3
+"Bacteroides gingivalis"	"Porphyromonas gingivalis"	"Coykendall et al., 1980"	2
-"Bacteroides goldsteinii"	"Parabacteroides goldsteinii"	"Song et al., 2006"	3
+"Bacteroides goldsteinii"	"Parabacteroides goldsteinii"	"Song et al., 2006"	2
 "Bacteroides gracilis"	"Campylobacter gracilis"	"Tanner et al., 1981"	2
 "Bacteroides heparinolyticus"	"Prevotella heparinolytica"	"Okuda et al., 1985"	2
 "Bacteroides hypermegas"	"Megamonas hypermegale"	"Harrison et al., 1963"	2
 "Bacteroides intermedius"	"Prevotella intermedia"	"Johnson et al., 1983"	2
-"Bacteroides levii"	"Porphyromonas levii"	"Johnson et al., 1983"	3
+"Bacteroides levii"	"Porphyromonas levii"	"Johnson et al., 1983"	2
 "Bacteroides loescheii"	"Prevotella loescheii"	"Holdeman et al., 1982"	2
-"Bacteroides macacae"	"Porphyromonas macacae"	"Coykendall et al., 1980"	3
+"Bacteroides macacae"	"Porphyromonas macacae"	"Coykendall et al., 1980"	2
-"Bacteroides massiliensis"	"Phocaeicola massiliensis"	"Fenner et al., 2016"	3
+"Bacteroides massiliensis"	"Phocaeicola massiliensis"	"Fenner et al., 2016"	2
 "Bacteroides melaninogenicus"	"Prevotella melaninogenica"	"Roy et al., 1982"	2
 "Bacteroides melaninogenicus intermedius"	"Prevotella intermedia"	"Holdeman et al., 1970"	2
-"Bacteroides melaninogenicus macacae"	"Porphyromonas macacae"	"Slots et al., 1980"	3
+"Bacteroides melaninogenicus macacae"	"Porphyromonas macacae"	"Slots et al., 1980"	2
-"Bacteroides merdae"	"Parabacteroides merdae"	"Johnson et al., 1986"	3
+"Bacteroides merdae"	"Parabacteroides merdae"	"Johnson et al., 1986"	2
 "Bacteroides microfusus"	"Rikenella microfusus"	"Kaneuchi et al., 1978"	3
 "Bacteroides multiacidus"	"Mitsuokella multacida"	"Mitsuoka et al., 1974"	2
 "Bacteroides nodosus"	"Dichelobacter nodosus"	"Mraz, 1963"	1
@@ -1366,19 +1366,19 @@
 "Bacteroides oralis"	"Prevotella oralis"	"Loesche et al., 1964"	2
 "Bacteroides oris"	"Prevotella oris"	"Holdeman et al., 1982"	2
 "Bacteroides oulorum"	"Prevotella oulorum"	"Shah et al., 1985"	2
-"Bacteroides paurosaccharolyticus"	"Phocaeicola paurosaccharolyticus"	"Ueki et al., 2011"	3
+"Bacteroides paurosaccharolyticus"	"Phocaeicola paurosaccharolyticus"	"Ueki et al., 2011"	2
 "Bacteroides pentosaceus"	"Prevotella buccae"	"Shah et al., 1982"	2
-"Bacteroides plebeius"	"Phocaeicola plebeius"	"Kitahara et al., 2005"	3
+"Bacteroides plebeius"	"Phocaeicola plebeius"	"Kitahara et al., 2005"	2
 "Bacteroides pneumosintes"	"Dialister pneumosintes"	"Holdeman et al., 1970"	2
 "Bacteroides praeacutus"	"Tissierella praeacuta"	"Holdeman et al., 1970"	2
-"Bacteroides putredinis"	"Alistipes putredinis"	"Kelly, 1957"	3
+"Bacteroides putredinis"	"Alistipes putredinis"	"Kelly, 1957"	2
 "Bacteroides ruminicola"	"Prevotella ruminicola"	"Bryant et al., 1958"	2
 "Bacteroides ruminicola brevis"	"Prevotella brevis"	"Bryant et al., 1958"	2
-"Bacteroides salanitronis"	"Phocaeicola salanitronis"	"Lan et al., 2006"	3
+"Bacteroides salanitronis"	"Phocaeicola salanitronis"	"Lan et al., 2006"	2
-"Bacteroides salivosus"	"Porphyromonas macacae"	"Love et al., 1987"	3
+"Bacteroides salivosus"	"Porphyromonas macacae"	"Love et al., 1987"	2
 "Bacteroides salyersae"	"Bacteroides salyersiae"	"Song et al., 2005"	2
-"Bacteroides sartorii"	"Phocaeicola sartorii"	"Clavel et al., 2012"	3
+"Bacteroides sartorii"	"Phocaeicola sartorii"	"Clavel et al., 2012"	2
-"Bacteroides splanchnicus"	"Odoribacter splanchnicus"	"Werner et al., 1975"	3
+"Bacteroides splanchnicus"	"Odoribacter splanchnicus"	"Werner et al., 1975"	2
 "Bacteroides succinogenes"	"Fibrobacter succinogenes"	"Hungate, 1950"	3
 "Bacteroides suis"	"Bacteroides pyogenes"	"Benno et al., 1983"	2
 "Bacteroides tectum"	"Bacteroides pyogenes"	"Love et al., 2019"	2
@@ -1386,7 +1386,7 @@
 "Bacteroides termitidis"	"Sebaldella termitidis"	"Holdeman et al., 1970"	3
 "Bacteroides ureolyticus"	"Campylobacter ureolyticus"	"Jackson et al., 1978"	2
 "Bacteroides veroralis"	"Prevotella veroralis"	"Watabe et al., 1983"	2
-"Bacteroides vulgatus"	"Phocaeicola vulgatus"	"Hahnke et al., 2016"	3
+"Bacteroides vulgatus"	"Phocaeicola vulgatus"	"Hahnke et al., 2016"	2
 "Bacteroides xylanolyticus"	"Hungatella xylanolytica"	"Scholten-Koerselman et al., 1988"	2
 "Bacteroides zoogleoformans"	"Prevotella zoogleoformans"	"Cato et al., 1982"	
 "Bacteroides zoogleoformans"	"Capsularis zoogleoformans"	"Cato et al., 1982"	3
@@ -1650,27 +1650,27 @@
 "Bolivinita subangularis"	"Saidovina subangularis"	"Brady, 1881"	3
 "Bolivinita subangularis lineata"	"Saidovina subangularis lineata"	"Cushman, 1933"	3
 "Borelis (Fasciolites) pygmaea"	"Neoalveolina pygmaea"	"Hanzawa, 1930"	3
-"Borrelia baltazardi"	"Borrelia baltazardii"	"Karimi et al., 1983"	3
+"Borrelia baltazardi"	"Borrelia baltazardii"	"Karimi et al., 1983"	2
-"Borrelia bavariensis"	"Borrelia garinii bavariensis"	"Margos et al., 2020"	3
+"Borrelia bavariensis"	"Borrelia garinii bavariensis"	"Margos et al., 2020"	2
-"Borrelia turdae"	"Borrelia turdi"	"Fukunaga et al., 1997"	3
+"Borrelia turdae"	"Borrelia turdi"	"Fukunaga et al., 1997"	2
-"Borreliella"	"Borrelia"	"Adeolu et al., 2015"	3
+"Borreliella"	"Borrelia"	"Adeolu et al., 2015"	2
-"Borreliella afzelii"	"Borrelia afzelii"	"Adeolu et al., 2018"	3
+"Borreliella afzelii"	"Borrelia afzelii"	"Adeolu et al., 2018"	2
-"Borreliella americana"	"Borrelia americana"	"Adeolu et al., 2018"	3
+"Borreliella americana"	"Borrelia americana"	"Adeolu et al., 2018"	2
 "Borreliella bavariensis"	"Borrelia bavariensis"	"Adeolu et al., 2015"	
-"Borreliella bavariensis"	"Borrelia garinii bavariensis"	"Adeolu et al., 2015"	3
+"Borreliella bavariensis"	"Borrelia garinii bavariensis"	"Adeolu et al., 2015"	2
-"Borreliella bissettiae"	"Borrelia bissettiae"	"Gupta, 2020"	3
+"Borreliella bissettiae"	"Borrelia bissettiae"	"Gupta, 2020"	2
-"Borreliella burgdorferi"	"Borrelia burgdorferi"	"Adeolu et al., 2015"	3
+"Borreliella burgdorferi"	"Borrelia burgdorferi"	"Adeolu et al., 2015"	2
-"Borreliella californiensis"	"Borrelia californiensis"	"Gupta, 2020"	3
+"Borreliella californiensis"	"Borrelia californiensis"	"Gupta, 2020"	2
-"Borreliella carolinensis"	"Borrelia carolinensis"	"Adeolu et al., 2015"	3
+"Borreliella carolinensis"	"Borrelia carolinensis"	"Adeolu et al., 2015"	2
-"Borreliella garinii"	"Borrelia garinii"	"Adeolu et al., 2015"	3
+"Borreliella garinii"	"Borrelia garinii"	"Adeolu et al., 2015"	2
-"Borreliella japonica"	"Borrelia japonica"	"Adeolu et al., 2015"	3
+"Borreliella japonica"	"Borrelia japonica"	"Adeolu et al., 2015"	2
-"Borreliella kurtenbachii"	"Borrelia kurtenbachii"	"Adeolu et al., 2015"	3
+"Borreliella kurtenbachii"	"Borrelia kurtenbachii"	"Adeolu et al., 2015"	2
-"Borreliella lanei"	"Borrelia lanei"	"Gupta, 2020"	3
+"Borreliella lanei"	"Borrelia lanei"	"Gupta, 2020"	2
-"Borreliella mayonii"	"Borrelia mayonii"	"Gupta, 2020"	3
+"Borreliella mayonii"	"Borrelia mayonii"	"Gupta, 2020"	2
-"Borreliella sinica"	"Borrelia sinica"	"Adeolu et al., 2015"	3
+"Borreliella sinica"	"Borrelia sinica"	"Adeolu et al., 2015"	2
-"Borreliella spielmanii"	"Borrelia spielmanii"	"Adeolu et al., 2015"	3
+"Borreliella spielmanii"	"Borrelia spielmanii"	"Adeolu et al., 2015"	2
-"Borreliella valaisiana"	"Borrelia valaisiana"	"Adeolu et al., 2018"	3
+"Borreliella valaisiana"	"Borrelia valaisiana"	"Adeolu et al., 2018"	2
-"Borreliella yangtzensis"	"Borrelia yangtzensis"	"Gupta, 2020"	3
+"Borreliella yangtzensis"	"Borrelia yangtzensis"	"Gupta, 2020"	2
 "Botryonipha aurantiaca"	"Nectria aurantiaca"	"Kuntze, 1891"	2
 "Botryonipha flavipes"	"Trichoderma flavipes"	"Kuntze, 1891"	2
 "Botryopyle setosa"	"Amphimelissa setosa"	"Cleve, 1899"	3
@@ -1857,9 +1857,9 @@
 "Buliminoides curta"	"Seiglieina curta"	"Seiglie, 1965"	3
 "Buliminoides laevigata"	"Fredsmithia laevigata"	"Seiglie, 1964"	3
 "Buliminoides milletti"	"Floresina milletti"	"Cushman, 1933"	3
-"Buliminus mantongensis"	"Giardia mantongensis"	"Kobelt, 1899"	3
+"Buliminus mantongensis"	"Giardia mantongensis"	"Kobelt, 1899"	2
-"Buliminus pharangensis"	"Giardia pharangensis"	"Dautzenberg et al., 1905"	3
+"Buliminus pharangensis"	"Giardia pharangensis"	"Dautzenberg et al., 1905"	2
-"Bulimus siamensis"	"Giardia siamensis"	"Redfield, 1853"	3
+"Bulimus siamensis"	"Giardia siamensis"	"Redfield, 1853"	2
 "Bulla ovum"	"Ovum ovum"	"Linnaeus, 1758"	3
 "Bullera aurantiaca"	"Dioszegia aurantiaca"	"Johri et al., 1984"	3
 "Bullera begoniae"	"Bulleribasidium begoniae"	"Nakase et al., 2004"	3
@@ -2009,7 +2009,7 @@
 "Caliciopsis calicioides"	"Exophiala calicioides"	"Fitzp, 1920"	2
 "Calidifontibacillus azotoformans"	"Schinkia azotoformans"	"Adiguzel et al., 2020"	2
 "Calidifontibacillus oryziterrae"	"Schinkia oryziterrae"	"Adiguzel et al., 2020"	2
-"Calliphora bicolor"	"Lucilia bicolor"	"Macquart, 1843"	3
+"Calliphora bicolor"	"Lucilia bicolor"	"Macquart, 1843"	2
 "Calomyxa longifila"	"Minakatella longifila"	"LGKrieglst, 1990"	3
 "Calonectria calami"	"Nectria calami"	"Henn et al., 1900"	2
 "Calonectria citrinoaurantia"	"Nectria citrinoaurantia"	"Sacc, 1883"	2
@@ -2302,7 +2302,7 @@
 "Cavostelium bisporum"	"Echinostelium bisporum"	"LSOlive et al., 1966"	3
 "Celeribacter manganoxidans"	"Pacificitalea manganoxidans"	"Wang et al., 2015"	2
 "Cellanthus biperforatus"	"Elphidium biperforatus"	"Whittaker et al., 1979"	3
-"Cellia pretoriensis"	"Anopheles pretoriensis"	"Gough, 1910"	3
+"Cellia pretoriensis"	"Anopheles pretoriensis"	"Gough, 1910"	2
 "Cellulomonas cartae"	"Cellulosimicrobium cellulans"	"Stackebrandt et al., 1980"	2
 "Cellulomonas cellulans"	"Cellulosimicrobium cellulans"	"Stackebrandt et al., 1988"	2
 "Cellulomonas fermentans"	"Actinotalea fermentans"	"Bagnara et al., 1985"	2
@@ -2522,11 +2522,11 @@
 "Chlamydonella distyla"	"Wilbertella distyla"	"Jankowski, 2007"	3
 "Chlamydonella polonica"	"Chlamydonellopsis polonica"	"Foissner et al., 1981"	3
 "Chlamydonella stricta"	"Wilbertiella stricta"	"Deroux, 1976"	3
-"Chlamydophila abortus"	"Chlamydia abortus"	"Everett et al., 1999"	3
+"Chlamydophila abortus"	"Chlamydia abortus"	"Everett et al., 1999"	2
-"Chlamydophila felis"	"Chlamydia felis"	"Everett et al., 1999"	3
+"Chlamydophila felis"	"Chlamydia felis"	"Everett et al., 1999"	2
-"Chlamydophila pecorum"	"Chlamydia pecorum"	"Everett et al., 1999"	3
+"Chlamydophila pecorum"	"Chlamydia pecorum"	"Everett et al., 1999"	2
-"Chlamydophila pneumoniae"	"Chlamydia pneumoniae"	"Everett et al., 1999"	3
+"Chlamydophila pneumoniae"	"Chlamydia pneumoniae"	"Everett et al., 1999"	2
-"Chlamydophila psittaci"	"Chlamydia psittaci"	"Everett et al., 1999"	3
+"Chlamydophila psittaci"	"Chlamydia psittaci"	"Everett et al., 1999"	2
 "Chlamydotomus beigelii"	"Geotrichum beigelii"	"Trevis, 1879"	3
 "Chlamydozyma pulcherrima"	"Metschnikowia pulcherrima"	"Wick, 1964"	3
 "Chlamydozyma reukaufii"	"Metschnikowia reukaufii"	"Wick, 1964"	3
@@ -2599,8 +2599,8 @@
 "Chrysalogonium piramidale"	"Acostina piramidale"	"Acosta, 1940"	3
 "Chryseobacterium arothri"	"Chryseobacterium hominis"	"Campbell et al., 2008"	2
 "Chryseobacterium greenlandense"	"Chryseobacterium aquaticum greenlandense"	"Loveland-Curtze et al., 2016"	2
-"Chryseobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"Vandamme et al., 1994"	3
+"Chryseobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"Vandamme et al., 1994"	2
-"Chryseobacterium miricola"	"Elizabethkingia miricola"	"Li et al., 2004"	3
+"Chryseobacterium miricola"	"Elizabethkingia miricola"	"Li et al., 2004"	2
 "Chryseomonas"	"Pseudomonas"	"Holmes et al., 1987"	1
 "Chryseomonas luteola"	"Pseudomonas luteola"	"Holmes et al., 1987"	1
 "Chryseomonas polytricha"	"Pseudomonas luteola"	"Holmes et al., 1986"	1
@@ -3331,11 +3331,11 @@
 "Cucurbitaria urceolus"	"Nectria urceolus"	"Kuntze, 1898"	2
 "Cucurbitaria uredinicola"	"Nectria uredinicola"	"Kuntze, 1898"	2
 "Cucurbitaria verrucosa"	"Nectria verrucosa"	"Kuntze, 1898"	2
-"Culex auratus"	"Aedes auratus"	"Leicester, 1908"	3
+"Culex auratus"	"Aedes auratus"	"Leicester, 1908"	2
-"Culex sticticus"	"Aedes sticticus"	"Meigen, 1838"	3
+"Culex sticticus"	"Aedes sticticus"	"Meigen, 1838"	2
-"Culex sudanensis"	"Aedes sudanensis"	"Theobald, 1911"	3
+"Culex sudanensis"	"Aedes sudanensis"	"Theobald, 1911"	2
-"Culex sylvaticus"	"Aedes sylvaticus"	"Meigen, 1818"	3
+"Culex sylvaticus"	"Aedes sylvaticus"	"Meigen, 1818"	2
-"Culicada annulipes"	"Aedes annulipes"	"Taylor, 1914"	3
+"Culicada annulipes"	"Aedes annulipes"	"Taylor, 1914"	2
 "Cuneolina angusta"	"Textulariella angusta"	"Cushman, 1919"	3
 "Cunninghamia infundibulifera"	"Choanephora infundibulifera"	"Curr, 1873"	3
 "Cupravidus yeoncheonense"	"Cupriavidus yeoncheonensis"	"Singh et al., 2015"	2
@@ -3456,11 +3456,11 @@
 "Cytophaga diffluens"	"Persicobacter diffluens"	"Reichenbach, 1989"	3
 "Cytophaga fermentans"	"Saccharicrinis fermentans"	"Bachmann, 1955"	3
 "Cytophaga flevensis"	"Flavobacterium flevense"	"Van der Meulen et al., 1974"	2
-"Cytophaga heparina"	"Pedobacter heparinus"	"Christensen, 1980"	3
+"Cytophaga heparina"	"Pedobacter heparinus"	"Christensen, 1980"	2
 "Cytophaga johnsonae"	"Flavobacterium johnsoniae"	"Stanier, 1947"	2
 "Cytophaga latercula"	"Aquimarina latercula"	"Lewin, 1969"	3
 "Cytophaga lytica"	"Cellulophaga lytica"	"Lewin, 1969"	3
-"Cytophaga marina"	"Tenacibaculum maritimum"	"Reichenbach, 1989"	3
+"Cytophaga marina"	"Tenacibaculum maritimum"	"Reichenbach, 1989"	2
 "Cytophaga marinoflava"	"Leeuwenhoekiella marinoflava"	"Reichenbach, 1989"	3
 "Cytophaga pectinovora"	"Flavobacterium pectinovorum"	"Reichenbach, 1989"	2
 "Cytophaga psychrophila"	"Flavobacterium psychrophilum"	"Reichenbach, 1989"	2
@@ -3514,11 +3514,11 @@
 "Defluviimonas pyrenivorans"	"Acidimangrovimonas pyrenivorans"	"Zhang et al., 2018"	2
 "Dehalospirillum"	"Sulfurospirillum"	"Scholz-Muramatsu et al., 2002"	2
 "Dehalospirillum multivorans"	"Sulfurospirillum multivorans"	"Scholz-Muramatsu et al., 2002"	2
-"Deinobacter"	"Deinococcus"	"Oyaizu et al., 1987"	3
+"Deinobacter"	"Deinococcus"	"Oyaizu et al., 1987"	2
-"Deinobacter grandis"	"Deinococcus grandis"	"Oyaizu et al., 1987"	3
+"Deinobacter grandis"	"Deinococcus grandis"	"Oyaizu et al., 1987"	2
 "Deinococcus erythromyxa"	"Kocuria rosea"	"Brooks et al., 1981"	2
-"Deinococcus mumbaiensis"	"Deinococcus ficus"	"Shashidhar et al., 2006"	3
+"Deinococcus mumbaiensis"	"Deinococcus ficus"	"Shashidhar et al., 2006"	2
-"Deinococcus xibeiensis"	"Deinococcus wulumuqiensis"	"Wang et al., 2010"	3
+"Deinococcus xibeiensis"	"Deinococcus wulumuqiensis"	"Wang et al., 2010"	2
 "Dekkeromyces aestuarii"	"Kluyveromyces aestuarii"	"Kock-Krat, 1982"	3
 "Dekkeromyces delphensis"	"Nakaseomyces delphensis"	"Novak et al., 1961"	3
 "Dekkeromyces dobzhanskii"	"Kluyveromyces dobzhanskii"	"Santa Maria et al., 1970"	3
@@ -3745,7 +3745,7 @@
 "Deuterammina williamsoni"	"Lepidodeuterammina williamsoni"	"Bronnimann et al., 1988"	3
 "Devosia nitraria"	"Devosia nitrariae"	"Xu et al., 2018"	2
 "Devosia subaequoris"	"Devosia soli"	"Lee, 2007"	2
-"Dexiogonimus ciureanus"	"Metagonimus ciureanus"	"Witenberg, 1929"	3
+"Dexiogonimus ciureanus"	"Metagonimus ciureanus"	"Witenberg, 1929"	2
 "Dexiotricha centralis"	"Dexiotrichides centralis"	"Stokes, 1885"	3
 "Diacanthocapsa brevithorax"	"Theocapsomma brevithorax"	"Dumitrica, 1970"	3
 "Diachaeella bulbillosa"	"Diachea bulbillosa"	"Hohn, 1909"	3
@@ -3772,11 +3772,11 @@
 "Diaphorobacter polyhydroxybutyrativorans"	"Diaphorobacter nitroreducens"	"Qiu et al., 2015"	2
 "Diatoma anceps"	"Meridion anceps"	"Kirchn"	3
 "Diatoma hyalina"	"Fragilaria hyalina"	"Kutzing"	3
-"Dibothriocephalus archeri"	"Diphyllobothrium archeri"	"Leiper et al., 1914"	3
+"Dibothriocephalus archeri"	"Diphyllobothrium archeri"	"Leiper et al., 1914"	2
-"Dibothriocephalus hians"	"Diphyllobothrium hians"	"Luhe, 1899"	3
+"Dibothriocephalus hians"	"Diphyllobothrium hians"	"Luhe, 1899"	2
-"Dibothriocephalus lashleyi"	"Diphyllobothrium lashleyi"	"Leiper et al., 1914"	3
+"Dibothriocephalus lashleyi"	"Diphyllobothrium lashleyi"	"Leiper et al., 1914"	2
-"Dibothriocephalus pygoscelis"	"Diphyllobothrium pygoscelis"	"Rennie et al., 1912"	3
+"Dibothriocephalus pygoscelis"	"Diphyllobothrium pygoscelis"	"Rennie et al., 1912"	2
-"Dibothriocephalus schistochilus"	"Diphyllobothrium schistochilus"	"Germanos, 1895"	3
+"Dibothriocephalus schistochilus"	"Diphyllobothrium schistochilus"	"Germanos, 1895"	2
 "Dicaeoma brassicae"	"Alternaria brassicae"	"Kuntze, 1898"	2
 "Dichotomomyces cejpii"	"Aspergillus cejpii"	"Scott, 1970"	2
 "Dickeya dieffenbachiae"	"Dickeya dadantii dieffenbachiae"	"Samson et al., 2005"	1
@@ -3938,7 +3938,7 @@
 "Diplodina pedicularis"	"Leptosphaeria pedicularis"	"Lind, 1924"	2
 "Diplodinium lunula"	"Gymnodinium lunula"	"Klebs, 1912"	3
 "Diplodinium uncinata"	"Blepharocorys uncinata"	"Fiorentini, 1890"	3
-"Diplogonoporus balaenopterae"	"Diphyllobothrium balaenopterae"	"Lonnberg, 1892"	3
+"Diplogonoporus balaenopterae"	"Diphyllobothrium balaenopterae"	"Lonnberg, 1892"	2
 "Diplophrys stercorea"	"Sorodiplophrys stercorea"	"Cienk, 1876"	3
 "Diplophysa saprolegniae"	"Olpidiopsis saprolegniae"	"Schrot, 1886"	3
 "Diploplenodomus piskorzii"	"Phoma piskorzii"	"Petr, 1923"	2
@@ -4105,7 +4105,7 @@
 "Drechslera spicifera"	"Curvularia spicifera"	"Arx, 1975"	2
 "Drechslera subpapendorfii"	"Curvularia subpapendorfii"	"Mouch, 1975"	2
 "Drechslera tripogonis"	"Curvularia tripogonis"	"Patil et al., 1972"	2
-"Drepanidotaenia dusmeti"	"Hymenolepis dusmeti"	"Lopez-Neyra, 1942"	3
+"Drepanidotaenia dusmeti"	"Hymenolepis dusmeti"	"Lopez-Neyra, 1942"	2
 "Drepanomonas simulans"	"Microthorax simulans"	"Kahl, 1926"	3
 "Drulanta edenshawi"	"Parahsuum edenshawi"	"Carter, 1988"	3
 "Drulanta mostleri"	"Parahsuum mostleri"	"Yeh, 1987"	3
@@ -4174,8 +4174,8 @@
 "Eidamia viridescens"	"Trichoderma viridescens"	"Horne et al., 1923"	2
 "Eilohedra weddellensis"	"Alabaminella weddellensis"	"Earland, 1936"	3
 "Electothigma acuminatus"	"Metopus acuminatus"	"Jankowski, 1967"	3
-"Elizabethkingia anophelis endophytica"	"Elizabethkingia anophelis"	"Garcia-Lopez et al., 2020"	3
+"Elizabethkingia anophelis endophytica"	"Elizabethkingia anophelis"	"Garcia-Lopez et al., 2020"	2
-"Elizabethkingia endophytica"	"Elizabethkingia anophelis"	"Kampfer et al., 2015"	3
+"Elizabethkingia endophytica"	"Elizabethkingia anophelis"	"Kampfer et al., 2015"	2
 "Elkelangia"	"Novosphingopyxis"	"Hordt et al., 2020"	2
 "Elkelangia baekryungensis"	"Novosphingopyxis baekryungensis"	"Hordt et al., 2020"	2
 "Ellipsolagena bidens"	"Parafissurina bidens"	"Cushman, 1930"	3
@@ -4255,7 +4255,7 @@
 "Emericella spectabilis"	"Aspergillus spectabilis"	"Chr, 1978"	2
 "Emericella unguis"	"Aspergillus unguis"	"Malloch et al., 1972"	2
 "Emmonsia crescens"	"Ajellomyces crescens"	"Emmons et al., 1960"	3
-"Empedobacter falsenii"	"Wautersiella falsenii"	"Zhang et al., 2014"	3
+"Empedobacter falsenii"	"Wautersiella falsenii"	"Zhang et al., 2014"	2
 "Enantiocristellaria navicula"	"Saracenaria navicula"	"DOrbigny, 1840"	3
 "Encephalitozoon cuniculi"	"Nosema cuniculi"	"Levaditi et al., 1923"	3
 "Encephalitozoon ixodis"	"Unikaryon ixodis"	"Weiser et al., 1975"	3
@@ -4341,7 +4341,7 @@
 "Enteridium splendens"	"Reticularia splendens"	"TMacbr, 1899"	3
 "Enterobacter aerogenes"	"Klebsiella aerogenes"	"Hormaeche et al., 1960"	1
 "Enterobacter agglomerans"	"Pantoea agglomerans"	"Ewing et al., 1972"	1
-"Enterobacter amnigenus"	"Lelliottia amnigena"	"Izard et al., 1981"	1
+"Enterobacter amnigenus"	"Lelliottia amnigena"	"Izard et al., 1981"	2
 "Enterobacter arachidis"	"Kosakonia arachidis"	"Madhaiyan et al., 2010"	1
 "Enterobacter cowanii"	"Kosakonia cowanii"	"Inoue et al., 2001"	1
 "Enterobacter dissolvens"	"Enterobacter cloacae dissolvens"	"Brenner et al., 1988"	1
@@ -4352,7 +4352,7 @@
 "Enterobacter massiliensis"	"Metakosakonia massiliensis"	"Lagier et al., 2014"	
 "Enterobacter massiliensis"	"Phytobacter massiliensis"	"Lagier et al., 2014"	1
 "Enterobacter muelleri"	"Enterobacter asburiae"	"Kampfer et al., 2015"	1
-"Enterobacter nimipressuralis"	"Lelliottia nimipressuralis"	"Brenner et al., 1988"	1
+"Enterobacter nimipressuralis"	"Lelliottia nimipressuralis"	"Brenner et al., 1988"	2
 "Enterobacter oligotrophica"	"Enterobacter oligotrophicus"	"Akita et al., 2020"	1
 "Enterobacter oryzae"	"Kosakonia oryzae"	"Peng et al., 2009"	1
 "Enterobacter oryzendophyticus"	"Kosakonia oryzendophytica"	"Hardoim et al., 2015"	1
@@ -4527,7 +4527,7 @@
 "Erwinia herbicola"	"Pantoea agglomerans"	"Dye, 1964"	1
 "Erwinia milletiae"	"Pantoea agglomerans"	"Magrou, 1937"	1
 "Erwinia nigrifluens"	"Brenneria nigrifluens"	"Wilson et al., 1957"	1
-"Erwinia nimipressuralis"	"Lelliottia nimipressuralis"	"Dye, 1969"	1
+"Erwinia nimipressuralis"	"Lelliottia nimipressuralis"	"Dye, 1969"	2
 "Erwinia paradisiaca"	"Dickeya paradisiaca"	"Fernandez-Borrero et al., 1970"	1
 "Erwinia persicinus"	"Erwinia persicina"	"Hao et al., 1990"	1
 "Erwinia quercina"	"Lonsdalea quercina"	"Hildebrand et al., 1967"	1
@@ -4844,33 +4844,33 @@
 "Flaviramulus ichthyoenteri"	"Wocania ichthyoenteri"	"Zhang et al., 2013"	3
 "Flavirhabdus"	"Lacinutrix"	"Shakeela et al., 2015"	3
 "Flavirhabdus iliipiscaria"	"Lacinutrix iliipiscaria"	"Shakeela et al., 2015"	3
-"Flavobacterium anatoliense"	"Myroides anatoliensis"	"Kacagan et al., 2013"	3
+"Flavobacterium anatoliense"	"Myroides anatoliensis"	"Kacagan et al., 2013"	2
 "Flavobacterium balustinum"	"Chryseobacterium balustinum"	"Harrison, 1929"	2
 "Flavobacterium bomensis"	"Flavobacterium bomense"	"Liu et al., 2019"	2
 "Flavobacterium branchiophila"	"Flavobacterium branchiophilum"	"Wakabayashi et al., 1989"	2
-"Flavobacterium breve"	"Empedobacter brevis"	"Holmes et al., 1982"	3
+"Flavobacterium breve"	"Empedobacter brevis"	"Holmes et al., 1982"	2
 "Flavobacterium capsulatum"	"Novosphingobium capsulatum"	"Leifson, 1962"	2
-"Flavobacterium ceti"	"Myroides ceti"	"Vela et al., 2013"	3
+"Flavobacterium ceti"	"Myroides ceti"	"Vela et al., 2013"	2
-"Flavobacterium cloacae"	"Myroides cloacae"	"Liu et al., 2017"	3
+"Flavobacterium cloacae"	"Myroides cloacae"	"Liu et al., 2017"	2
 "Flavobacterium daemonensis"	"Flavobacterium daemonense"	"Ngo et al., 2015"	2
 "Flavobacterium esteraromaticum"	"Microbacterium esteraromaticum"	"Bergey et al., 1930"	2
-"Flavobacterium ferrugineum"	"Terrimonas ferruginea"	"Sickles et al., 1934"	3
+"Flavobacterium ferrugineum"	"Terrimonas ferruginea"	"Sickles et al., 1934"	2
 "Flavobacterium gleum"	"Chryseobacterium gleum"	"Holmes et al., 1984"	2
 "Flavobacterium gondwanense"	"Psychroflexus gondwanensis"	"Dobson et al., 1993"	3
 "Flavobacterium halmephilium"	"Halomonas halmophila"	"Elazari-Volcani, 1940"	1
 "Flavobacterium halmophilum"	"Halomonas halmophila"	"Corrig Elazari-Volcani, 1940"	1
-"Flavobacterium heparinum"	"Pedobacter heparinus"	"Payza et al., 1956"	3
+"Flavobacterium heparinum"	"Pedobacter heparinus"	"Payza et al., 1956"	2
 "Flavobacterium indologenes"	"Chryseobacterium indologenes"	"Yabuuchi et al., 1983"	2
 "Flavobacterium indoltheticum"	"Chryseobacterium indoltheticum"	"Campbell et al., 1951"	2
 "Flavobacterium jejuensis"	"Flavobacterium jejuense"	"Park et al., 2016"	2
 "Flavobacterium johnsonae"	"Flavobacterium johnsoniae"	"Bernardet et al., 1996"	2
 "Flavobacterium kyungheensis"	"Flavobacterium kyungheense"	"Son et al., 2014"	2
 "Flavobacterium marinotypicum"	"Microbacterium maritypicum"	"ZoBell et al., 1944"	2
-"Flavobacterium marinum"	"Myroides aquimaris"	"Song et al., 2013"	3
+"Flavobacterium marinum"	"Myroides aquimaris"	"Song et al., 2013"	2
-"Flavobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"King, 1959"	3
+"Flavobacterium meningosepticum"	"Elizabethkingia meningoseptica"	"King, 1959"	2
-"Flavobacterium mizutaii"	"Sphingobacterium mizutaii"	"Holmes et al., 1988"	3
+"Flavobacterium mizutaii"	"Sphingobacterium mizutaii"	"Holmes et al., 1988"	2
-"Flavobacterium multivorum"	"Sphingobacterium multivorum"	"Holmes et al., 1981"	3
+"Flavobacterium multivorum"	"Sphingobacterium multivorum"	"Holmes et al., 1981"	2
-"Flavobacterium odoratum"	"Myroides odoratus"	"Stutzer, 1929"	3
+"Flavobacterium odoratum"	"Myroides odoratus"	"Stutzer, 1929"	2
 "Flavobacterium okeanokoites"	"Planomicrobium okeanokoites"	"ZoBell et al., 1944"	
 "Flavobacterium okeanokoites"	"Planococcus okeanokoites"	"ZoBell et al., 1944"	2
 "Flavobacterium qiangtangensis"	"Flavobacterium qiangtangense"	"Huang et al., 2015"	2
@@ -4878,12 +4878,12 @@
 "Flavobacterium salegens"	"Salegentibacter salegens"	"Dobson et al., 1993"	3
 "Flavobacterium scophthalmum"	"Chryseobacterium scophthalmum"	"Mudarris et al., 1994"	2
 "Flavobacterium spartansii"	"Flavobacterium tructae"	"Loch et al., 2019"	2
-"Flavobacterium spiritivorum"	"Sphingobacterium spiritivorum"	"Holmes et al., 1982"	3
+"Flavobacterium spiritivorum"	"Sphingobacterium spiritivorum"	"Holmes et al., 1982"	2
 "Flavobacterium tangerina"	"Flavobacterium tangerinum"	"Li et al., 2020"	2
-"Flavobacterium thalpophilum"	"Sphingobacterium thalpophilum"	"Holmes et al., 1983"	3
+"Flavobacterium thalpophilum"	"Sphingobacterium thalpophilum"	"Holmes et al., 1983"	2
 "Flavobacterium uliginosum"	"Zobellia uliginosa"	"ZoBell et al., 1944"	3
 "Flavobacterium viscosus"	"Flavobacterium viscosum"	"Li et al., 2020"	2
-"Flavobacterium yabuuchiae"	"Sphingobacterium spiritivorum"	"Holmes et al., 1988"	3
+"Flavobacterium yabuuchiae"	"Sphingobacterium spiritivorum"	"Holmes et al., 1988"	2
 "Flavobacterium zhairuonensis"	"Flavobacterium zhairuonense"	"Debnath et al., 2020"	2
 "Flectobacillus glomeratus"	"Polaribacter glomeratus"	"McGuire et al., 1988"	3
 "Flectobacillus marinus"	"Cyclobacterium marinum"	"Borrall et al., 1978"	3
@@ -4895,8 +4895,8 @@
 "Flexibacter filiformis"	"Chitinophaga filiformis"	"Reichenbach, 1989"	3
 "Flexibacter japonensis"	"Chitinophaga japonensis"	"Fujita et al., 1997"	3
 "Flexibacter litoralis"	"Bernardetia litoralis"	"Lewin, 1969"	3
-"Flexibacter maritimus"	"Tenacibaculum maritimum"	"Wakabayashi et al., 1989"	3
+"Flexibacter maritimus"	"Tenacibaculum maritimum"	"Wakabayashi et al., 1989"	2
-"Flexibacter ovolyticus"	"Tenacibaculum ovolyticum"	"Hansen et al., 1992"	3
+"Flexibacter ovolyticus"	"Tenacibaculum ovolyticum"	"Hansen et al., 1992"	2
 "Flexibacter polymorphus"	"Garritya polymorpha"	"Lewin, 1974"	3
 "Flexibacter psychrophilus"	"Flavobacterium psychrophilum"	"Bernardet et al., 1989"	2
 "Flexibacter roseolus"	"Hugenholtzia roseola"	"Lewin et al., 2016"	3
@@ -5338,7 +5338,7 @@
 "Gordonia rubropertinctus"	"Gordonia rubripertincta"	"Stackebrandt et al., 1989"	2
 "Gordonibacter faecihominis"	"Gordonibacter urolithinfaciens"	"Jin et al., 2015"	2
 "Gottfriedia acidiceler"	"Gottfriedia acidiceleris"	"Gupta et al., 2020"	2
-"Grabhamia australis"	"Aedes australis"	"Strickland, 1911"	3
+"Grabhamia australis"	"Aedes australis"	"Strickland, 1911"	2
 "Grahamella"	"Bartonella"	"Ristic et al., 1984"	2
 "Grahamella peromysci"	"Bartonella peromysci"	"Ristic et al., 1984"	2
 "Grahamella talpae"	"Bartonella talpae"	"Ristic et al., 1984"	2
@@ -5486,20 +5486,20 @@
 "Haloarcobacter ebronensis"	"Halarcobacter ebronensis"	"Perez-Cataluna et al., 2019"	
 "Haloarcobacter ebronensis"	"Arcobacter ebronensis"	"Perez-Cataluna et al., 2019"	2
 "Haloarcula mukohataei"	"Halomicrobium mukohataei"	"Ihara et al., 1997"	3
-"Halobacterium cutirubrum"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium cutirubrum"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium denitrificans"	"Haloferax denitrificans"	"Tomlinson et al., 1986"	3
 "Halobacterium distributum"	"Halorubrum distributum"	"Zvyagintseva et al., 1989"	3
 "Halobacterium distributus"	"Halorubrum distributum"	"Zvyagintseva et al., 1989"	3
-"Halobacterium halobium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium halobium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium lacusprofundi"	"Halorubrum lacusprofundi"	"Franzmann et al., 1989"	3
 "Halobacterium mediterranei"	"Haloferax mediterranei"	"Rodriguez-Valera et al., 1983"	3
 "Halobacterium pharaonis"	"Natronomonas pharaonis"	"Soliman et al., 1983"	3
-"Halobacterium piscisalsi"	"Halobacterium salinarum"	"Yachai et al., 2008"	3
+"Halobacterium piscisalsi"	"Halobacterium salinarum"	"Yachai et al., 2008"	2
 "Halobacterium saccharovorum"	"Halorubrum saccharovorum"	"Tomlinson et al., 1977"	3
-"Halobacterium salinarium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	3
+"Halobacterium salinarium"	"Halobacterium salinarum"	"Elazari-Volcani, 1957"	2
 "Halobacterium sodomense"	"Halorubrum sodomense"	"Oren, 1983"	3
 "Halobacterium trapanicum"	"Halorubrum trapanicum"	"Elazari-Volcani, 1957"	3
-"Halobacterium vallismortis"	"Haloarcula vallismortis"	"Gonzalez et al., 1979"	3
+"Halobacterium vallismortis"	"Haloarcula vallismortis"	"Gonzalez et al., 1979"	2
 "Halobacterium volcanii"	"Haloferax volcanii"	"Mullakhanbhai et al., 1975"	3
 "Halobacteroides acetoethylicus"	"Halanaerobium acetethylicum"	"Rengpipat et al., 1989"	2
 "Halobacteroides lacunaris"	"Halanaerobacter lacunarum"	"Zhilina et al., 1992"	2
@@ -5780,7 +5780,7 @@
 "Hendersonia pinicola"	"Hendersonula pinicola"	"Trotter, 1972"	2
 "Hendersonia symploci"	"Hendersonula symploci"	"Berk et al., 1873"	2
 "Hennebertia ovalis"	"Wardomyces ovalis"	"Morelet, 1969"	3
-"Hepatiarius longissimus"	"Opisthorchis longissimus"	"Feizullaev, 1961"	3
+"Hepatiarius longissimus"	"Opisthorchis longissimus"	"Feizullaev, 1961"	2
 "Heptameria acuta"	"Leptosphaeria acuta"	"Cooke, 1889"	2
 "Heptameria albopunctata"	"Leptosphaeria albopunctata"	"Cooke, 1889"	2
 "Heptameria artemisiae"	"Leptosphaeria artemisiae"	"Cooke, 1889"	2
@@ -5853,7 +5853,7 @@
 "Heteroconium chaetospira"	"Cladophialophora chaetospira"	"Ellis, 1976"	2
 "Heterolepa haidingeri"	"Cibicides haidingeri"	"DOrbigny, 1846"	3
 "Heteropatellina frustratiformis"	"Ungulatelloides frustratiformis"	"McCulloch, 1977"	3
-"Heterophyes yokogawai"	"Metagonimus yokogawai"	"Katsurada, 1912"	3
+"Heterophyes yokogawai"	"Metagonimus yokogawai"	"Katsurada, 1912"	2
 "Heterospiroloculina bikiniensis"	"Inaequalina bikiniensis"	"McCulloch, 1977"	3
 "Heterospiroloculina culebraensis"	"Inaequalina culebraensis"	"McCulloch, 1977"	3
 "Heterosporium algarum"	"Cladosporium algarum"	"Cooke et al., 1890"	2
@@ -5972,8 +5972,8 @@
 "Huaishuia"	"Celeribacter"	"Wang et al., 2012"	2
 "Huaishuia halophila"	"Celeribacter halophilus"	"Wang et al., 2012"	2
 "Hughesiella euricoi"	"Ceratocystis euricoi"	"Bat et al., 1956"	3
-"Hulecoeteomyia fluviatilis"	"Aedes fluviatilis"	"Leicester, 1908"	3
+"Hulecoeteomyia fluviatilis"	"Aedes fluviatilis"	"Leicester, 1908"	2
-"Hulecoeteomyia milsoni"	"Aedes milsoni"	"Taylor, 1916"	3
+"Hulecoeteomyia milsoni"	"Aedes milsoni"	"Taylor, 1916"	2
 "Humicoccus"	"Nakamurella"	"Yoon et al., 2007"	2
 "Humicoccus flavidus"	"Nakamurella flavida"	"Yoon et al., 2007"	2
 "Humicola minima"	"Ochroconis minima"	"Fassat, 1967"	2
@@ -6942,7 +6942,7 @@
 "Leifsonia pindariensis"	"Microterricola pindariensis"	"Reddy et al., 2008"	2
 "Leiotrocha serpularum"	"Cyclochaeta serpularum"	"Fabre-Domergue, 1888"	3
 "Leisingera nanhaiensis"	"Sedimentitalea nanhaiensis"	"Sun et al., 2014"	2
-"Lelliottia aquatilis"	"Lelliottia jeotgali"	"Kampfer et al., 2018"	1
+"Lelliottia aquatilis"	"Lelliottia jeotgali"	"Kampfer et al., 2018"	2
 "Lembus armatus"	"Philasterides armatus"	"Kahl, 1926"	3
 "Lembus kenti"	"Cohnilembus kenti"	"Kahl, 1931"	3
 "Lembus pusillus"	"Pseudocohnilembus pusillus"	"Quennerstedt, 1869"	3
@@ -7208,7 +7208,7 @@
 "Lonsdalea quercina iberica"	"Lonsdalea iberica"	"Brady et al., 2012"	1
 "Lonsdalea quercina populi"	"Lonsdalea populi"	"Toth et al., 2013"	1
 "Lonsdalea quercina quercina"	"Lonsdalea quercina"	"Brady et al., 2012"	1
-"Loossia dobrogiensis"	"Metagonimus dobrogiensis"	"Ciurea, 1915"	3
+"Loossia dobrogiensis"	"Metagonimus dobrogiensis"	"Ciurea, 1915"	2
 "Lophocorys neatum"	"Lophocyrtis neatum"	"Sanfilippo, 1990"	3
 "Lophophyton gallinae"	"Microsporum gallinae"	"Matr et al., 1899"	3
 "Loxocephalus colpidiopsis"	"Dexiotricha colpidiopsis"	"Kahl, 1926"	3
@@ -7490,7 +7490,7 @@
 "Mesoflavibacter sabulilitoris"	"Mesoflavibacter zeaxanthinifaciens sabulilitoris"	"Park et al., 2014"	3
 "Mesomycoplasma molaris"	"Mesomycoplasma molare"	"Gupta et al., 2018"	3
 "Mesonia maritimus"	"Mesonia maritima"	"Sung et al., 2017"	3
-"Mesoplasma pleciae"	"Acholeplasma pleciae"	"Tully et al., 1994"	3
+"Mesoplasma pleciae"	"Acholeplasma pleciae"	"Tully et al., 1994"	2
 "Metacarinina charlesensis"	"Laticarinina charlesensis"	"McCulloch, 1977"	3
 "Metacarinina chathamensis"	"Laticarinina chathamensis"	"McCulloch, 1977"	3
 "Metacarinina hoodensis"	"Laticarinina hoodensis"	"McCulloch, 1977"	3
@@ -7882,7 +7882,7 @@
 "Monosporium sclerotiale"	"Scedosporium sclerotiale"	"Pepere, 1914"	3
 "Monosporium sepedonioides"	"Chrysosporium sepedonioides"	"Harz, 1872"	3
 "Moorella thermoautotrophica"	"Moorella thermoacetica"	"Collins et al., 1994"	2
-"Moraxella anatipestifer"	"Riemerella anatipestifer"	"Bruner et al., 1954"	3
+"Moraxella anatipestifer"	"Riemerella anatipestifer"	"Bruner et al., 1954"	2
 "Moraxella phenylpyruvica"	"Psychrobacter phenylpyruvicus"	"Bovre et al., 1967"	1
 "Moraxella urethralis"	"Oligella urethralis"	"Lautrop et al., 1970"	2
 "Morella entamoebae"	"Sphaerita entamoebae"	"Perez Reyes, 1964"	3
@@ -7898,7 +7898,7 @@
 "Mrazekia niphargi"	"Microsporidium niphargi"	"Poisson, 1924"	3
 "Mrazekia piscicola"	"Jirovecia piscicola"	"Cepede, 1924"	3
 "Mrazekia tetraspora"	"Scipionospora tetraspora"	"Leger et al., 1922"	3
-"Mucidus africanus"	"Aedes africanus"	"Theobald, 1901"	3
+"Mucidus africanus"	"Aedes africanus"	"Theobald, 1901"	2
 "Mucor angarensis"	"Circinella angarensis"	"Schostak, 1897"	3
 "Mucor arrhizus"	"Rhizopus arrhizus"	"Hagem, 1908"	2
 "Mucor assamensis"	"Hyphomucor assamensis"	"Mehrotra et al., 1970"	3
@@ -7926,7 +7926,7 @@
 "Muricauda antarctica"	"Muricauda taeanensis"	"Wu et al., 2013"	3
 "Muricauda lutea"	"Croceivirga lutea"	"Wang et al., 2017"	3
 "Muriicola lacisalsi"	"Maritimibacter lacisalsi"	"Wang et al., 2021"	2
-"Musca azurea"	"Lucilia azurea"	"Doleschall, 1858"	3
+"Musca azurea"	"Lucilia azurea"	"Doleschall, 1858"	2
 "Mya nitens"	"Ervilia nitens"	"Montagu, 1808"	3
 "Myceloblastanon albicans"	"Candida albicans"	"Ota, 1927"	2
 "Myceloblastanon guilliermondii"	"Meyerozyma guilliermondii"	"Ota, 1927"	3
@@ -8221,7 +8221,7 @@
 "Mycterotrix ovata"	"Maryna ovata"	"Gelei, 1950"	3
 "Myllocercion rhodanon"	"Schadelfusslerus rhodanon"	"Foreman, 1968"	3
 "Myrionecta rubrum"	"Mesodinium rubrum"	"Jankowski, 1976"	3
-"Myroides xuanwuensis"	"Myroides odoratimimus xuanwuensis"	"Zhang et al., 2014"	3
+"Myroides xuanwuensis"	"Myroides odoratimimus xuanwuensis"	"Zhang et al., 2014"	2
 "Myxococcus coralloides"	"Corallococcus coralloides"	"Thaxter, 1892"	2
 "Myxococcus disciformis"	"Archangium disciforme"	"Thaxter, 1904"	2
 "Myxococcus flavescens"	"Myxococcus virescens"	"Yamanaka et al., 1990"	2
@@ -8231,8 +8231,8 @@
 "Myxotrichum johnstonii"	"Gymnoascus johnstonii"	"Massee et al., 1902"	3
 "Myzocytium humicola"	"Myzocytiopsis humicola"	"Barron et al., 1975"	3
 "Myzocytium vermicola"	"Myzocytiopsis vermicola"	"Fisch, 1892"	3
-"Myzorhynchus minutus"	"Anopheles minutus"	"Theobald, 1903"	3
+"Myzorhynchus minutus"	"Anopheles minutus"	"Theobald, 1903"	2
-"Myzorhynchus pallidus"	"Anopheles pallidus"	"Swellengrebel, 1919"	3
+"Myzorhynchus pallidus"	"Anopheles pallidus"	"Swellengrebel, 1919"	2
 "Mzabimyces"	"Halopolyspora"	"Saker et al., 2015"	2
 "Mzabimyces algeriensis"	"Halopolyspora algeriensis"	"Saker et al., 2015"	2
 "Naematelia aurantia"	"Tremella aurantia"	"Burt, 1921"	3
@@ -9265,8 +9265,8 @@
 "Orcadella operculata"	"Licea operculata"	"Wingate, 1889"	3
 "Orcadella parasitica"	"Licea parasitica"	"Hagelst, 1942"	3
 "Orcadella pusilla"	"Licea pusilla"	"Hagelst, 1942"	3
-"Oribaculum"	"Porphyromonas"	"Moore et al., 1994"	3
+"Oribaculum"	"Porphyromonas"	"Moore et al., 1994"	2
-"Oribaculum catoniae"	"Porphyromonas catoniae"	"Moore et al., 1994"	3
+"Oribaculum catoniae"	"Porphyromonas catoniae"	"Moore et al., 1994"	2
 "Ornatispora frondicola"	"Stachybotrys frondicola"	"Hyde et al., 1999"	2
 "Ornatispora gamsii"	"Stachybotrys gamsii"	"Hyde et al., 1999"	2
 "Ornatispora nepalensis"	"Stachybotrys nepalensis"	"Whitton et al., 2012"	2
@@ -9602,7 +9602,7 @@
 "Pedobacter huanghensis"	"Daejeonella huanghensis"	"Qiu et al., 2014"	3
 "Pedobacter luteus"	"Daejeonella lutea"	"Oh et al., 2013"	3
 "Pedobacter oryzae"	"Daejeonella oryzae"	"Jeon et al., 2009"	3
-"Pedobacter piscium"	"Pedobacter antarcticus"	"Steyn et al., 2014"	3
+"Pedobacter piscium"	"Pedobacter antarcticus"	"Steyn et al., 2014"	2
 "Pedobacter ruber"	"Daejeonella rubra"	"Margesin et al., 2013"	3
 "Pedobacter saltans"	"Pseudopedobacter saltans"	"Steyn et al., 1998"	3
 "Pedobacter tournemirensis"	"Arcticibacter tournemirensis"	"Urios et al., 2013"	3
@@ -9828,7 +9828,7 @@
 "Petersenia andreei"	"Sirolpidium andreei"	"Sparrow, 1936"	3
 "Petersenia catenophlyctidis"	"Cornumyces catenophlyctidis"	"Sundaram, 1968"	3
 "Petersenia irregularis"	"Cornumyces irregularis"	"Sparrow, 1943"	3
-"Petraeus vignei"	"Giardia vignei"	"Rochebrune, 1882"	3
+"Petraeus vignei"	"Giardia vignei"	"Rochebrune, 1882"	2
 "Petriella boulangeri"	"Microascus boulangeri"	"Curzi, 1930"	3
 "Petriellidium boydii"	"Pseudallescheria boydii"	"Malloch, 1970"	2
 "Petriellidium desertorum"	"Scedosporium desertorum"	"Arx et al., 1973"	3
@@ -9850,8 +9850,8 @@
 "Phacellium geranii"	"Graphium geranii"	"Braun, 1993"	3
 "Phacellium ligulariae"	"Graphium ligulariae"	"Braun, 1993"	3
 "Phacellium trifolii"	"Graphium trifolii"	"Braun, 1993"	3
-"Phaenicia azurea"	"Lucilia azurea"	"Robineau-Desvoidy, 1863"	3
+"Phaenicia azurea"	"Lucilia azurea"	"Robineau-Desvoidy, 1863"	2
-"Phaenicia pallescens"	"Lucilia pallescens"	"Shannon, 1924"	3
+"Phaenicia pallescens"	"Lucilia pallescens"	"Shannon, 1924"	2
 "Phaenicosphaera mammilla"	"Hegleria mammilla"	"Sheng et al., 1985"	3
 "Phaeobacter aquaemixtae"	"Leisingera aquaemixtae"	"Park et al., 2014"	2
 "Phaeobacter arcticus"	"Pseudophaeobacter arcticus"	"Zhang et al., 2008"	2
@@ -9895,7 +9895,7 @@
 "Phloeophthora syringae"	"Phytophthora syringae"	"Kleb, 1906"	3
 "Phloeospora trifolii"	"Leptosphaeria trifolii"	"Cavara, 1878"	2
 "Phlyctospora persoonii"	"Elaphomyces persoonii"	"Corda, 1854"	3
-"Phocaeicola chinchillae"	"Phocaeicola sartorii"	"Garcia-Lopez et al., 2020"	3
+"Phocaeicola chinchillae"	"Phocaeicola sartorii"	"Garcia-Lopez et al., 2020"	2
 "Phoma acuta"	"Leptosphaeria acuta"	"Fuckel, 1870"	2
 "Phoma errabunda"	"Leptosphaeria errabunda"	"Desm, 1849"	2
 "Phoma macrocapsa"	"Leptosphaeria macrocapsa"	"Trail, 1886"	2
@@ -10127,7 +10127,7 @@
 "Plagiotricha camelus"	"Trichoda camelus"	"Bory, 1824"	3
 "Plagiotricha sinuata"	"Trichoda sinuata"	"Bory, 1824"	3
 "Plagiotricha succisa"	"Psilotricha succisa"	"Bory, 1824"	3
-"Planaria punctata"	"Fasciola punctata"	"Muller, 1776"	3
+"Planaria punctata"	"Fasciola punctata"	"Muller, 1776"	2
 "Planctomyces brasiliensis"	"Rubinisphaera brasiliensis"	"Schlesner, 1990"	3
 "Planctomyces limnophilus"	"Planctopirus limnophila"	"Hirsch et al., 1986"	3
 "Planctomyces maris"	"Gimesia maris"	"Bauld et al., 1980"	3
@@ -10432,8 +10432,8 @@
 "Porphyrobacter mercurialis"	"Croceibacterium mercuriale"	"Coil et al., 2016"	2
 "Porphyrobacter neustonensis"	"Erythrobacter neustonensis"	"Fuerst et al., 2020"	2
 "Porphyrobacter sanguineus"	"Erythrobacter sanguineus"	"Hiraishi et al., 2002"	2
-"Porphyromonas cansulci"	"Porphyromonas crevioricanis"	"Collins et al., 1994"	3
+"Porphyromonas cansulci"	"Porphyromonas crevioricanis"	"Collins et al., 1994"	2
-"Porphyromonas salivosa"	"Porphyromonas macacae"	"Love et al., 1992"	3
+"Porphyromonas salivosa"	"Porphyromonas macacae"	"Love et al., 1992"	2
 "Posadasia esteriformis"	"Coccidioides esteriformis"	"Canton, 1898"	3
 "Poseidonibacter lekithochrous"	"Arcobacter lekithochrous"	"Perez-Cataluna et al., 2019"	2
 "Pottsiocles hannae"	"Manuelophrya hannae"	"Guhl, 1985"	3
@@ -10450,7 +10450,7 @@
 "Prauserella flava"	"Prauserella salsuginis"	"Li et al., 2009"	2
 "Prevotella oulora"	"Prevotella oulorum"	"Shah et al., 1990"	2
 "Prevotella ruminicola brevis"	"Prevotella brevis"	"Shah et al., 1990"	2
-"Prevotella tannerae"	"Alloprevotella tannerae"	"Moore et al., 1994"	3
+"Prevotella tannerae"	"Alloprevotella tannerae"	"Moore et al., 1994"	2
 "Prevotella zoogleoformans"	"Capsularis zoogleoformans"	"Shah et al., 1994"	3
 "Primorskyibacter insulae"	"Pseudoprimorskyibacter insulae"	"Park et al., 2015"	2
 "Procandida albicans"	"Candida albicans"	"Novak et al., 1961"	2
@@ -11111,7 +11111,7 @@
 "Rectocibicidella robertsi"	"Dyocibicides robertsi"	"McLean, 1956"	3
 "Rectoglandulina rotundata"	"Pseudonodosaria rotundata"	"Reuss, 1850"	3
 "Recurvoides trochamminiformis"	"Recurvoidatus trochamminiformis"	"Saidova, 1961"	3
-"Reedomyia sudanensis"	"Aedes sudanensis"	"Theobald, 1913"	3
+"Reedomyia sudanensis"	"Aedes sudanensis"	"Theobald, 1913"	2
 "Reichenbachia"	"Reichenbachiella"	"Nedashkovskaya et al., 2003"	3
 "Reichenbachia agariperforans"	"Reichenbachiella agariperforans"	"Nedashkovskaya et al., 2003"	3
 "Remaneica gonzalezi"	"Remaneicella gonzalezi"	"Seiglie, 1964"	3
@@ -11462,7 +11462,7 @@
 "Rotalina truncatulinoides"	"Globorotalia truncatulinoides"	"DOrbigny, 1839"	3
 "Rotamorphina minuta"	"Valvulineria minuta"	"Schubert, 1904"	3
 "Rothia dentocariosus"	"Rothia dentocariosa"	"Georg et al., 1967"	2
-"Roubaudiella caerulea"	"Lucilia caerulea"	"Seguy, 1925"	3
+"Roubaudiella caerulea"	"Lucilia caerulea"	"Seguy, 1925"	2
 "Rozella itersoniliae"	"Pleotrachelus itersoniliae"	"Barr et al., 1980"	3
 "Rozella septigena"	"Rozellopsis septigena"	"Cornu, 1872"	3
 "Rozella simulans"	"Rozellopsis simulans"	"Fisch, 1882"	3
@@ -11790,16 +11790,16 @@
 "Septotrochammina gonzalezi"	"Remaneicella gonzalezi"	"Seiglie, 1964"	3
 "Serpens"	"Pseudomonas"	"Hespell, 1977"	1
 "Serpens flexibilis"	"Pseudomonas flexibilis"	"Hespell, 1977"	1
-"Serpula"	"Brachyspira"	"Stanton et al., 1991"	3
+"Serpula"	"Brachyspira"	"Stanton et al., 1991"	2
-"Serpula hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1991"	3
+"Serpula hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1991"	2
-"Serpula innocens"	"Brachyspira innocens"	"Stanton et al., 1991"	3
+"Serpula innocens"	"Brachyspira innocens"	"Stanton et al., 1991"	2
-"Serpulina"	"Brachyspira"	"Stanton, 1992"	3
+"Serpulina"	"Brachyspira"	"Stanton, 1992"	2
-"Serpulina alvinipulli"	"Brachyspira alvinipulli"	"Stanton et al., 1998"	3
+"Serpulina alvinipulli"	"Brachyspira alvinipulli"	"Stanton et al., 1998"	2
-"Serpulina hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1992"	3
+"Serpulina hyodysenteriae"	"Brachyspira hyodysenteriae"	"Stanton et al., 1992"	2
-"Serpulina innocens"	"Brachyspira innocens"	"Stanton et al., 1992"	3
+"Serpulina innocens"	"Brachyspira innocens"	"Stanton et al., 1992"	2
-"Serpulina intermedia"	"Brachyspira intermedia"	"Stanton et al., 1997"	3
+"Serpulina intermedia"	"Brachyspira intermedia"	"Stanton et al., 1997"	2
-"Serpulina murdochii"	"Brachyspira murdochii"	"Stanton et al., 1997"	3
+"Serpulina murdochii"	"Brachyspira murdochii"	"Stanton et al., 1997"	2
-"Serpulina pilosicoli"	"Brachyspira pilosicoli"	"Trott et al., 1996"	3
+"Serpulina pilosicoli"	"Brachyspira pilosicoli"	"Trott et al., 1996"	2
 "Serratia glossinae"	"Serratia fonticola"	"Geiger et al., 2010"	1
 "Serratia marcescens sakuensis"	"Serratia marcescens"	"Ajithkumar et al., 2003"	1
 "Serratia marinorubra"	"Serratia rubidaea"	"ZoBell et al., 1944"	1
@@ -12111,12 +12111,12 @@
 "Sphaerulina amicta"	"Appendichordella amicta"	"Kohlm, 1962"	3
 "Sphaerulina tanaceti"	"Leptosphaeria tanaceti"	"Shoemaker, 1976"	2
 "Sphinctocystis elliptica"	"Cymatopleura elliptica"	"Kuntze"	3
-"Sphingobacterium antarcticum"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	3
+"Sphingobacterium antarcticum"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	2
-"Sphingobacterium antarcticus"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	3
+"Sphingobacterium antarcticus"	"Pedobacter antarcticus"	"Shivaji et al., 1992"	2
-"Sphingobacterium heparinum"	"Pedobacter heparinus"	"Takeuchi et al., 1993"	3
+"Sphingobacterium heparinum"	"Pedobacter heparinus"	"Takeuchi et al., 1993"	2
-"Sphingobacterium mizutae"	"Sphingobacterium mizutaii"	"Yabuuchi et al., 1983"	3
+"Sphingobacterium mizutae"	"Sphingobacterium mizutaii"	"Yabuuchi et al., 1983"	2
-"Sphingobacterium pakistanensis"	"Sphingobacterium pakistanense"	"Ahmed et al., 2015"	3
+"Sphingobacterium pakistanensis"	"Sphingobacterium pakistanense"	"Ahmed et al., 2015"	2
-"Sphingobacterium piscium"	"Pedobacter antarcticus"	"Takeuchi et al., 1993"	3
+"Sphingobacterium piscium"	"Pedobacter antarcticus"	"Takeuchi et al., 1993"	2
 "Sphingobium algicola"	"Sphingobium limneticum"	"Lee et al., 2017"	2
 "Sphingobium barthaii"	"Sphingobium fuliginis"	"Maeda et al., 2015"	2
 "Sphingobium chinhatense"	"Sphingobium indicum"	"Dadhwal et al., 2020"	2
@@ -12415,7 +12415,7 @@
 "Staurosphaera pusilla"	"Stigmosphaerostylus pusilla"	"Hinde, 1899"	3
 "Staurosphaera sedecimporata"	"Emiluvia sedecimporata"	"Rust, 1885"	3
 "Staurosphaera trispinosa"	"Staurolonche trispinosa"	"Kozur et al., 1979"	3
-"Stegomyia wellmanii"	"Aedes wellmanii"	"Theobald, 1910"	3
+"Stegomyia wellmanii"	"Aedes wellmanii"	"Theobald, 1910"	2
 "Steinia balladynula"	"Oxytricha balladynula"	"Kahl, 1932"	3
 "Steinia candens"	"Cyrtohymena candens"	"Kahl, 1932"	3
 "Steinia citrina"	"Cyrtohymena citrina"	"Berger et al., 1987"	3
@@ -12487,7 +12487,7 @@
 "Stemphylium uredinis"	"Alternaria uredinis"	"Thirum, 1947"	2
 "Stenella gynoxidicola"	"Cladosporium gynoxidicola"	"Mulder, 1982"	2
 "Stenopterobia delicatissima"	"Surirella delicatissima"	"Van Heurck, 1896"	3
-"Stenoscutus africanus"	"Aedes africanus"	"Theobald, 1909"	3
+"Stenoscutus africanus"	"Aedes africanus"	"Theobald, 1909"	2
 "Stenothermobacter"	"Nonlabens"	"Lau et al., 2006"	3
 "Stenothermobacter spongiae"	"Nonlabens spongiae"	"Lau et al., 2006"	3
 "Stenotrophomonas africana"	"Stenotrophomonas maltophilia"	"Drancourt et al., 1997"	1
@@ -12889,7 +12889,7 @@
 "Strombidium viride"	"Limnostrombidium viride"	"Kahl, 1932"	3
 "Strombilidium tonsuratum"	"Strobilidium tonsuratum"	"Meunier, 1907"	3
 "Strongylidium wilberti"	"Hemiamphisiella wilberti"	"Foissner, 1982"	3
-"Strophalosia warwicki"	"Capillaria warwicki"	"Maxwell, 1954"	3
+"Strophalosia warwicki"	"Capillaria warwicki"	"Maxwell, 1954"	2
 "Stylocapsa catenarum"	"Plicaforacapsa catenarum"	"Matsuoka, 1982"	3
 "Stylocapsa oblongula"	"Kilinora oblongula"	"Kocher, 1981"	3
 "Stylocapsa spiralis"	"Kilinora spiralis"	"Matsuoka, 1982"	3
@@ -12986,7 +12986,7 @@
 "Tachysoma siseris"	"Oxytricha siseris"	"Stiller, 1974"	3
 "Tachysoma tricornis"	"Oxytricha tricornis"	"Milne, 1886"	3
 "Taeniolella boppii"	"Cladophialophora boppii"	"Borelli, 1983"	2
-"Taeniorhynchus africanus"	"Aedes africanus"	"Neveu-Lemaire, 1906"	3
+"Taeniorhynchus africanus"	"Aedes africanus"	"Neveu-Lemaire, 1906"	2
 "Talaromyces brevicompactus"	"Hamigera brevicompactus"	"Kong, 1999"	3
 "Talaromyces byssochlamydoides"	"Rasamsonia byssochlamydoides"	"Stolk et al., 1972"	3
 "Talaromyces cejpii"	"Aspergillus cejpii"	"Milko, 1964"	2
@@ -13539,8 +13539,8 @@
 "Tremella simplex"	"Phaeotremella simplex"	"Jacks et al., 1940"	3
 "Tremella translucens"	"Sirotrema translucens"	"Gordon, 1938"	3
 "Treponema caldaria"	"Treponema caldarium"	"Abt et al., 2013"	2
-"Treponema hyodysenteriae"	"Brachyspira hyodysenteriae"	"Harris et al., 1972"	3
+"Treponema hyodysenteriae"	"Brachyspira hyodysenteriae"	"Harris et al., 1972"	2
-"Treponema innocens"	"Brachyspira innocens"	"Kinyon et al., 1979"	3
+"Treponema innocens"	"Brachyspira innocens"	"Kinyon et al., 1979"	2
 "Treponema stenostrepta"	"Treponema stenostreptum"	"Abt et al., 2013"	2
 "Tretomphalus bermudezi"	"Cymbaloporetta bermudezi"	"Sellier de Civrieux, 1976"	3
 "Tretomphalus concinnus"	"Tretomphaloides concinnus"	"Brady, 1884"	3
@@ -14161,7 +14161,7 @@
 "Wautersia paucula"	"Cupriavidus pauculus"	"Vaneechoutte et al., 2004"	2
 "Wautersia respiraculi"	"Cupriavidus respiraculi"	"Vaneechoutte et al., 2004"	2
 "Wautersia taiwanensis"	"Cupriavidus taiwanensis"	"Vaneechoutte et al., 2004"	2
-"Weeksella zoohelcum"	"Bergeyella zoohelcum"	"Holmes et al., 1987"	3
+"Weeksella zoohelcum"	"Bergeyella zoohelcum"	"Holmes et al., 1987"	2
 "Weiseria spinosa"	"Golbergia spinosa"	"Golberg, 1971"	3
 "Weissella jogaejeotgali"	"Weissella thailandensis"	"Lee et al., 2015"	2
 "Weissella kimchii"	"Weissella cibaria"	"Choi et al., 2002"	2

data-raw/mo.md5

@@ -1 +1 @@
-638a06636d8b547c2cb9d1ec243ecb7e
+348a6773a1e8e1e7255ca8961581a766

data-raw/reproduction_of_microorganisms.R

@@ -168,32 +168,6 @@ rm(ref_taxonomy)
 rm(data_col.bak)
 rm(data_dsmz.bak)
 
-mo_found_in_NL <- c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternaria", "Anaerosalibacter", "Ancylostoma", 
-                    "Angiostrongylus", "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus", 
-                    "Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus", "Beauveria", 
-                    "Bilophilia", "Blastocystis", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Candida", "Capillaria",
-                    "Capnocytophaga", "Catabacter", "Cdc", "Chaetomium", "Chilomastix", "Chryseobacterium",
-                    "Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis", "Conidiobolus",
-                    "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex", "Dermatobia", "Dicrocoelium", 
-                    "Dioctophyma", "Diphyllobothrium", "Dipylidium", "Dirofilaria", "Dracunculus", "Echinococcus", 
-                    "Echinostoma", "Elisabethkingia", "Enterobius", "Enteromonas", "Euascomycetes", "Exophiala",
-                    "Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium",
-                    "Giardia", "Gnathostoma", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces", 
-                    "Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania", "Lelliottia",
-                    "Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus", "Malassezia", 
-                    "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium", "Molonomonas", 
-                    "Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma", "Nanophetus", "Nattrassia",
-                    "Necator", "Nectria", "Novospingobium", "Ochroconis", "Oesophagostomum", "Oidiodendron", "Onchocerca",
-                    "Opisthorchis", "Opistorchis", "Paragonimus", "Paramyxovirus", "Pediculus", "Phlebotomus",
-                    "Phocanema", "Phoma", "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella", 
-                    "Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
-                    "Rhodotorula", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes", "Schistosoma", 
-                    "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Stachybotrys",
-                    "Stenotrophomononas", "Stomatococcus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
-                    "Ternidens", "Torulopsis", "Toxocara", "Toxoplasma", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
-                    "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
-                    "Trombicula", "Trypanosoma", "Tunga", "Ureaplasma", "Wuchereria")
-
 MOs <- data_total %>%
   filter(
     (
@@ -205,7 +179,7 @@ MOs <- data_total %>%
           & !order %in% c("Eurotiales", "Microascales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
     )
     # or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
-    | genus %in% mo_found_in_NL
+    | genus %in% MO_PREVALENT_GENERA
   ) %>%
   # really no Plantae (e.g. Dracunculus exist both as worm and as plant)
   filter(kingdom != "Plantae") %>% 
@@ -398,7 +372,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% mo_found_in_NL
+       | genus %in% MO_PREVALENT_GENERA
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/reproduction_of_microorganisms_update.R

@@ -276,18 +276,7 @@ MOs <- MOs %>%
                      "Firmicutes",
                      "Actinobacteria",
                      "Sarcomastigophora")
-       | genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Apophysomyces",
+       | genus %in% MO_PREVALENT_GENERA
-                      "Arachnia", "Aspergillus", "Aureobacterium", "Aureobasidium", "Bacteroides", "Basidiobolus",
-                      "Beauveria", "Blastocystis", "Branhamella", "Calymmatobacterium", "Candida", "Capnocytophaga",
-                      "Catabacter", "Chaetomium", "Chryseobacterium", "Chryseomonas", "Chrysonilia", "Cladophialophora",
-                      "Cladosporium", "Conidiobolus", "Cryptococcus", "Curvularia", "Exophiala", "Exserohilum",
-                      "Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium", "Hendersonula", "Hypomyces",
-                      "Koserella", "Lelliottia", "Leptosphaeria", "Leptotrichia", "Malassezia", "Malbranchea",
-                      "Mortierella", "Mucor", "Mycocentrospora", "Mycoplasma", "Nectria", "Ochroconis",
-                      "Oidiodendron", "Phoma", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella", "Pseudallescheria", 
-                      "Rhizomucor", "Rhizopus", "Rhodotorula", "Scolecobasidium", "Scopulariopsis", "Scytalidium", 
-                      "Sporobolomyces", "Stachybotrys", "Stomatococcus", "Treponema", "Trichoderma", "Trichophyton", 
-                      "Trichosporon", "Tritirachium", "Ureaplasma")
        | rank %in% c("kingdom", "phylum", "class", "order", "family"))
     ~ 2,
     TRUE ~ 3

data-raw/reproduction_of_rsi_translation.R

@@ -24,6 +24,7 @@
 # ==================================================================== #
 
 # This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
+# Run it with source("data-raw/reproduction_of_rsi_translation.R")
 
 library(dplyr)
 library(readr)
@@ -32,9 +33,9 @@ library(AMR)
 
 # Install the WHONET software on Windows (http://www.whonet.org/software.html),
 # and copy the folder C:\WHONET\Codes to data-raw/WHONET/Codes
-DRGLST <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"))
+DRGLST <- read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
-DRGLST1 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"))
+DRGLST1 <- read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"), show_col_types = FALSE)
-ORGLIST <- readr::read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"))
+ORGLIST <- read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
 
 # create data set for generic rules (i.e., AB-specific but not MO-specific)
 rsi_generic <- DRGLST %>%
@@ -128,11 +129,30 @@ rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m
 rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
 rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
 
+# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
+# EUCAST 2021 guideline: S <= 8 and R > 8
+#           WHONET file: S <= 8 and R >= 16
+# this will make an MIC of 12 I, which should be R, so:
+eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
+                       rsi_translation$method == "MIC" &
+                       log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0 &
+                       !is.na(rsi_translation$breakpoint_R))
+old_R <- rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE]
+old_S <- rsi_translation[eucast_mics, "breakpoint_S", drop = TRUE]
+new_R <- 2 ^ (log2(old_R) - 1)
+new_R[new_R < old_S | is.na(as.mic(new_R))] <- old_S[new_R < old_S | is.na(as.mic(new_R))]
+rsi_translation[eucast_mics, "breakpoint_R"] <- new_R
+eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
+                        rsi_translation$method == "DISK" &
+                        rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0 &
+                        !is.na(rsi_translation$breakpoint_R))
+rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
+
 # Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
 rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
 rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
 
 # save to package
-usethis::use_data(rsi_translation, overwrite = TRUE)
+usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
 rm(rsi_translation)
 devtools::load_all(".")

data-raw/rsi.md5

@@ -1 +1 @@
-d8083b68d4e492ea8e87c1eae4da4196
+75a10b41a8bd4f4788520f3407431e66

data-raw/toxoplasma.R

@@ -0,0 +1,68 @@
+microorganisms <- microorganisms |> bind_rows(
+  # Toxoplasma
+  data.frame(mo = "P_TXPL_GOND", # species
+             fullname = "Toxoplasma gondii",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "gondii",
+             subspecies = "",
+             rank = "species",
+             ref = "Nicolle et al., 1908",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "P_TXPL", # genus
+             fullname = "Toxoplasma",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "Toxoplasma",
+             species = "",
+             subspecies = "",
+             rank = "genus",
+             ref = "Nicolle et al., 1909",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[FAM]_SRCCYSTD", # family
+             fullname = "Sarcocystidae",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "Sarcocystidae",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "family",
+             ref = "Poche, 1913",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  data.frame(mo = "[ORD]_EUCCCDRD", # order
+             fullname = "Eucoccidiorida",
+             kingdom = "(unknown kingdom)",
+             phylum = "Apicomplexa",
+             class = "Conoidasida",
+             order = "Eucoccidiorida",
+             family = "",
+             genus = "",
+             species = "",
+             subspecies = "",
+             rank = "order",
+             ref = "Leger et al., 1910",
+             species_id = NA_real_,
+             source = "manually added",
+             prevalence = 2,
+             stringsAsFactors = FALSE),
+  ) |> 
+  arrange(fullname)

data-raw/translations.tsv

@@ -1,269 +1,272 @@
-pattern	regular_expr	case_sensitive	affect_ab_name	affect_mo_name	de	nl	es	it	fr	pt	da	sv	ru
+pattern	regular_expr	case_sensitive	affect_ab_name	affect_mo_name	zh	da	nl	fr	de	el	it	ja	pl	pt	ru	es	sv	tr	uk
-Coagulase-negative Staphylococcus	TRUE	TRUE	FALSE	TRUE	Koagulase-negative Staphylococcus	Coagulase-negatieve Staphylococcus	Staphylococcus coagulasa negativo	Staphylococcus negativo coagulasi	Staphylococcus à coagulase négative	Staphylococcus coagulase negativo	Koagulase-negative stafylokokker	Koagulasnegativa stafylokocker	Коагулазоотрицательный стафилококк
+language name English	FALSE	FALSE	FALSE	FALSE	Chinese	Danish	Dutch	French	German	Greek	Italian	Japanese	Polish	Portuguese	Russian	Spanish	Swedish	Turkish	Ukrainian
-Coagulase-positive Staphylococcus	TRUE	TRUE	FALSE	TRUE	Koagulase-positive Staphylococcus	Coagulase-positieve Staphylococcus	Staphylococcus coagulasa positivo	Staphylococcus positivo coagulasi	Staphylococcus à coagulase positif	Staphylococcus coagulase positivo	Koagulase-positive stafylokokker	Koagulaspositiva stafylokocker	Коагулазоположительный стафилококк
+language name	FALSE	FALSE	FALSE	FALSE	汉语	Dansk	Nederlands	Français	Deutsch	Ελληνικά	Italiano	日本語	Polski	Português	Русский	Español	Svenska	Türkçe	украї́нська
-Beta-haemolytic Streptococcus	TRUE	TRUE	FALSE	TRUE	Beta-hämolytischer Streptococcus	Beta-hemolytische Streptococcus	Streptococcus Beta-hemolítico	Streptococcus Beta-emolitico	Streptococcus Bêta-hémolytique	Streptococcus Beta-hemolítico	Beta-haemolytiske streptokokker	Beta-hemolytiska streptokocker	Бета-гемолитический стрептококк
+Coagulase-negative Staphylococcus	TRUE	TRUE	FALSE	TRUE	凝固酶阴性葡萄球菌	Koagulase-negative stafylokokker	Coagulase-negatieve Staphylococcus	Staphylococcus à coagulase négative	Koagulase-negative Staphylococcus	Σταφυλόκοκκος με αρνητική πηκτικότητα	Staphylococcus negativo coagulasi	コアグラーゼ陰性ブドウ球菌	Staphylococcus koagulazoujemny	Staphylococcus coagulase negativo	Коагулазоотрицательный стафилококк	Staphylococcus coagulasa negativo	Koagulasnegativa stafylokocker	Koagülaz-negatif Stafilokok	Коагулазонегативний стафілокок
-unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	unbekannte Gramnegativen	onbekende Gram-negatieven	Gram negativos desconocidos	Gram negativi sconosciuti	Gram négatifs inconnus	Gram negativos desconhecidos	ukendte Gram-negative	okända gramnegativa bakterier	неизвестные грамотрицательные
+Coagulase-positive Staphylococcus	TRUE	TRUE	FALSE	TRUE	凝固酶阳性葡萄球菌	Koagulase-positive stafylokokker	Coagulase-positieve Staphylococcus	Staphylococcus à coagulase positif	Koagulase-positive Staphylococcus	Σταφυλόκοκκος θετικός στην πήξη	Staphylococcus positivo coagulasi	コアグラーゼ陽性ブドウ球菌	Staphylococcus koagulazo-dodatni	Staphylococcus coagulase positivo	Коагулазоположительный стафилококк	Staphylococcus coagulasa positivo	Koagulaspositiva stafylokocker	Koagülaz-pozitif Stafilokok	Коагулазопозитивний стафілокок
-unknown Gram-positives	TRUE	TRUE	FALSE	TRUE	unbekannte Grampositiven	onbekende Gram-positieven	Gram positivos desconocidos	Gram positivi sconosciuti	Gram positifs inconnus	Gram positivos desconhecidos	ukendte Gram-positive	okända Gram-positiva	неизвестные грамположительные
+Beta-haemolytic Streptococcus	TRUE	TRUE	FALSE	TRUE	β-溶血性链球菌	Beta-haemolytiske streptokokker	Beta-hemolytische Streptococcus	Streptococcus Bêta-hémolytique	Beta-hämolytischer Streptococcus	Β-αιμολυτικός στρεπτόκοκκος	Streptococcus Beta-emolitico	ベータ溶血性レンサ球菌	Streptococcus beta-hemolityczny	Streptococcus Beta-hemolítico	Бета-гемолитический стрептококк	Streptococcus Beta-hemolítico	Beta-hemolytiska streptokocker	Beta-hemolitik Streptokok	Бета-гемолітичний стрептокок
-unknown fungus	TRUE	TRUE	FALSE	TRUE	unbekannter Pilze	onbekende schimmel	hongo desconocido	fungo sconosciuto	champignon inconnu	fungo desconhecido	ukendt svamp	Okänd svamp	неизвестный грибок
+unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	不明革兰氏阴性菌	ukendte Gram-negative	onbekende Gram-negatieven	Gram négatifs inconnus	unbekannte Gramnegativen	άγνωστοι αρνητικοί κατά Gram	Gram negativi sconosciuti	不明なグラム陰性菌	Nieznane bakterie Gram-ujemne	Gram negativos desconhecidos	неизвестные грамотрицательные	Gram negativos desconocidos	okända gramnegativa bakterier	bilinmeyen Gram-negatifler	невідомі грамнегативні
-unknown yeast	TRUE	TRUE	FALSE	TRUE	unbekannte Hefe	onbekende gist	levadura desconocida	lievito sconosciuto	levure inconnue	levedura desconhecida	ukendt gær	Okänd jäst	неизвестные дрожжи
+unknown Gram-positives	TRUE	TRUE	FALSE	TRUE	不明革兰氏阳性菌	ukendte Gram-positive	onbekende Gram-positieven	Gram positifs inconnus	unbekannte Grampositiven	άγνωστοι θετικοί κατά Gram	Gram positivi sconosciuti	未知のグラム陽性菌	Nieznane bakterie Gram-dodatnie	Gram positivos desconhecidos	неизвестные грамположительные	Gram positivos desconocidos	okända Gram-positiva	bilinmeyen Gram-pozitifler	невідомі грампозитивні
-unknown name	TRUE	TRUE	FALSE	TRUE	unbekannte Name	onbekende naam	nombre desconocido	nome sconosciuto	nom inconnu	nome desconhecido	ukendt navn	okänt namn	неизвестное название
+unknown fungus	TRUE	TRUE	FALSE	TRUE	未知真菌	ukendt svamp	onbekende schimmel	champignon inconnu	unbekannter Pilze	άγνωστος μύκητας	fungo sconosciuto	未知真菌	Nieznany grzyb	fungo desconhecido	неизвестный грибок	hongo desconocido	Okänd svamp	bilinmeyen mantar	невідомий гриб
-unknown kingdom	TRUE	TRUE	FALSE	TRUE	unbekanntes Reich	onbekend koninkrijk	reino desconocido	regno sconosciuto	règme inconnu	reino desconhecido	ukendt kongerige	okänt rike	неизвестное царство
+unknown yeast	TRUE	TRUE	FALSE	TRUE	未知酵母菌	ukendt gær	onbekende gist	levure inconnue	unbekannte Hefe	άγνωστος ζυμομύκητας	lievito sconosciuto	未知酵母	Nieznany drożdżak	levedura desconhecida	неизвестные дрожжи	levadura desconocida	Okänd jäst	bilinmeyen maya	невідомі дріжджі
-unknown phylum	TRUE	TRUE	FALSE	TRUE	unbekannter Stamm	onbekend fylum	filo desconocido	phylum sconosciuto	embranchement inconnu	filo desconhecido	ukendt stamme	okänt fylum	неизвестный филум
+unknown name	TRUE	TRUE	FALSE	TRUE	不明名称	ukendt navn	onbekende naam	nom inconnu	unbekannte Name	άγνωστο όνομα	nome sconosciuto	名称未知	nieznana nazwa	nome desconhecido	неизвестное название	nombre desconocido	okänt namn	bilinmeyen isim	невідома назва
-unknown class	TRUE	TRUE	FALSE	TRUE	unbekannte Klasse	onbekende klasse	clase desconocida	classe sconosciuta	classe inconnue	classe desconhecida	ukendt klasse	okänd klass	неизвестный класс
+unknown kingdom	TRUE	TRUE	FALSE	TRUE	未知王国	ukendt kongerige	onbekend koninkrijk	règme inconnu	unbekanntes Reich	άγνωστο βασίλειο	regno sconosciuto	未知の王国	nieznane królestwo	reino desconhecido	неизвестное царство	reino desconocido	okänt rike	bilinmeyen krallık	невідоме царство
-unknown order	TRUE	TRUE	FALSE	TRUE	unbekannte Ordnung	onbekende orde	orden desconocido	ordine sconosciuto	ordre inconnu	ordem desconhecido	ukendt orden	okänd ordning	неизвестный порядок
+unknown phylum	TRUE	TRUE	FALSE	TRUE	未知门	ukendt stamme	onbekend fylum	embranchement inconnu	unbekannter Stamm	άγνωστο φύλο	phylum sconosciuto	未知の門	nieznany azyl	filo desconhecido	неизвестный филум	filo desconocido	okänt fylum	bilinmeyen filum	невідомий відділ
-unknown family	TRUE	TRUE	FALSE	TRUE	unbekannte Familie	onbekende familie	familia desconocida	famiglia sconosciuta	famille inconnue	família desconhecida	ukendt familie	okänd familj	неизвестное семейство
+unknown class	TRUE	TRUE	FALSE	TRUE	未知类	ukendt klasse	onbekende klasse	classe inconnue	unbekannte Klasse	άγνωστη τάξη	classe sconosciuta	未知のクラス	Nieznana klasa	classe desconhecida	неизвестный класс	clase desconocida	okänd klass	bilinmeyen sınıf	невідомий клас
-unknown genus	TRUE	TRUE	FALSE	TRUE	unbekannte Gattung	onbekend geslacht	género desconocido	genere sconosciuto	genre inconnu	gênero desconhecido	ukendt slægt	okänt släkte	неизвестный род
+unknown order	TRUE	TRUE	FALSE	TRUE	未知目	ukendt orden	onbekende orde	ordre inconnu	unbekannte Ordnung	άγνωστη τάξη	ordine sconosciuto	未知の目	nieznany rząd	ordem desconhecido	неизвестный порядок	orden desconocido	okänd ordning	bilinmeyen sipariş	невідомий порядок
-unknown species	TRUE	TRUE	FALSE	TRUE	unbekannte Art	onbekende soort	especie desconocida	specie sconosciute	espèce inconnue	espécies desconhecida	ukendt art	okänd art	неизвестный вид
+unknown family	TRUE	TRUE	FALSE	TRUE	未知科	ukendt familie	onbekende familie	famille inconnue	unbekannte Familie	άγνωστη οικογένεια	famiglia sconosciuta	未知ファミリー	nieznana rodzina	família desconhecida	неизвестное семейство	familia desconocida	okänd familj	bilinmeyen aile	невідома родина
-unknown subspecies	TRUE	TRUE	FALSE	TRUE	unbekannte Unterart	onbekende ondersoort	subespecie desconocida	sottospecie sconosciute	sous-espèce inconnue	subespécies desconhecida	ukendt underart	okänd underart	неизвестный подвид
+unknown genus	TRUE	TRUE	FALSE	TRUE	未知属	ukendt slægt	onbekend geslacht	genre inconnu	unbekannte Gattung	άγνωστο γένος	genere sconosciuto	未知属	nieznany rodzaj	gênero desconhecido	неизвестный род	género desconocido	okänt släkte	bilinmeyen cins	невідомий рід
-unknown rank	TRUE	TRUE	FALSE	TRUE	unbekannter Rang	onbekende rang	rango desconocido	grado sconosciuto	rang inconnu	classificação desconhecido	ukendt rang	okänd rang	неизвестный ранг
+unknown species	TRUE	TRUE	FALSE	TRUE	未知种	ukendt art	onbekende soort	espèce inconnue	unbekannte Art	άγνωστο είδος	specie sconosciute	未知種	nieznany gatunek	espécies desconhecida	неизвестный вид	especie desconocida	okänd art	bilinmeyen türler	невідомий вид
- group 	TRUE	TRUE	FALSE	TRUE	 Gruppe 	 groep 	 grupo 	 gruppo 	 groupe 	 grupo 	 gruppe 	 grupp 	 группа 
+unknown subspecies	TRUE	TRUE	FALSE	TRUE	未知亚种	ukendt underart	onbekende ondersoort	sous-espèce inconnue	unbekannte Unterart	άγνωστο υποείδος	sottospecie sconosciute	亜種不明	nieznany podgatunek	subespécies desconhecida	неизвестный подвид	subespecie desconocida	okänd underart	bilinmeyen alt türler	невідомий підвид
-CoNS	FALSE	TRUE	FALSE	TRUE	KNS	CNS	SCN				KNS	KNS	КОС
+unknown rank	TRUE	TRUE	FALSE	TRUE	未知等级	ukendt rang	onbekende rang	rang inconnu	unbekannter Rang	άγνωστη τάξη	grado sconosciuto	未知ランク	nieznany stopień	classificação desconhecido	неизвестный ранг	rango desconocido	okänd rang	bilinmeyen rütbe	невідомий ранг
-CoPS	FALSE	TRUE	FALSE	TRUE	KPS	CPS	SCP				KPS	KPS	КПС
+ group 	TRUE	TRUE	FALSE	TRUE	 组 	 gruppe 	 groep 	 groupe 	 Gruppe 	 ομάδα 	 gruppo 	 グループ	 grupa 	 grupo 	 группа 	 grupo 	 grupp 	 Grup 	 група
-Gram-negative	TRUE	TRUE	FALSE	FALSE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo	Gram-negativ	Gram-negativ	Грамотрицательные
+CoNS	FALSE	TRUE	FALSE	TRUE		KNS	CNS		KNS	CoNS		グラム陰性	CoNS		КОС	SCN	KNS	KNS	КНС
-Gram-positive	TRUE	TRUE	FALSE	FALSE	Grampositiv	Gram-positief	Gram positivo	Gram positivo	Gram positif	Gram positivo	Gram-positiv	Gram-positiv	Грамположительные
+CoPS	FALSE	TRUE	FALSE	TRUE		KPS	CPS		KPS	CoPS		グラム陽性	CoPS		КПС	SCP	KPS	KPS	КПС
-^Bacteria$	TRUE	TRUE	FALSE	FALSE	Bakterien	Bacteriën	Bacterias	Batteri	Bactéries	Bactérias	Bakterier	Bakterier	Бактерии
+Gram-negative	TRUE	TRUE	FALSE	FALSE	革兰氏阴性	Gram-negativ	Gram-negatief	Gram négatif	Gramnegativ	Αρνητικό κατά Gram	Gram negativo	^細菌$	Gram-ujemne	Gram negativo	Грамотрицательные	Gram negativo	Gram-negativ	Gram-negatif	Грамнегативні
-^Fungi$	TRUE	TRUE	FALSE	FALSE	Pilze	Schimmels	Hongos	Funghi	Champignons	Fungos	Støbeforme	Svampar	Грибы
+Gram-positive	TRUE	TRUE	FALSE	FALSE	革兰氏阳性	Gram-positiv	Gram-positief	Gram positif	Grampositiv	Θετικό κατά Gram	Gram positivo	^真菌$	Gram-dodatnie	Gram positivo	Грамположительные	Gram positivo	Gram-positiv	Gram-pozitif	Грампозитивні
-^Yeasts$	TRUE	TRUE	FALSE	FALSE	Hefen	Gisten	Levaduras	Lieviti	Levures	Leveduras	Gær	Jästdjur	Животные
+^Bacteria$	TRUE	TRUE	FALSE	FALSE	^细菌$	Bakterier	Bacteriën	Bactéries	Bakterien	^Βακτήρια$	Batteri	^酵母$	^Bakterie$	Bactérias	Бактерии	Bacterias	Bakterier	^Bakteri$	Бактерії
-^Protozoa$	TRUE	TRUE	FALSE	FALSE	Protozoen	Protozoën	Protozoarios	Protozoi	Protozoaires	Protozoários	Protozoer	Protozoer	Протозоа
+^Fungi$	TRUE	TRUE	FALSE	FALSE	^真菌$	Støbeforme	Schimmels	Champignons	Pilze	^Μύκητες$	Funghi	^原生動物$	^Grzyby$	Fungos	Грибы	Hongos	Svampar	^Mantarlar$	Гриби
-biogroup	TRUE	TRUE	FALSE	FALSE	Biogruppe	biogroep	biogrupo	biogruppo	biogroupe	biogrupo	biogruppe	biogrupp	биогруппа
+^Yeasts$	TRUE	TRUE	FALSE	FALSE	^酵母菌$	Gær	Gisten	Levures	Hefen	^Ζυμομύκητες$	Lieviti	バイオグループ	^Drożdże$	Leveduras	Животные	Levaduras	Jästdjur	^Mayalar$	Дріжджі
-biotype	TRUE	TRUE	FALSE	FALSE	Biotyp		biotipo	biotipo		biótipo	biotype	biotyp	биотип
+^Protozoa$	TRUE	TRUE	FALSE	FALSE	^原生动物$	Protozoer	Protozoën	Protozoaires	Protozoen	^Πρωτόζωα$	Protozoi	生物型	^Protozoa$	Protozoários	Протозоа	Protozoarios	Protozoer	^Protozoa$	Найпростіші
-vegetative	TRUE	TRUE	FALSE	FALSE	vegetativ	vegetatief	vegetativo	vegetativo	végétatif	vegetativo	vegetativ	vegetativ	вегетативный
+biogroup	TRUE	TRUE	FALSE	FALSE	生物群	biogruppe	biogroep	biogroupe	Biogruppe	βιοομάδα	biogruppo	植物型	biogrupa	biogrupo	биогруппа	biogrupo	biogrupp	biyogrup	біогрупа
-([([ ]*?)group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1groep	\\1grupo	\\1gruppo	\\1groupe	\\1grupo	\\1gruppe	\\1grupp	\\1группа
+biotype	TRUE	TRUE	FALSE	FALSE	生物型	biotype			Biotyp	βιότυπος	biotipo	([([ ]*?))) グループ	biotyp	biótipo	биотип	biotipo	biotyp	biyotip	біотип
-([([ ]*?)Group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1Groep	\\1Grupo	\\1Gruppo	\\1Groupe	\\1Grupo	\\1Gruppe	\\1Grupp	\\1Группа
+vegetative	TRUE	TRUE	FALSE	FALSE	无性系	vegetativ	vegetatief	végétatif	vegetativ	βλαστικός	vegetativo	([[ ]*?)グループ	wegetatywna	vegetativo	вегетативный	vegetativo	vegetativ	vejetatif	вегетативний
-no .*growth	TRUE	FALSE	FALSE	FALSE	keine? .*wachstum	geen .*groei	no .*crecimientonon	sem .*crescimento	pas .*croissance	sem .*crescimento	ingen .*vækst	ingen .*tillväxt	отсутствие.*роста
+([([ ]*?)group	TRUE	TRUE	FALSE	FALSE	([([]*?)组	\\1gruppe	\\1groep	\\1groupe	\\1Gruppe	([([ ]*?)ομάδα	\\1gruppo		([([ ]*?)grupa	\\1grupo	\\1группа	\\1grupo	\\1grupp	([([ ]*?)grup	\\1група
-no|not	TRUE	FALSE	FALSE	FALSE	keine?	geen|niet	no|sin	sem	non	sem	nej|ikke	nej|inte	нет?
+([([ ]*?)Group	TRUE	TRUE	FALSE	FALSE	([([]*?)组	\\1Gruppe	\\1Groep	\\1Groupe	\\1Gruppe	([([ ]*;)ομάδα	\\1Gruppo	ない	([([ ]*?)Grupa	\\1Grupo	\\1Группа	\\1Grupo	\\1Grupp	([([ ]*?)Grup	\\1Група
-Intermediate	TRUE	FALSE	FALSE	FALSE	Mittlere	Intermediair	Intermedio						
+no .*growth	TRUE	FALSE	FALSE	FALSE	无.*生长	ingen .*vækst	geen .*groei	pas .*croissance	keine? .*wachstum	όχι .*αύξηση	sem .*crescimento	中間体	brak .*wzrostu	sem .*crescimento	отсутствие.*роста	no .*crecimientonon	ingen .*tillväxt	büyüme yok	відсутність .*росту
-Susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	Empfindlich, erh Belastung	Gevoelig bij verh. blootstelling							
+no|not	TRUE	FALSE	FALSE	FALSE	不|不	nej|ikke	geen|niet	non	keine?	no|not	sem	感受性の高い、被ばく量の増加	nie|nie	sem	нет?	no|sin	nej|inte	hayır|değil|hayir|degil	ні
-susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	empfindlich, erh Belastung	gevoelig bij verh. blootstelling							
+Intermediate	TRUE	FALSE	FALSE	FALSE	中级	Mellemliggende	Intermediair		Mittlere	Ενδιάμεση		影響を受けやすい。	Pośrednia			Intermedio		Orta seviye	Знижена чутливість
-Susceptible	TRUE	FALSE	FALSE	FALSE	Empfindlich	Gevoelig	Susceptible						
+Susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	易感，暴露增加	Modtagelig, øget eksp.	Gevoelig bij verh. blootstelling		Empfindlich, erh Belastung	Ευάλωτος, αυξημένη έκθεση		影響を受けやすい	Podatne, zwiększone narażenie					Duyarlı, enk. maruziyet	Чутливий до підвищеної експозиції
-Incr. exposure	TRUE	FALSE	FALSE	FALSE	Empfindlich, erh Belastung	'Incr. exposure'	'Incr. exposure'						
+susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	易感，接触增加	modtagelig, øget eksp.	gevoelig bij verh. blootstelling		empfindlich, erh Belastung	Ευαίσθητος, αυξημένη έκθεση		曝露量増加	podatny, zwiększone narażenie					duyarlı, enk. maruziyet	чутливий до підвищеної експозиції
-Resistant	TRUE	FALSE	FALSE	FALSE	Resistent	Resistent	Resistente						
+Susceptible	TRUE	FALSE	FALSE	FALSE	易受影响	Modtagelig	Gevoelig		Empfindlich	Ευαίσθητο		耐性	Podatny			Susceptible		Duyarlı	Чутливий
-antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	antibioticum	antibiótico	antibiotico	antibiotique	antibiótico	antibiotikum	antibiotika	антибиотик
+Incr. exposure	TRUE	FALSE	FALSE	FALSE	暴露增加	Øget eksponering	'Incr. exposure'		Empfindlich, erh Belastung	Αυξημένη έκθεση		抗生物質	Większe narażenie			'Incr. exposure'		Enk. maruziyet	Підвищена експозиція
-Antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	Antibioticum	Antibiótico	Antibiotico	Antibiotique	Antibiótico	Antibiotikum	Antibiotika	Антибиотик
+Resistant	TRUE	FALSE	FALSE	FALSE	耐药性	Resistent	Resistent		Resistent	Ανθεκτικός		抗生物質	Odporny			Resistente		Dayanıklı	Стійкий
-Drug	TRUE	TRUE	FALSE	FALSE	Medikament	Middel	Fármaco	Droga	Médicament	Droga	Lægemiddel	Läkemedel	Лекарство
+antibiotic	TRUE	TRUE	FALSE	FALSE	抗生素	antibiotikum	antibioticum	antibiotique	Antibiotikum	αντιβιοτικό	antibiotico	薬剤	antybiotyk	antibiótico	антибиотик	antibiótico	antibiotika	Antibiyotik	антибіотик
-drug	TRUE	TRUE	FALSE	FALSE	Medikament	middel	fármaco	droga	médicament	droga	lægemiddel	läkemedel	лекарство
+Antibiotic	TRUE	TRUE	FALSE	FALSE	抗生素	Antibiotikum	Antibioticum	Antibiotique	Antibiotikum	Αντιβιοτικό	Antibiotico	薬剤	Antybiotyk	Antibiótico	Антибиотик	Antibiótico	Antibiotika	Antibiyotik	Антибіотик
-Frequency	FALSE	TRUE	FALSE	FALSE	Zahl	Aantal	Frecuencia	Frequenza	Fréquence	Frequência	Frekvens	Frekvens	Частота
+Drug	TRUE	TRUE	FALSE	FALSE	药物	Lægemiddel	Middel	Médicament	Medikament	Φάρμακο	Droga	頻度	Lek	Droga	Лекарство	Fármaco	Läkemedel	İlaç	Лікарський засіб
-Minimum Inhibitory Concentration (mg/L)	FALSE	FALSE	FALSE	FALSE	Minimale Hemm-Konzentration (mg/L)	Minimale inhiberende concentratie (mg/L)	Concentración mínima inhibitoria (mg/L)	Concentrazione minima inibitoria (mg/L)	Concentration minimale inhibitrice (mg/L)	Concentração Inibitória Mínima (mg/L)	Mindste hæmmende koncentration (mg/L)	Minsta hämmande koncentration (mg/L)	Минимальная ингибирующая концентрация (мг/л)
+drug	TRUE	TRUE	FALSE	FALSE	药物	lægemiddel	middel	médicament	Medikament	φάρμακο	droga	最小発育阻止濃度(mg / L)	lek	droga	лекарство	fármaco	läkemedel	İlaç	лікарський засіб
-Disk diffusion diameter (mm)	FALSE	FALSE	FALSE	FALSE	Durchmesser der Scheibenzone (mm)	Diameter diskzone (mm)	Diámetro de difusión en disco (mm)	Diametro di diffusione del disco (mm)	Diamètre de diffusion en disque (mm)	Diâmetro de difusão do disco (mm)	Diskdiffusionsdiameter (mm)	Diskdiffusionsdiameter (mm)	Диаметр диффузии диска (мм)
+Frequency	FALSE	TRUE	FALSE	FALSE	使用频率	Frekvens	Aantal	Fréquence	Zahl	Συχνότητα	Frequenza	ディスク拡散径(mm)	Częstotliwość	Frequência	Частота	Frecuencia	Frekvens	Frekans	Частота
-Antimicrobial Interpretation	FALSE	FALSE	FALSE	FALSE	Antimikrobielle Auswertung	Antimicrobiële interpretatie	Interpretación antimicrobiana	Interpretazione antimicrobica	Interprétation antimicrobienne	Interpretação Antimicrobiana	Antimikrobiel fortolkning	Antimikrobiell tolkning	Антимикробная интерпретация
+Minimum Inhibitory Concentration (mg/L)	FALSE	FALSE	FALSE	FALSE	最小抑菌浓度(mg/L)	Mindste hæmmende koncentration (mg/L)	Minimale inhiberende concentratie (mg/L)	Concentration minimale inhibitrice (mg/L)	Minimale Hemm-Konzentration (mg/L)	Ελάχιστη ανασταλτική συγκέντρωση (mg/L)	Concentrazione minima inibitoria (mg/L)	抗菌性解釈	Minimalne stężenie hamujące (mg/L)	Concentração Inibitória Mínima (mg/L)	Минимальная ингибирующая концентрация (мг/л)	Concentración mínima inhibitoria (mg/L)	Minsta hämmande koncentration (mg/L)	Minimum İnhibitör Konsantrasyon (mg/L)	Мінімальна інгібуюча концентрація (мг/мл)
-4-aminosalicylic acid	FALSE	TRUE	TRUE	FALSE	4-Aminosalicylsäure	4-aminosalicylzuur	Ácido 4-aminosalicílico	Acido 4-aminosalicilico	Acide 4-aminosalicylique	Ácido 4-aminosalicílico	4-aminosalicylsyre	4-aminosalicylsyra	4-аминосалициловая кислота
+Disk diffusion diameter (mm)	FALSE	FALSE	FALSE	FALSE	磁盘扩散直径(mm)	Diskdiffusionsdiameter (mm)	Diameter diskzone (mm)	Diamètre de diffusion en disque (mm)	Durchmesser der Scheibenzone (mm)	Διάμετρος διάχυσης δίσκου (mm)	Diametro di diffusione del disco (mm)	割合	Średnica dyfuzji dysku (mm)	Diâmetro de difusão do disco (mm)	Диаметр диффузии диска (мм)	Diámetro de difusión en disco (mm)	Diskdiffusionsdiameter (mm)	Disk difüzyon çapı (mm)	Зона затримки росту (мм)
-Adefovir dipivoxil	FALSE	TRUE	TRUE	FALSE	Adefovir Dipivoxil	Adefovir	Adefovir dipivoxil	Adefovir dipivoxil	Adéfovir dipivoxil	Adefovir dipivoxil	Adefovir dipivoxil	Adefovir dipivoxil	Адефовир дипивоксил
+Antimicrobial Interpretation	FALSE	FALSE	FALSE	FALSE	抗菌性解释	Antimikrobiel fortolkning	Antimicrobiële interpretatie	Interprétation antimicrobienne	Antimikrobielle Auswertung	Αντιμικροβιακή ερμηνεία	Interpretazione antimicrobica	4-アミノサリチル酸	Interpretacja antybakteryjna	Interpretação Antimicrobiana	Антимикробная интерпретация	Interpretación antimicrobiana	Antimikrobiell tolkning	Antimikrobiyal Yorumlama	Фенотипи чутливості
-Aldesulfone sodium	FALSE	TRUE	TRUE	FALSE	Aldesulfon-Natrium	Aldesulfon	Aldesulfona sódica	Aldesulfone sodio	Aldésulfone sodique	Aldesulfona de sódio	Aldesulfon-natrium	Aldesulfonnatrium	Альдесульфон натрия
+Percentage	FALSE	FALSE	FALSE	FALSE	百分比	Procentdel	Percentage	Pourcentage	Prozentsatz	Ποσοστό	Percentuale	アデホビル・ジピボキシル	Procent	Percentagem	Процент	Porcentaje	Procentuell andel	Yüzde	Відсоток
-Amikacin	FALSE	TRUE	TRUE	FALSE	Amikacin	Amikacine	Amikacina	Amikacin	Amikacine	Amikacin	Amikacin	Amikacin	Амикацин
+4-aminosalicylic acid	FALSE	TRUE	TRUE	FALSE	4-氨基水杨酸	4-aminosalicylsyre	4-aminosalicylzuur	Acide 4-aminosalicylique	4-Aminosalicylsäure	4-αμινοσαλικυλικό οξύ	Acido 4-aminosalicilico	アルデスルホンナトリウム	Kwas 4-aminosalicylowy	Ácido 4-aminosalicílico	4-аминосалициловая кислота	Ácido 4-aminosalicílico	4-aminosalicylsyra	4-aminosalisilik asit	4-Аміносаліцилова кислота
-Amoxicillin	FALSE	TRUE	TRUE	FALSE	Amoxicillin	Amoxicilline	Amoxicilina	Amoxicillina	Amoxicilline	Amoxicilina	Amoxicillin	Amoxicillin	Амоксициллин
+Adefovir dipivoxil	FALSE	TRUE	TRUE	FALSE	阿德福韦酯	Adefovir dipivoxil	Adefovir	Adéfovir dipivoxil	Adefovir Dipivoxil	Adefovir dipivoxil	Adefovir dipivoxil	アミカシン	Adefovir dipivoxil	Adefovir dipivoxil	Адефовир дипивоксил	Adefovir dipivoxil	Adefovir dipivoxil	Adefovir dipivoksil	Адефовір діпівоксил
-Amoxicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Amoxicillin/Beta-Lactamase-Hemmer	Amoxicilline/enzymremmer	Amoxicilina/inhib. de la beta-lactamasa	Amoxicillina/inib. d. beta-lattamasi	Amoxicilline/inhib. de bêta-lactamase	Amoxicilina/inibid. da beta-lactamase	Amoxicillin/beta-lactamasehæmmer	Amoxicillin/betalaktamashämmare	Амоксициллин/ингибитор бета-лактамаз
+Aldesulfone sodium	FALSE	TRUE	TRUE	FALSE	醛缩酮钠	Aldesulfon-natrium	Aldesulfon	Aldésulfone sodique	Aldesulfon-Natrium	Αλδεσουλφονικό νάτριο	Aldesulfone sodio	アモキシシリン	Sól sodowa aldesulfonu	Aldesulfona de sódio	Альдесульфон натрия	Aldesulfona sódica	Aldesulfonnatrium	Aldesülfon sodyum	Альденсульфон натрію
-Amphotericin B	FALSE	TRUE	TRUE	FALSE	Amphotericin B	Amfotericine B	Anfotericina B	Amfotericina B	Amphotéricine B	Anfotericina B	Amfotericin B	Amfotericin B	Амфотерицин В
+Amikacin	FALSE	TRUE	TRUE	FALSE	阿米卡星	Amikacin	Amikacine	Amikacine	Amikacin	Amikacin	Amikacin	アモキシシリン／β-ラクタマーゼ阻害剤	Amikacyna	Amikacin	Амикацин	Amikacina	Amikacin	Amikasin	Амікацин
-Ampicillin	FALSE	TRUE	TRUE	FALSE	Ampicillin	Ampicilline	Ampicilina	Ampicillina	Ampicilline	Ampicilina	Ampicillin	Ampicillin	Ампициллин
+Amoxicillin	FALSE	TRUE	TRUE	FALSE	阿莫西林	Amoxicillin	Amoxicilline	Amoxicilline	Amoxicillin	Αμοξικιλλίνη	Amoxicillina	アムホテリシンB	Amoxicillin	Amoxicilina	Амоксициллин	Amoxicilina	Amoxicillin	Amoksisilin	Амоксицилін
-Ampicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Ampicillin/Beta-Laktamase-Hemmer	Ampicilline/enzymremmer	Ampicilina/inhib. de la beta-lactamasa	Ampicillina/inib. d. beta-lattamasi	Ampicilline/inhib. de bêta-lactamase	Ampicilina/inibid. da beta-lactamase	Ampicillin/beta-lactamasehæmmer	Ampicillin/beta-laktamashämmare	Ампициллин/ингибитор бета-лактамазы
+Amoxicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	阿莫西林/β-内酰胺酶抑制剂	Amoxicillin/beta-lactamasehæmmer	Amoxicilline/enzymremmer	Amoxicilline/inhib. de bêta-lactamase	Amoxicillin/Beta-Lactamase-Hemmer	Αμοξικιλλίνη/αναστολέας της β-λακταμάσης	Amoxicillina/inib. d. beta-lattamasi	アンピシリン	Amoksycylina/inhibitor beta-laktamazy	Amoxicilina/inibid. da beta-lactamase	Амоксициллин/ингибитор бета-лактамаз	Amoxicilina/inhib. de la beta-lactamasa	Amoxicillin/betalaktamashämmare	Amoksisilin/beta-laktamaz inhibitörü	Амоксицилін/інгібітор бета-лактамаз
-Anidulafungin	FALSE	TRUE	TRUE	FALSE	Anidulafungin	Anidulafungine	Anidulafungina	Anidulafungin	Anidulafungine	Anidulafungin	Anidulafungin	Anidulafungin	Анидулафунгин
+Amphotericin B	FALSE	TRUE	TRUE	FALSE	两性霉素B	Amfotericin B	Amfotericine B	Amphotéricine B	Amphotericin B	Αμφοτερικίνη Β	Amfotericina B	アンピシリン／β-ラクタマーゼ阻害剤	Amfoterycyna B	Anfotericina B	Амфотерицин В	Anfotericina B	Amfotericin B	Amfoterisin B	Амфотерицин В
-Azidocillin	FALSE	TRUE	TRUE	FALSE	Azidocillin	Azidocilline	Azidocilina	Azidocillina	Azidocilline	Azidocillin	Azidocillin	Azidocillin	Азидоциллин
+Ampicillin	FALSE	TRUE	TRUE	FALSE	氨苄西林	Ampicillin	Ampicilline	Ampicilline	Ampicillin	Αµπικιλλίνη	Ampicillina	アニデュラファンギン	Ampicylina	Ampicilina	Ампициллин	Ampicilina	Ampicillin	Ampisilin	Ампіцилін
-Azithromycin	FALSE	TRUE	TRUE	FALSE	Azithromycin	Azitromycine	Azitromicina	Azitromicina	Azithromycine	Azitromicina	Azithromycin	Azitromycin	Азитромицин
+Ampicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	氨苄西林/β-内酰胺酶抑制剂	Ampicillin/beta-lactamasehæmmer	Ampicilline/enzymremmer	Ampicilline/inhib. de bêta-lactamase	Ampicillin/Beta-Laktamase-Hemmer	Αμπικιλλίνη/αναστολέας β-λακταμάσης	Ampicillina/inib. d. beta-lattamasi	アジドシリン	Ampicylina/inhibitor beta-laktamazy	Ampicilina/inibid. da beta-lactamase	Ампициллин/ингибитор бета-лактамазы	Ampicilina/inhib. de la beta-lactamasa	Ampicillin/beta-laktamashämmare	Ampisilin/beta-laktamaz inhibitörü	Ампіцилін/інгібітор бета-лактамаз
-Azlocillin	FALSE	TRUE	TRUE	FALSE	Azlocillin	Azlocilline	Azlocilina	Azlocillina	Azlocilline	Azlocillin	Azlocillin	Azlocillin	Азлоциллин
+Anidulafungin	FALSE	TRUE	TRUE	FALSE	阿尼芬净	Anidulafungin	Anidulafungine	Anidulafungine	Anidulafungin	Ανιδουλαφουνγκίνη	Anidulafungin	アジスロマイシン	Anidulafungina	Anidulafungin	Анидулафунгин	Anidulafungina	Anidulafungin	Anidulafungin	Анідулафунгін
-Bacampicillin	FALSE	TRUE	TRUE	FALSE	Bacampicillin	Bacampicilline	Bacampicilina	Bacampicillina	Bacampicilline	Bacampicilina	Bacampicillin	Bacampicillin	Бакампициллин
+Azidocillin	FALSE	TRUE	TRUE	FALSE	阿奇霉素	Azidocillin	Azidocilline	Azidocilline	Azidocillin	Αζιδοκιλλίνη	Azidocillina	アズロシリン	Azidocillin	Azidocillin	Азидоциллин	Azidocilina	Azidocillin	Azidosilin	Азидоцилін
-Bacitracin	FALSE	TRUE	TRUE	FALSE	Bacitracin	Bacitracine	Bacitracina	Bacitracina	Bacitracine	Bacitracin	Bacitracin	Bacitracin	Бацитрацин
+Azithromycin	FALSE	TRUE	TRUE	FALSE	阿奇霉素	Azithromycin	Azitromycine	Azithromycine	Azithromycin	Αζιθρομυκίνη	Azitromicina	バカンピシリン	Azithromycin	Azitromicina	Азитромицин	Azitromicina	Azitromycin	Azitromisin	Азитроміцин
-Benzathine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Benzylpenicillin	Benzylpenicillinebenzathine	Bencilpenicilina benzatínica	Benzatina benzilpenicillina	Benzathine benzylpénicilline	Benzatina benzatina benzilpenicilina	Benzathinbenzylpenicillin	Benzathinbenzylpenicillin	Бензатин бензилпенициллин
+Azlocillin	FALSE	TRUE	TRUE	FALSE	阿洛西林	Azlocillin	Azlocilline	Azlocilline	Azlocillin	Αζλοκιλλίνη	Azlocillina	バシトラシン	Azlocillin	Azlocillin	Азлоциллин	Azlocilina	Azlocillin	Azlocillin	Азлоцилін
-Benzathine phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Phenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine	Fenoximetilpenicilina benzatínica	Benzatina fenossimetilpenicillina	Phénoxyméthylpénicilline benzathine	Benzatina fenoximetilpenicilina	Benzathinfenoxymethylpenicillin	Bensathinfenoximetylpenicillin	Бензатин феноксиметилпенициллин
+Bacampicillin	FALSE	TRUE	TRUE	FALSE	巴卡比林	Bacampicillin	Bacampicilline	Bacampicilline	Bacampicillin	Μπακαμπικιλλίνη	Bacampicillina	ベンズシン・ベンジルペニシリン	Bakampicylina	Bacampicilina	Бакампициллин	Bacampicilina	Bacampicillin	Bacampicillin	Бакампіцилін
-Benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzylpenicillin	Benzylpenicilline	Bencilpenicilina	Benzilpenicillina	Benzylpénicilline	Benzilpenicilina	Benzylpenicillin	Bensylpenicillin	Бензилпенициллин
+Bacitracin	FALSE	TRUE	TRUE	FALSE	阿奇霉素	Bacitracin	Bacitracine	Bacitracine	Bacitracin	Bacitracin	Bacitracina	ベンザチンフェノキシメチルペニシリン	Bacytracyna	Bacitracin	Бацитрацин	Bacitracina	Bacitracin	Basitrasin	Бацитрацин
-Calcium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Kalzium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de calcio	Calcio aminosalicilato	Aminosalicylate de calcium	Aminosalicilato de cálcio	Calciumaminosalicylat	Kalciumaminosalicylat	Аминосалицилат кальция
+Benzathine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	苄丝肼青霉素	Benzathinbenzylpenicillin	Benzylpenicillinebenzathine	Benzathine benzylpénicilline	Benzathin-Benzylpenicillin	Βενζαθίνη βενζυλπενικιλλίνη	Benzatina benzilpenicillina	ベンジルペニシリン	Benzylpenicylina benzylowa	Benzatina benzatina benzilpenicilina	Бензатин бензилпенициллин	Bencilpenicilina benzatínica	Benzathinbenzylpenicillin	Benzatin benzilpenisilin	Бензатину бензилпеніцилін
-Capreomycin	FALSE	TRUE	TRUE	FALSE	Capreomycin	Capreomycine	Capreomicina	Capreomicina	Capréomycine	Capreomicina	Capreomycin	Kapreomycin	Капреомицин
+Benzathine phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	苄星苯氧甲基青霉素	Benzathinfenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine	Phénoxyméthylpénicilline benzathine	Benzathin-Phenoxymethylpenicillin	Βενζαθίνη φαινοξυμεθυλοπενικιλλίνη	Benzatina fenossimetilpenicillina	アミノサリチル酸カルシウム	Fenoksymetylopenicylina benzylowa	Benzatina fenoximetilpenicilina	Бензатин феноксиметилпенициллин	Fenoximetilpenicilina benzatínica	Bensathinfenoximetylpenicillin	Benzatin fenoksimetilpenisilin	Бензатину феноксиметилпеніцилін
-Carbenicillin	FALSE	TRUE	TRUE	FALSE	Carbenicillin	Carbenicilline	Carbenicilina	Carbenicillina	Carbénicilline	Carbenicilina	Carbenicillin	Karbenicillin	Карбенициллин
+Benzylpenicillin	FALSE	TRUE	TRUE	FALSE	苄基青霉素	Benzylpenicillin	Benzylpenicilline	Benzylpénicilline	Benzylpenicillin	Benzylpenicillin	Benzilpenicillina	カプレオマイシン	Benzylpenicylina	Benzilpenicilina	Бензилпенициллин	Bencilpenicilina	Bensylpenicillin	Benzilpenisilin	Бензилпеніцилін
-Carindacillin	FALSE	TRUE	TRUE	FALSE	Carindacillin	Carindacilline	Carindacilina	Carindacillina	Carindacilline	Carindacillin	Carindacillin	Carindacillin	Кариндациллин
+Calcium aminosalicylate	FALSE	TRUE	TRUE	FALSE	氨基水杨酸钙	Calciumaminosalicylat	Aminosalicylzuur	Aminosalicylate de calcium	Kalzium-Aminosalicylat	Αμινοσαλικυλικό ασβέστιο	Calcio aminosalicilato	カルベニシリン	Aminosalicylan wapnia	Aminosalicilato de cálcio	Аминосалицилат кальция	Aminosalicilato de calcio	Kalciumaminosalicylat	Kalsiyum aminosalisilat	Кальцію аміносаліцилат
-Caspofungin	FALSE	TRUE	TRUE	FALSE	Caspofungin	Caspofungine	Caspofungina	Caspofungin	Caspofungine	Caspofungin	Caspofungin	Caspofungin	Каспофунгин
+Capreomycin	FALSE	TRUE	TRUE	FALSE	氨水杨酸钙	Capreomycin	Capreomycine	Capréomycine	Capreomycin	Καπρεομυκίνη	Capreomicina	カリンダシリン	Kapreomycyna	Capreomicina	Капреомицин	Capreomicina	Kapreomycin	Kapreomisin	Капреоміцин
-Ce(f|ph)acetrile	TRUE	TRUE	TRUE	FALSE	Cefacetril	Cefacetril	Cefacetrilo	Cefacetrile	Céphacétrile	Cephacetrile	Cephacetril	Cephacetril	Цефацетрил
+Carbenicillin	FALSE	TRUE	TRUE	FALSE	羧基青霉素	Carbenicillin	Carbenicilline	Carbénicilline	Carbenicillin	Καρβενικιλλίνη	Carbenicillina	カスポファンギン	Karbenicylina	Carbenicilina	Карбенициллин	Carbenicilina	Karbenicillin	Karbenisilin	Карбеніцилін
-Ce(f|ph)alotin	TRUE	TRUE	TRUE	FALSE	Cefalotin	Cefalotine	Cefalotina	Cefalotina	Céphalotine	Cefalotina	Cephalotin	Cefalotin	Цефалотин
+Carindacillin	FALSE	TRUE	TRUE	FALSE	卡林达西林	Carindacillin	Carindacilline	Carindacilline	Carindacillin	Carindacillin	Carindacillina	セファセトリル	Karindacillin	Carindacillin	Кариндациллин	Carindacilina	Carindacillin	Karindasilin	Кариндацилін
-Ce(f|ph)amandole	TRUE	TRUE	TRUE	FALSE	Cefamandol	Cefamandol	Cefamandole	Cephamandole	Céphamandole	Cephamandole	Cephamandol	Cephamandol	Цефамандол
+Caspofungin	FALSE	TRUE	TRUE	FALSE	氨苄青霉素	Caspofungin	Caspofungine	Caspofungine	Caspofungin	Caspofungin	Caspofungin	セファロチン	Kaspofungina	Caspofungin	Каспофунгин	Caspofungina	Caspofungin	Caspofungin	Каспофунгін
-Ce(f|ph)apirin	TRUE	TRUE	TRUE	FALSE	Cefapirin	Cefapirine	Cefapirina	Cefapirina	Céphapirine	Cephapirin	Cephapirin	Cephapirin	Цефапирин
+Ce(f|ph)acetrile	TRUE	TRUE	TRUE	FALSE	头孢乙腈	Cephacetril	Cefacetril	Céphacétrile	Cefacetril	Κεφακετρίλη	Cefacetrile	セファマンドール	Cefacetrile	Cephacetrile	Цефацетрил	Cefacetrilo	Cephacetril	Sefasetril	Цефацетрил
-Ce(f|ph)azedone	TRUE	TRUE	TRUE	FALSE	Cefazedon	Cefazedon	Cefazedona	Cefazedone	Céphazédone	Cephazedone	Cephazedon	Cephazedon	Цефазедон
+Ce(f|ph)alotin	TRUE	TRUE	TRUE	FALSE	头孢罗丁	Cephalotin	Cefalotine	Céphalotine	Cefalotin	Κεφαλοτίνη	Cefalotina	セファピリン	Cefalotyna	Cefalotina	Цефалотин	Cefalotina	Cefalotin	Sefalotin	Цефалотин
-Ce(f|ph)azolin	TRUE	TRUE	TRUE	FALSE	Cefazolin	Cefazoline	Cefazolina	Cephazolin	Céphazoline	Cephazolin	Cephazolin	Cephazolin	Цефазолин
+Ce(f|ph)amandole	TRUE	TRUE	TRUE	FALSE	头孢曼多	Cephamandol	Cefamandol	Céphamandole	Cefamandol	Κεφαμανδόλη	Cephamandole	セファゼドン	Cefamandol	Cephamandole	Цефамандол	Cefamandole	Cephamandol	Cefamandole	Цефамандол
-Ce(f|ph)alothin	TRUE	TRUE	TRUE	FALSE	Cefalothin	Cefalotine	Cefalotina	Cefalotina	Céphalothine	Cephalothin	Cephalothin	Kefalotin	Цефалотин
+Ce(f|ph)apirin	TRUE	TRUE	TRUE	FALSE	头孢匹林	Cephapirin	Cefapirine	Céphapirine	Cefapirin	Κεφαπιρίνη	Cefapirina	セファゾリン	Cefapiryna	Cephapirin	Цефапирин	Cefapirina	Cephapirin	Sefapirin	Цефапірин
-Ce(f|ph)alexin	TRUE	TRUE	TRUE	FALSE	Cefalexin	Cefalexine	Cefalexina	Cephalexin	Céphalexine	Cephalexin	Cephalexin	Cephalexin	Цефалексин
+Ce(f|ph)azedone	TRUE	TRUE	TRUE	FALSE	头孢唑酮	Cephazedon	Cefazedon	Céphazédone	Cefazedon	Κεφαζεδόνη	Cefazedone	セファロチン	Cefazedon	Cephazedone	Цефазедон	Cefazedona	Cephazedon	Sefazedon	Цефазедон
-Ce(f|ph)epime	TRUE	TRUE	TRUE	FALSE	Cefepim	Cefepim	Cefepime	Cephepime	Céphépime	Cephepime	Cephepime	Cephepim	Цефепим
+Ce(f|ph)azolin	TRUE	TRUE	TRUE	FALSE	头孢唑啉	Cephazolin	Cefazoline	Céphazoline	Cefazolin	Κεφαζολίνη	Cephazolin	セファレキシン	Cefazolin	Cephazolin	Цефазолин	Cefazolina	Cephazolin	Sefazolin	Цефазолін
-Ce(f|ph)ixime	TRUE	TRUE	TRUE	FALSE	Cefixim	Cefixim	Cefixima	Cephixime	Céphixime	Cephixime	Cephixim	Cephixim	Цефиксим
+Ce(f|ph)alothin	TRUE	TRUE	TRUE	FALSE	头孢罗丁	Cephalothin	Cefalotine	Céphalothine	Cefalothin	Κεφαλοθίνη	Cefalotina	セフェパイム	Cefalotyna	Cephalothin	Цефалотин	Cefalotina	Kefalotin	Cefalothin	Цефалотин
-Ce(f|ph)menoxime	TRUE	TRUE	TRUE	FALSE	Cefmenoxim	Cefmenoxim	Cefmenoxima	Cephmenoxime	Céphénoxime	Cephmenoxime	Cephmenoxim	Cephmenoxim	Цефменоксим
+Ce(f|ph)alexin	TRUE	TRUE	TRUE	FALSE	头孢莱辛	Cephalexin	Cefalexine	Céphalexine	Cefalexin	Κεφαλεξίνη	Cephalexin	セフィキシム	Cefaleksyna	Cephalexin	Цефалексин	Cefalexina	Cephalexin	Cefalexin	Цефалексин
-Ce(f|ph)metazole	TRUE	TRUE	TRUE	FALSE	Cefmetazol	Cefmetazol	Cefmetazol	Cephmetazole	Céphmétazole	Cefmetazole	Cephmetazol	Cephmetazol	Цефметазол
+Ce(f|ph)epime	TRUE	TRUE	TRUE	FALSE	头孢吡肟	Cephepime	Cefepim	Céphépime	Cefepim	Κεφεπίμη	Cephepime	セフメノキシム	Cefepime	Cephepime	Цефепим	Cefepime	Cephepim	Sefepim	Цефепім
-Ce(f|ph)odizime	TRUE	TRUE	TRUE	FALSE	Cefodizim	Cefodizim	Cefodixima	Cephodizime	Céphodizime	Cephodizime	Cephodizim	Cephodizim	Цефодизим
+Ce(f|ph)ixime	TRUE	TRUE	TRUE	FALSE	头孢克肟	Cephixim	Cefixim	Céphixime	Cefixim	Cefixime	Cephixime	セフメタゾール	Cefixime	Cephixime	Цефиксим	Cefixima	Cephixim	Cefixime	Цефіксим
-Ce(f|ph)onicid	TRUE	TRUE	TRUE	FALSE	Cefonicid	Cefonicide	Cefonicida	Cephonicid	Céphonicide	Cefonicid	Cephonicid	Cephonicid	Цефонизид
+Ce(f|ph)menoxime	TRUE	TRUE	TRUE	FALSE	头孢米诺肟	Cephmenoxim	Cefmenoxim	Céphénoxime	Cefmenoxim	Cefmenoxime	Cephmenoxime	セフォジジム	Cefmenoksym	Cephmenoxime	Цефменоксим	Cefmenoxima	Cephmenoxim	Sefmenoksim	Цефменоксим
-Ce(f|ph)operazone	TRUE	TRUE	TRUE	FALSE	Cefoperazon	Cefoperazon	Cefoperazona	Cephoperazone	Céphopérazone	Cephoperazone	Cephoperazon	Cephoperazon	Цефоперазон
+Ce(f|ph)metazole	TRUE	TRUE	TRUE	FALSE	头孢美唑	Cephmetazol	Cefmetazol	Céphmétazole	Cefmetazol	Cefmetazole	Cephmetazole	セフォニキッド	Cefmetazol	Cefmetazole	Цефметазол	Cefmetazol	Cephmetazol	Sefmetazol	Цефметазол
-Ce(f|ph)operazone/beta-lactamase inhibitor	TRUE	TRUE	TRUE	FALSE	Cefoperazon/Beta-Lactamase-Hemmer	Cefoperazon/enzymremmer	Cefoperazona/inhib. de betalactamasas	Cephoperazone/inib. d. beta-lattamasi	Céphopérazone/inhib. de bêta-lactamase	Cephoperazona/inibid. da beta-lactamase	Cephoperazon/beta-lactamasehæmmer	Cefoperazon/beta-laktamashämmare	Цефоперазон/ингибитор бета-лактамаз
+Ce(f|ph)odizime	TRUE	TRUE	TRUE	FALSE	头孢地嗪	Cephodizim	Cefodizim	Céphodizime	Cefodizim	Cefodizime	Cephodizime	セフォペラゾン	Cefodizime	Cephodizime	Цефодизим	Cefodixima	Cephodizim	Sefodizim	Цефодізим
-Ce(f|ph)otaxime	TRUE	TRUE	TRUE	FALSE	Cefotaxim	Cefotaxim	Cefotaxima	Cephotaxime	Céphotaxime	Cephotaxime	Cephotaxim	Cephotaxim	Цефотаксим
+Ce(f|ph)onicid	TRUE	TRUE	TRUE	FALSE	头孢尼西	Cephonicid	Cefonicide	Céphonicide	Cefonicid	Cefonicid	Cephonicid		Cefonicid	Cefonicid	Цефонизид	Cefonicida	Cephonicid	Cefonicid	Цефоніцид
-Ce(f|ph)oxitin	TRUE	TRUE	TRUE	FALSE	Cefoxitin	Cefoxitine	Cefoxitina	Cefossitina	Céphoxitine	Cephoxitin	Cephoxitin	Cephoxitin	Цефокситин
+Ce(f|ph)operazone	TRUE	TRUE	TRUE	FALSE	头孢哌酮	Cephoperazon	Cefoperazon	Céphopérazone	Cefoperazon	Κεφοπεραζόνη	Cephoperazone	セフォタキシム	Cefoperazon	Cephoperazone	Цефоперазон	Cefoperazona	Cephoperazon	Sefoperazon	Цефоперазон
-Ce(f|ph)pirome	TRUE	TRUE	TRUE	FALSE	Cefpirom	Cefpirom	Cephpirome	Cephpirome	Céphpirome	Cefpirome	Cephpirom	Cephpirom	Цефпиром
+Ce(f|ph)operazone/beta-lactamase inhibitor	TRUE	TRUE	TRUE	FALSE	头孢哌酮/β-内酰胺酶抑制剂	Cephoperazon/beta-lactamasehæmmer	Cefoperazon/enzymremmer	Céphopérazone/inhib. de bêta-lactamase	Cefoperazon/Beta-Lactamase-Hemmer	Κεφοπεραζόνη/αναστολέας της β-λακταμάσης	Cephoperazone/inib. d. beta-lattamasi		Cefoperazon/inhibitor beta-laktamazy	Cephoperazona/inibid. da beta-lactamase	Цефоперазон/ингибитор бета-лактамаз	Cefoperazona/inhib. de betalactamasas	Cefoperazon/beta-laktamashämmare	Sefoperazon/beta-laktamaz inhibitörü	Цефоперазон/інгібітор бета-лактамаз
-Ce(f|ph)podoxime	TRUE	TRUE	TRUE	FALSE	Cefpodoxim	Cefpodoxim	Cefpodoxima	Cephpodoxime	Céphpodoxime	Cephpodoxime	Cephpodoxim	Cephpodoxim	Цефподоксим
+Ce(f|ph)otaxime	TRUE	TRUE	TRUE	FALSE	头孢噻肟	Cephotaxim	Cefotaxim	Céphotaxime	Cefotaxim	Κεφοταξίμη	Cephotaxime	セフピロム	Cefotaksym	Cephotaxime	Цефотаксим	Cefotaxima	Cephotaxim	Sefotaksim	Цефотаксим
-Ce(f|ph)radine	TRUE	TRUE	TRUE	FALSE	Cefradin	Cefradine	Cefradina	Cefradina	Céphradine	Cephradine	Cephradin	Cephradin	Цефрадин
+Ce(f|ph)oxitin	TRUE	TRUE	TRUE	FALSE	头孢西丁	Cephoxitin	Cefoxitine	Céphoxitine	Cefoxitin	Κεφοξιτίνη	Cefossitina	セフポドキシム	Cefoksytyna	Cephoxitin	Цефокситин	Cefoxitina	Cephoxitin	Cefoxitin	Цефокситин
-Ce(f|ph)sulodin	TRUE	TRUE	TRUE	FALSE	Cefsulodin	Cefsulodine	Cefsulodina	Cephsulodin	Céphsulodine	Cephsulodin	Cephsulodin	Cephsulodin	Цефсулодин
+Ce(f|ph)pirome	TRUE	TRUE	TRUE	FALSE	头孢匹罗	Cephpirom	Cefpirom	Céphpirome	Cefpirom	Κεφπιρόμη	Cephpirome	セフラジン	Cefpirom	Cefpirome	Цефпиром	Cephpirome	Cephpirom	Sefpirom	Цефпіром
-Ce(f|ph)tazidime	TRUE	TRUE	TRUE	FALSE	Ceftazidim	Ceftazidim	Ceftazidima	Ceftazidima	Céphtazidime	Ceftazidima	Cephtazidim	Cephtazidim	Цефтазидим
+Ce(f|ph)podoxime	TRUE	TRUE	TRUE	FALSE	头孢泊肟	Cephpodoxim	Cefpodoxim	Céphpodoxime	Cefpodoxim	Κεφποδοξίμη	Cephpodoxime	セフスロジン	Cefpodoxime	Cephpodoxime	Цефподоксим	Cefpodoxima	Cephpodoxim	Sefpodoksim	Цефподоксим
-Ce(f|ph)tezole	TRUE	TRUE	TRUE	FALSE	Ceftezol	Ceftezol	Ceftezol	Cephtezole	Céphtézole	Ceftezole	Cephtezol	Cephtezole	Цефтезол
+Ce(f|ph)radine	TRUE	TRUE	TRUE	FALSE	头孢拉定	Cephradin	Cefradine	Céphradine	Cefradin	Cefradine	Cefradina	セフタジジム	Cefradyna	Cephradine	Цефрадин	Cefradina	Cephradin	Sefradin	Цефрадін
-Ce(f|ph)tizoxime	TRUE	TRUE	TRUE	FALSE	Ceftizoxim	Ceftizoxim	Ceftizoxima	Cephtizoxime	Céphtizoxime	Cephtizoxime	Cephtizoxim	Cephtizoxim	Цефтизоксим
+Ce(f|ph)sulodin	TRUE	TRUE	TRUE	FALSE	头孢苏洛丁	Cephsulodin	Cefsulodine	Céphsulodine	Cefsulodin	Cefsulodin	Cephsulodin	セフテゾール	Cefsulodin	Cephsulodin	Цефсулодин	Cefsulodina	Cephsulodin	Cefsulodin	Цефсулодин
-Ce(f|ph)triaxone	TRUE	TRUE	TRUE	FALSE	Ceftriaxon	Ceftriaxon	Ceftriaxona	Ceftriaxone	Céphtriaxone	Cefhtriaxone	Cephtriaxon	Ceftriaxon	Цефтриаксон
+Ce(f|ph)tazidime	TRUE	TRUE	TRUE	FALSE	头孢噻肟	Cephtazidim	Ceftazidim	Céphtazidime	Ceftazidim	Κεφταζιδίμη	Ceftazidima	セフティゾキシム	Ceftazidime	Ceftazidima	Цефтазидим	Ceftazidima	Cephtazidim	Seftazidim	Цефтазидим
-Ce(f|ph)uroxime	TRUE	TRUE	TRUE	FALSE	Cefuroxim	Cefuroxim	Cefuroxima	Cefuroxima	Céphuroxime	Cephuroxime	Cephuroxim	Cefuroxim	Цефуроксим
+Ce(f|ph)tezole	TRUE	TRUE	TRUE	FALSE	头孢特唑	Cephtezol	Ceftezol	Céphtézole	Ceftezol	Ceftezole	Cephtezole	セフトリアキソン	Ceftezol	Ceftezole	Цефтезол	Ceftezol	Cephtezole	Seftezol	Цефтезол
-Ce(f|ph)uroxime/metronidazole	TRUE	TRUE	TRUE	FALSE	Cefuroxim/Metronidazol	Cefuroxim/andere antibacteriele middelen	Cefuroxima/metronidazol	Cefuroxima/metronidazolo	Céphuroxime/métronidazole	Cephuroxime/metronidazol	Cefuroxim/metronidazol	Cefuroxim/metronidazol	Цефуроксим/метронидазол
+Ce(f|ph)tizoxime	TRUE	TRUE	TRUE	FALSE	头孢唑肟	Cephtizoxim	Ceftizoxim	Céphtizoxime	Ceftizoxim	Ceftizoxime	Cephtizoxime	セフロキシム	Ceftizoxime	Cephtizoxime	Цефтизоксим	Ceftizoxima	Cephtizoxim	Seftizoksim	Цефтизоксим
-Chloramphenicol	FALSE	TRUE	TRUE	FALSE	Chloramphenicol	Chlooramfenicol	Cloranfenicol	Cloramfenicolo	Chloramphénicol	Cloranfenicol	Kloramfenicol	Kloramfenikol	Хлорамфеникол
+Ce(f|ph)triaxone	TRUE	TRUE	TRUE	FALSE	头孢曲松	Cephtriaxon	Ceftriaxon	Céphtriaxone	Ceftriaxon	Ceftriaxone	Ceftriaxone		Ceftriakson	Cefhtriaxone	Цефтриаксон	Ceftriaxona	Ceftriaxon	Ceftriaxone	Цефтриаксон
-Chlortetracycline	FALSE	TRUE	TRUE	FALSE	Chlortetracyclin	Chloortetracycline	Clortetraciclina	Clorotetraciclina	Chlortétracycline	Chlortetracycline	Chlortetracyclin	Klortetracyklin	Хлортетрациклин
+Ce(f|ph)uroxime	TRUE	TRUE	TRUE	FALSE	头孢呋辛	Cephuroxim	Cefuroxim	Céphuroxime	Cefuroxim	Κεφουροξίμη	Cefuroxima	クロラムフェニコール	Cefuroksym	Cephuroxime	Цефуроксим	Cefuroxima	Cefuroxim	Sefuroksim	Цефуроксим
-Cinoxacin	FALSE	TRUE	TRUE	FALSE	Cinoxacin	Cinoxacine	Cinoxacina	Cinoxacina	Cinoxacine	Cinoxacin	Cinoxacin	Cinoxacin	Циноксацин
+Ce(f|ph)uroxime/metronidazole	TRUE	TRUE	TRUE	FALSE	头孢呋辛/甲硝唑	Cefuroxim/metronidazol	Cefuroxim/andere antibacteriele middelen	Céphuroxime/métronidazole	Cefuroxim/Metronidazol	Κεφουροξίμη/μετρονιδαζόλη	Cefuroxima/metronidazolo	クロルテトラサイクリン	Cefuroksym/metronidazol	Cephuroxime/metronidazol	Цефуроксим/метронидазол	Cefuroxima/metronidazol	Cefuroxim/metronidazol	Sefuroksim/metronidazol	Цефуроксим/метронідазол
-Ciprofloxacin	FALSE	TRUE	TRUE	FALSE	Ciprofloxacin	Ciprofloxacine	Ciprofloxacina	Ciprofloxacina	Ciprofloxacine	Ciprofloxacin	Ciprofloxacin	Ciprofloxacin	Ципрофлоксацин
+Chloramphenicol	FALSE	TRUE	TRUE	FALSE	氯霉素	Kloramfenicol	Chlooramfenicol	Chloramphénicol	Chloramphenicol	Χλωραμφενικόλη	Cloramfenicolo	シノキサシン	Chloramfenikol	Cloranfenicol	Хлорамфеникол	Cloranfenicol	Kloramfenikol	Kloramfenikol	Хлорамфенікол
-Clarithromycin	FALSE	TRUE	TRUE	FALSE	Clarithromycin	Claritromycine	Claritromicina	Claritromicina	Clarithromycine	Claritromicina	Clarithromycin	Claritromycin	Кларитромицин
+Chlortetracycline	FALSE	TRUE	TRUE	FALSE	金霉素	Chlortetracyclin	Chloortetracycline	Chlortétracycline	Chlortetracyclin	Χλωροτετρακυκλίνη	Clorotetraciclina	シプロフロキサシン	Chlortetracyklina	Chlortetracycline	Хлортетрациклин	Clortetraciclina	Klortetracyklin	Klortetrasiklin	Хлортетрациклін
-Clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	Clavulaanzuur	Ácido clavulánico	Acido clavulanico	Acide clavulanique	Ácido clavulânico	Clavulansyre	Clavulansyra	Клавулановая кислота
+Cinoxacin	FALSE	TRUE	TRUE	FALSE	西诺沙星	Cinoxacin	Cinoxacine	Cinoxacine	Cinoxacin	Cinoxacin	Cinoxacina	クラリスロマイシン	Cinoxacin	Cinoxacin	Циноксацин	Cinoxacina	Cinoxacin	Cinoxacin	Циноксацин
-clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	clavulaanzuur	ácido clavulánico	acido clavulanico	acide clavulanique	ácido clavulânico	clavulansyre	clavulansyra	клавулановая кислота
+Ciprofloxacin	FALSE	TRUE	TRUE	FALSE	环丙沙星	Ciprofloxacin	Ciprofloxacine	Ciprofloxacine	Ciprofloxacin	Σιπροφλοξασίνη	Ciprofloxacina	クラビュラン酸	Ciprofloksacyna	Ciprofloxacin	Ципрофлоксацин	Ciprofloxacina	Ciprofloxacin	Siprofloksasin	Ципрофлоксацин
-Clindamycin	FALSE	TRUE	TRUE	FALSE	Clindamycin	Clindamycine	Clindamicina	Clindamicina	Clindamycine	Clindamicina	Clindamycin	Clindamycin	Клиндамицин
+Clarithromycin	FALSE	TRUE	TRUE	FALSE	克拉霉素	Clarithromycin	Claritromycine	Clarithromycine	Clarithromycin	Κλαριθρομυκίνη	Claritromicina	クラビュラン酸	Klarytromycyna	Claritromicina	Кларитромицин	Claritromicina	Claritromycin	Klaritromisin	Кларитроміцин
-Clometocillin	FALSE	TRUE	TRUE	FALSE	Clometocillin	Clometocilline	Clometocilina	Clometocillina	Clométocilline	Clometocillin	Clometocillin	Klometocillin	Клометоциллин
+Clavulanic acid	FALSE	TRUE	TRUE	FALSE	克拉维酸	Clavulansyre	Clavulaanzuur	Acide clavulanique	Clavulansäure	Κλαβουλανικό οξύ	Acido clavulanico	クリンダマイシン	Kwas klawulanowy	Ácido clavulânico	Клавулановая кислота	Ácido clavulánico	Clavulansyra	Klavulanik asit	Клавуланова кислота
-Clotrimazole	FALSE	TRUE	TRUE	FALSE	Clotrimazol	Clotrimazol	Clotrimazol	Clotrimazolo	Clotrimazole	Clotrimazole	Clotrimazol	Klotrimazol	Клотримазол
+clavulanic acid	FALSE	TRUE	TRUE	FALSE	克拉维酸	clavulansyre	clavulaanzuur	acide clavulanique	Clavulansäure	Κλαβουλανικό οξύ	acido clavulanico	クロメトシリン	kwas klawulanowy	ácido clavulânico	клавулановая кислота	ácido clavulánico	clavulansyra	klavulanik asit	клавуланова кислота
-Cloxacillin	FALSE	TRUE	TRUE	FALSE	Cloxacillin	Cloxacilline	Cloxacilina	Cloxacillina	Cloxacilline	Cloxacillin	Cloxacillin	Kloxacillin	Клоксациллин
+Clindamycin	FALSE	TRUE	TRUE	FALSE	克林霉素	Clindamycin	Clindamycine	Clindamycine	Clindamycin	Clindamycin	Clindamicina	クロトリマゾール	Klindamycyna	Clindamicina	Клиндамицин	Clindamicina	Clindamycin	Klindamisin	Кліндаміцин
-Colistin	FALSE	TRUE	TRUE	FALSE	Colistin	Colistine	Colistina	Colistina	Colistine	Colistin	Colistin	Kolistin	Колистин
+Clometocillin	FALSE	TRUE	TRUE	FALSE	克罗米修斯（	Clometocillin	Clometocilline	Clométocilline	Clometocillin	Clometocillin	Clometocillina	クロキサシリン	Clometocillin	Clometocillin	Клометоциллин	Clometocilina	Klometocillin	Clometocillin	Клометоцилін
-Dapsone	FALSE	TRUE	TRUE	FALSE	Dapson	Dapson	Dapsona	Dapsone	Dapsone	Dapsone	Dapson	Dapson	Дапсон
+Clotrimazole	FALSE	TRUE	TRUE	FALSE	克霉唑	Clotrimazol	Clotrimazol	Clotrimazole	Clotrimazol	Κλοτριμαζόλη	Clotrimazolo	コリスチン	Klotrimazol	Clotrimazole	Клотримазол	Clotrimazol	Klotrimazol	Klotrimazol	Клотримазол
-Daptomycin	FALSE	TRUE	TRUE	FALSE	Daptomycin	Daptomycine	Daptomicina	Daptomicina	Daptomycine	Daptomicina	Daptomycin	Daptomycin	Даптомицин
+Cloxacillin	FALSE	TRUE	TRUE	FALSE	克罗西林	Cloxacillin	Cloxacilline	Cloxacilline	Cloxacillin	Κλοξακιλλίνη	Cloxacillina	ダプソン	Cloxacillin	Cloxacillin	Клоксациллин	Cloxacilina	Kloxacillin	Cloxacillin	Клоксацилін
-Dibekacin	FALSE	TRUE	TRUE	FALSE	Dibekacin	Dibekacine	Dibekacina	Dibekacin	Dibekacine	Dibekacin	Dibekacin	Dibekacin	Дибекацин
+Colistin	FALSE	TRUE	TRUE	FALSE	唑啉酮	Colistin	Colistine	Colistine	Colistin	Κολιστίνη	Colistina	ダプトマイシン	Kolistyna	Colistin	Колистин	Colistina	Kolistin	Kolistin	Колістин
-Dicloxacillin	FALSE	TRUE	TRUE	FALSE	Dicloxacillin	Dicloxacilline	Dicloxacilina	Dicloxacillina	Dicloxacilline	Dicloxacilina	Dicloxacillin	Dikloxacillin	Диклоксациллин
+Dapsone	FALSE	TRUE	TRUE	FALSE	多普生	Dapson	Dapson	Dapsone	Dapson	Δαψόνη	Dapsone	ジベカシン	Dapson	Dapsone	Дапсон	Dapsona	Dapson	Dapson	Дапсон
-Dirithromycin	FALSE	TRUE	TRUE	FALSE	Dirithromycin	Diritromycine	Diritromicina	Diritromicina	Dirithromycine	Diritromicina	Dirithromycin	Diritromycin	Диритромицин
+Daptomycin	FALSE	TRUE	TRUE	FALSE	达托霉素	Daptomycin	Daptomycine	Daptomycine	Daptomycin	Daptomycin	Daptomicina	ジクロキサシリン	Daptomycyna	Daptomicina	Даптомицин	Daptomicina	Daptomycin	Daptomisin	Даптоміцин
-Econazole	FALSE	TRUE	TRUE	FALSE	Econazol	Econazol	Econazol	Econazolo	Econazole	Econazole	Econazol	Ekonazol	Эконазол
+Dibekacin	FALSE	TRUE	TRUE	FALSE	迪贝卡星	Dibekacin	Dibekacine	Dibekacine	Dibekacin	Dibekacin	Dibekacin	ジリスロマイシン	Dibekacin	Dibekacin	Дибекацин	Dibekacina	Dibekacin	Dibekacin	Дібекацин
-Enoxacin	FALSE	TRUE	TRUE	FALSE	Enoxacin	Enoxacine	Enoxacina	Enoxacina	Enoxacine	Enoxacin	Enoxacin	Enoxacin	Эноксацин
+Dicloxacillin	FALSE	TRUE	TRUE	FALSE	迪卡西林	Dicloxacillin	Dicloxacilline	Dicloxacilline	Dicloxacillin	Dicloxacillin	Dicloxacillina	エコナゾール	Dikloxacillin	Dicloxacilina	Диклоксациллин	Dicloxacilina	Dikloxacillin	Dikloksasilin	Диклоксацилін
-Epicillin	FALSE	TRUE	TRUE	FALSE	Epicillin	Epicilline	Epicilina	Epicillina	Epicilline	Epicilina	Epicillin	Epicillin	Эпициллин
+Dirithromycin	FALSE	TRUE	TRUE	FALSE	迪里红霉素	Dirithromycin	Diritromycine	Dirithromycine	Dirithromycin	Dirithromycin	Diritromicina	エノキサシン	Dirytromycyna	Diritromicina	Диритромицин	Diritromicina	Diritromycin	Diritromisin	Диритроміцин
-Erythromycin	FALSE	TRUE	TRUE	FALSE	Erythromycin	Erytromycine	Eritromicina	Eritromicina	Erythromycine	Eritromicina	Erythromycin	Erytromycin	Эритромицин
+Econazole	FALSE	TRUE	TRUE	FALSE	胺鲜胺	Econazol	Econazol	Econazole	Econazol	Econazole	Econazolo	エピシリン	Ekonazol	Econazole	Эконазол	Econazol	Ekonazol	Ekonazol	Еконазол
-Ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	Ethambutol/Isoniazid	Ethambutol/isoniazide	Etambutol/isoniazida	Etambutolo/isoniazide	Ethambutol/isoniazide	Ethambutol/isoniazid	Ethambutol/isoniazid	Etambutol/isoniazid	Этамбутол/изониазид
+Enoxacin	FALSE	TRUE	TRUE	FALSE	伊诺沙星	Enoxacin	Enoxacine	Enoxacine	Enoxacin	Enoxacin	Enoxacina	エリスロマイシン	Enoxacin	Enoxacin	Эноксацин	Enoxacina	Enoxacin	Enoksasin	Еноксацин
-Fleroxacin	FALSE	TRUE	TRUE	FALSE	Fleroxacin	Fleroxacine	Fleroxacina	Fleroxacina	Fléroxacine	Fleroxacina	Fleroxacin	Fleroxacin	Флероксацин
+Epicillin	FALSE	TRUE	TRUE	FALSE	伊比西林	Epicillin	Epicilline	Epicilline	Epicillin	Epicillin	Epicillina	エタンブトール／イソニアジド	Epicillin	Epicilina	Эпициллин	Epicilina	Epicillin	Episilin	Епіцилін
-Flucloxacillin	FALSE	TRUE	TRUE	FALSE	Flucloxacillin	Flucloxacilline	Flucloxacilina	Flucloxacillina	Flucloxacilline	Flucloxacillin	Flucloxacillin	Flucloxacillin	Флуклоксациллин
+Erythromycin	FALSE	TRUE	TRUE	FALSE	红霉素	Erythromycin	Erytromycine	Erythromycine	Erythromycin	Ερυθρομυκίνη	Eritromicina	フレロキサシン	Erytromycyna	Eritromicina	Эритромицин	Eritromicina	Erytromycin	Eritromisin	Еритроміцин
-Fluconazole	FALSE	TRUE	TRUE	FALSE	Fluconazol	Fluconazol	Fluconazol	Fluconazolo	Fluconazole	Fluconazole	Fluconazol	Flukonazol	Флуконазол
+Ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	乙胺丁醇/异烟肼	Ethambutol/isoniazid	Ethambutol/isoniazide	Ethambutol/isoniazide	Ethambutol/Isoniazid	Αιθαμβουτόλη/ισονιαζίδη	Etambutolo/isoniazide	フルクロキサシリン	Etambutol/izoniazyd	Ethambutol/isoniazid	Этамбутол/изониазид	Etambutol/isoniazida	Etambutol/isoniazid	Etambutol/izoniazid	Етамбутол/ізоніазид
-Flucytosine	FALSE	TRUE	TRUE	FALSE	Flucytosin	Fluorocytosine	Flucitosina	Flucytosine	Flucytosine	Flucytosine	Flucytosin	Flucytosin	Флуцитозин
+Fleroxacin	FALSE	TRUE	TRUE	FALSE	氨甲喋呤	Fleroxacin	Fleroxacine	Fléroxacine	Fleroxacin	Φλεροξακίνη	Fleroxacina	フルコナゾール	Fleroksacyna	Fleroxacina	Флероксацин	Fleroxacina	Fleroxacin	Fleroxacin	Флероксацин
-Flurithromycin	FALSE	TRUE	TRUE	FALSE	Flurithromycin	Fluritromycine	Fluritromicina	Fluritromicina	Flurithromycine	Fluritromicina	Flurithromycin	Fluritromycin	Флуритромицин
+Flucloxacillin	FALSE	TRUE	TRUE	FALSE	氟氯西林	Flucloxacillin	Flucloxacilline	Flucloxacilline	Flucloxacillin	Flucloxacillin	Flucloxacillina	フルシトシン	Flucloxacillin	Flucloxacillin	Флуклоксациллин	Flucloxacilina	Flucloxacillin	Flukloksasilin	Флуклоксацилін
-Fosfomycin	FALSE	TRUE	TRUE	FALSE	Fosfomycin	Fosfomycine	Fosfomicina	Fosfomicina	Fosfomycine	Fosfomycin	Fosfomycin	Fosfomycin	Фосфомицин
+Fluconazole	FALSE	TRUE	TRUE	FALSE	氟康唑	Fluconazol	Fluconazol	Fluconazole	Fluconazol	Φλουκοναζόλη	Fluconazolo	フルリスロマイシン	Flukonazol	Fluconazole	Флуконазол	Fluconazol	Flukonazol	Flukonazol	Флуконазол
-Fusidic acid	FALSE	TRUE	TRUE	FALSE	Fusidinsäure	Fusidinezuur	Ácido fusídico	Acido fusidico	Acide fusidique	Ácido fusídico	Fusidinsyre	Fusidinsyra	Фузидовая кислота
+Flucytosine	FALSE	TRUE	TRUE	FALSE	氨甲喋呤	Flucytosin	Fluorocytosine	Flucytosine	Flucytosin	Φλουκυτοσίνη	Flucytosine	ホスホマイシン	Flucytozyna	Flucytosine	Флуцитозин	Flucitosina	Flucytosin	Flusitozin	Флуцитозин
-Gatifloxacin	FALSE	TRUE	TRUE	FALSE	Gatifloxacin	Gatifloxacine	Gatifloxacina	Gatifloxacina	Gatifloxacine	Gatifloxacin	Gatifloxacin	Gatifloxacin	Гатифлоксацин
+Flurithromycin	FALSE	TRUE	TRUE	FALSE	氟利霉素	Flurithromycin	Fluritromycine	Flurithromycine	Flurithromycin	Φλουριθρομυκίνη	Fluritromicina	フシジン酸	Flurithromycin	Fluritromicina	Флуритромицин	Fluritromicina	Fluritromycin	Fluritromisin	Флуритроміцин
-Gemifloxacin	FALSE	TRUE	TRUE	FALSE	Gemifloxacin	Gemifloxacine	Gemifloxacina	Gemifloxacina	Gemifloxacine	Gemifloxacin	Gemifloxacin	Gemifloxacin	Гемифлоксацин
+Fosfomycin	FALSE	TRUE	TRUE	FALSE	福斯霉素	Fosfomycin	Fosfomycine	Fosfomycine	Fosfomycin	Φοσφομυκίνη	Fosfomicina	ガチフロキサシン	Fosfomycyna	Fosfomycin	Фосфомицин	Fosfomicina	Fosfomycin	Fosfomisin	Фосфоміцин
-Gentamicin	FALSE	TRUE	TRUE	FALSE	Gentamicin	Gentamicine	Gentamicina	Gentamicina	Gentamicine	Gentamicina	Gentamicin	Gentamicin	Гентамицин
+Fusidic acid	FALSE	TRUE	TRUE	FALSE	夫西地酸	Fusidinsyre	Fusidinezuur	Acide fusidique	Fusidinsäure	Φουσιδικό οξύ	Acido fusidico	ゲミフロキサシン	Kwas fusydynowy	Ácido fusídico	Фузидовая кислота	Ácido fusídico	Fusidinsyra	Fusidik asit	Фузидова кислота
-Grepafloxacin	FALSE	TRUE	TRUE	FALSE	Grepafloxacin	Grepafloxacine	Grepafloxacina	Grepafloxacina	Grepafloxacine	Grepafloxacin	Grepafloxacin	Grepafloxacin	Грепафлоксацин
+Gatifloxacin	FALSE	TRUE	TRUE	FALSE	加替沙星	Gatifloxacin	Gatifloxacine	Gatifloxacine	Gatifloxacin	Gatifloxacin	Gatifloxacina	ゲンタマイシン	Gatifloxacin	Gatifloxacin	Гатифлоксацин	Gatifloxacina	Gatifloxacin	Gatifloksasin	Гатифлоксацин
-Hachimycin	FALSE	TRUE	TRUE	FALSE	Hachimycin	Hachimycine	Hachimycin	Hachimycin	Hachimycine	Hachimycin	Hachimycin	Hachimycin	Хатимицин
+Gemifloxacin	FALSE	TRUE	TRUE	FALSE	吉非沙星	Gemifloxacin	Gemifloxacine	Gemifloxacine	Gemifloxacin	Gemifloxacin	Gemifloxacina	グレパフロキサシン	Gemifloksacyna	Gemifloxacin	Гемифлоксацин	Gemifloxacina	Gemifloxacin	Gemifloksasin	Геміфлоксацин
-Hetacillin	FALSE	TRUE	TRUE	FALSE	Hetacillin	Hetacilline	Hetacilina	Hetacillin	Hétacilline	Hetacillin	Hetacillin	Hetacillin	Гетациллин
+Gentamicin	FALSE	TRUE	TRUE	FALSE	庆大霉素	Gentamicin	Gentamicine	Gentamicine	Gentamicin	Gentamicin	Gentamicina	ハチマイシン	Gentamicin	Gentamicina	Гентамицин	Gentamicina	Gentamicin	Gentamisin	Гентаміцин
-Imipenem/cilastatin	FALSE	TRUE	TRUE	FALSE	Imipenem/Cilastatin	Imipenem/enzymremmer	Imipenem/cilastatina	Imipenem/cilastatina	Imipénème/cilastatine	Imipenem/coteltelatina	Imipenem/cilastatin	Imipenem/cilastatin	Имипенем/циластатин
+Grepafloxacin	FALSE	TRUE	TRUE	FALSE	格雷帕沙星	Grepafloxacin	Grepafloxacine	Grepafloxacine	Grepafloxacin	Grepafloxacin	Grepafloxacina	ヘタシリン	Grepafloksacyna	Grepafloxacin	Грепафлоксацин	Grepafloxacina	Grepafloxacin	Grepafloksasin	Грепафлоксацин
-Inosine pranobex	FALSE	TRUE	TRUE	FALSE	Inosin-Pranobex	Inosiplex	Inosina pranobex	Inosina pranobex	Inosine pranobex	Pranobex inosine	Inosin pranobex	Inosin pranobex	Инозин пранобекс
+Hachimycin	FALSE	TRUE	TRUE	FALSE	哈奇霉素	Hachimycin	Hachimycine	Hachimycine	Hachimycin	Hachimycin	Hachimycin	イミペネム／シラスタチン	Hachimycin	Hachimycin	Хатимицин	Hachimycin	Hachimycin	Hachimycin	Хачиміцин
-Isepamicin	FALSE	TRUE	TRUE	FALSE	Isepamicin	Isepamicine	Isepamicina	Isepamicina	Isepamicine	Isepamicina	Isepamicin	Isepamicin	Исепамицин
+Hetacillin	FALSE	TRUE	TRUE	FALSE	赫拉西林	Hetacillin	Hetacilline	Hétacilline	Hetacillin	Hetacillin	Hetacillin	イノシン・プラノベックス	Hetacylina	Hetacillin	Гетациллин	Hetacilina	Hetacillin	Hetasilin	Гетацилін
-Isoconazole	FALSE	TRUE	TRUE	FALSE	Isoconazol	Isoconazol	Isoconazol	Isoconazolo	Isoconazole	Isoconazole	Isoconazol	Isokonazol	Изоконазол
+Imipenem/cilastatin	FALSE	TRUE	TRUE	FALSE	亚胺培南/西司他丁	Imipenem/cilastatin	Imipenem/enzymremmer	Imipénème/cilastatine	Imipenem/Cilastatin	Ιμιπενέμη/σιλαστατίνη	Imipenem/cilastatina	イセパマイシン	Imipenem/cilastatyna	Imipenem/coteltelatina	Имипенем/циластатин	Imipenem/cilastatina	Imipenem/cilastatin	İmipenem/silastatin	Іміпенем/циластатин
-Isoniazid	FALSE	TRUE	TRUE	FALSE	Isoniazid	Isoniazide	Isoniazida	Isoniazide	Isoniazide	Isoniazid	Isoniazid	Isoniazid	Изониазид
+Inosine pranobex	FALSE	TRUE	TRUE	FALSE	肌苷帕诺贝斯	Inosin pranobex	Inosiplex	Inosine pranobex	Inosin-Pranobex	Ινοσίνη pranobex	Inosina pranobex	イソコナゾール	Pranobeks inozyny	Pranobex inosine	Инозин пранобекс	Inosina pranobex	Inosin pranobex	İnosin pranobeks	Інозин пранобекс
-Itraconazole	FALSE	TRUE	TRUE	FALSE	Itraconazol	Itraconazol	Itraconazol	Itraconazolo	Itraconazole	Itraconazole	Itraconazol	Itrakonazol	Итраконазол
+Isepamicin	FALSE	TRUE	TRUE	FALSE	伊西帕米星	Isepamicin	Isepamicine	Isepamicine	Isepamicin	Isepamicin	Isepamicina	イソニアジド	Isepamicin	Isepamicina	Исепамицин	Isepamicina	Isepamicin	İzepamisin	Ізепаміцин
-Josamycin	FALSE	TRUE	TRUE	FALSE	Josamycin	Josamycine	Josamicina	Josamicina	Josamycine	Josamycin	Josamycin	Josamycin	Джозамицин
+Isoconazole	FALSE	TRUE	TRUE	FALSE	氨甲蝶呤	Isoconazol	Isoconazol	Isoconazole	Isoconazol	Ισοκοναζόλη	Isoconazolo	イトラコナゾール	Izokonazol	Isoconazole	Изоконазол	Isoconazol	Isokonazol	İzokonazol	Ізоконазол
-Kanamycin	FALSE	TRUE	TRUE	FALSE	Kanamycin	Kanamycine	Kanamicina	Kanamicina	Kanamycine	Kanamycin	Kanamycin	Kanamycin	Канамицин
+Isoniazid	FALSE	TRUE	TRUE	FALSE	伊索尼克酸	Isoniazid	Isoniazide	Isoniazide	Isoniazid	Ιζονιαζίδη	Isoniazide	ホサマイシン	Izoniazyd	Isoniazid	Изониазид	Isoniazida	Isoniazid	İzoniazid	Ізоніазид
-Ketoconazole	FALSE	TRUE	TRUE	FALSE	Ketoconazol	Ketoconazol	Ketoconazol	Ketoconazolo	Kétoconazole	Ketoconazole	Ketoconazol	Ketokonazol	Кетоконазол
+Itraconazole	FALSE	TRUE	TRUE	FALSE	伊曲康唑	Itraconazol	Itraconazol	Itraconazole	Itraconazol	Ιτρακοναζόλη	Itraconazolo	カナマイシン	Itrakonazol	Itraconazole	Итраконазол	Itraconazol	Itrakonazol	İtrakonazol	Ітраконазол
-Levofloxacin	FALSE	TRUE	TRUE	FALSE	Levofloxacin	Levofloxacine	Levofloxacina	Levofloxacina	Lévofloxacine	Levofloxacin	Levofloxacin	Levofloxacin	Левофлоксацин
+Josamycin	FALSE	TRUE	TRUE	FALSE	肌注	Josamycin	Josamycine	Josamycine	Josamycin	Josamycin	Josamicina	ケトコナゾール	Josamycin	Josamycin	Джозамицин	Josamicina	Josamycin	Josamycin	Джозаміцин
-Lincomycin	FALSE	TRUE	TRUE	FALSE	Lincomycin	Lincomycine	Lincomicina	Lincomicina	Lincomycine	Lincomycin	Lincomycin	Lincomycin	Линкомицин
+Kanamycin	FALSE	TRUE	TRUE	FALSE	卡那霉素	Kanamycin	Kanamycine	Kanamycine	Kanamycin	Kanamycin	Kanamicina	レボフロキサシン	Kanamycin	Kanamycin	Канамицин	Kanamicina	Kanamycin	Kanamisin	Канаміцин
-Lomefloxacin	FALSE	TRUE	TRUE	FALSE	Lomefloxacin	Lomefloxacine	Lomefloxacina	Lomefloxacina	Loméfloxacine	Lomefloxacin	Lomefloxacin	Lomefloxacin	Ломефлоксацин
+Ketoconazole	FALSE	TRUE	TRUE	FALSE	酮康唑	Ketoconazol	Ketoconazol	Kétoconazole	Ketoconazol	Κετοκοναζόλη	Ketoconazolo	リンコマイシン	Ketokonazol	Ketoconazole	Кетоконазол	Ketoconazol	Ketokonazol	Ketokonazol	Кетоконазол
-Lysozyme	FALSE	TRUE	TRUE	FALSE	Lysozym	Lysozym	Lisozima	Lisozima	Lysozyme	Lysozyme	Lysozym	Lysozym	Лизоцим
+Levofloxacin	FALSE	TRUE	TRUE	FALSE	氧氟沙星	Levofloxacin	Levofloxacine	Lévofloxacine	Levofloxacin	Λεβοφλοξασίνη	Levofloxacina	ロメフロキサシン	Levofloxacin	Levofloxacin	Левофлоксацин	Levofloxacina	Levofloxacin	Levofloksasin	Левофлоксацин
-Mandelic acid	FALSE	TRUE	TRUE	FALSE	Mandelsäure	Amandelzuur	Ácido mandélico	Acido mandelico	Acide mandélique	Ácido mandélico	Mandelinsyre	Mandelsyra	Мандаловая кислота
+Lincomycin	FALSE	TRUE	TRUE	FALSE	林可霉素	Lincomycin	Lincomycine	Lincomycine	Lincomycin	Lincomycin	Lincomicina	リゾチーム	Lincomycyna	Lincomycin	Линкомицин	Lincomicina	Lincomycin	Lincomycin	Лінкоміцин
-Metampicillin	FALSE	TRUE	TRUE	FALSE	Metampicillin	Metampicilline	Metampicilina	Metampicillina	Métampicilline	Metampicilina	Metampicillin	Metampicillin	Метампициллин
+Lomefloxacin	FALSE	TRUE	TRUE	FALSE	洛美沙星	Lomefloxacin	Lomefloxacine	Loméfloxacine	Lomefloxacin	Λομεφλοξασίνη	Lomefloxacina	マンデル酸	Lomefloxacin	Lomefloxacin	Ломефлоксацин	Lomefloxacina	Lomefloxacin	Lomefloksasin	Ломефлоксацин
-Meticillin	FALSE	TRUE	TRUE	FALSE	Meticillin	Meticilline	Meticilina	Meticillina	Méticilline	Meticillin	Meticillin	Meticillin	Метициллин
+Lysozyme	FALSE	TRUE	TRUE	FALSE	硫酸钠	Lysozym	Lysozym	Lysozyme	Lysozym	Λυσοζύμη	Lisozima	メタンピシリン	Lizozym	Lysozyme	Лизоцим	Lisozima	Lysozym	Lizozim	Лізоцим
-Metisazone	FALSE	TRUE	TRUE	FALSE	Metisazon	Metisazon	Metisazona	Metisazone	Métisazone	Metisazone	Metisazon	Metisazon	Метисазон
+Mandelic acid	FALSE	TRUE	TRUE	FALSE	扁桃酸	Mandelinsyre	Amandelzuur	Acide mandélique	Mandelsäure	Μανδελικό οξύ	Acido mandelico	メチシリン	Kwas migdałowy	Ácido mandélico	Мандаловая кислота	Ácido mandélico	Mandelsyra	Mandelik asit	Мигдалева кислота
-Metronidazole	FALSE	TRUE	TRUE	FALSE	Metronidazol	Metronidazol	Metronidazol	Metronidazolo	Métronidazole	Metronidazol	Metronidazol	Metronidazol	Метронидазол
+Metampicillin	FALSE	TRUE	TRUE	FALSE	氨苄青霉素	Metampicillin	Metampicilline	Métampicilline	Metampicillin	Metampicillin	Metampicillina	メチサゾン	Metampicylina	Metampicilina	Метампициллин	Metampicilina	Metampicillin	Metampisilin	Метампіцилін
-Mezlocillin	FALSE	TRUE	TRUE	FALSE	Mezlocillin	Mezlocilline	Mezlocilina	Mezlocillina	Mezlocilline	Mezlocillin	Mezlocillin	Mezlocillin	Мезлоциллин
+Meticillin	FALSE	TRUE	TRUE	FALSE	美西林	Meticillin	Meticilline	Méticilline	Meticillin	Μετικιλλίνη	Meticillina	メトロニダゾール	Meticillin	Meticillin	Метициллин	Meticilina	Meticillin	Metisilin	Метицилін
-Micafungin	FALSE	TRUE	TRUE	FALSE	Micafungin	Micafungine	Micafungina	Micafungin	Micafungine	Micafungin	Micafungin	Micafungin	Микафунгин
+Metisazone	FALSE	TRUE	TRUE	FALSE	氨甲喋呤	Metisazon	Metisazon	Métisazone	Metisazon	Μετισαζόνη	Metisazone	メスロシリン	Metisazon	Metisazone	Метисазон	Metisazona	Metisazon	Metisazon	Метисазон
-Miconazole	FALSE	TRUE	TRUE	FALSE	Miconazol	Miconazol	Miconazol	Miconazolo	Miconazole	Miconazole	Miconazol	Miconazol	Миконазол
+Metronidazole	FALSE	TRUE	TRUE	FALSE	甲硝唑	Metronidazol	Metronidazol	Métronidazole	Metronidazol	Μετρονιδαζόλη	Metronidazolo	ミカファンギン	Metronidazol	Metronidazol	Метронидазол	Metronidazol	Metronidazol	Metronidazol	Метронідазол
-Midecamycin	FALSE	TRUE	TRUE	FALSE	Midecamycin	Midecamycine	Midecamicina	Midecamicina	Midecamycine	Midecamycin	Midecamycin	Midecamycin	Мидекамицин
+Mezlocillin	FALSE	TRUE	TRUE	FALSE	氨甲蝶呤	Mezlocillin	Mezlocilline	Mezlocilline	Mezlocillin	Mezlocillin	Mezlocillina	ミコナゾール	Mezlocillin	Mezlocillin	Мезлоциллин	Mezlocilina	Mezlocillin	Mezlosilin	Мезлоцилін
-Miocamycin	FALSE	TRUE	TRUE	FALSE	Miocamycin	Miocamycine	Miocamycin	Miocamicina	Miocamycine	Miocamicina	Miocamycin	Miocamycin	Миокамицин
+Micafungin	FALSE	TRUE	TRUE	FALSE	咪蒙灵	Micafungin	Micafungine	Micafungine	Micafungin	Micafungin	Micafungin	ミデカマイシン	Micafungin	Micafungin	Микафунгин	Micafungina	Micafungin	Mikafungin	Мікафунгін
-Moxifloxacin	FALSE	TRUE	TRUE	FALSE	Moxifloxacin	Moxifloxacine	Moxifloxacina	Moxifloxacin	Moxifloxacine	Moxifloxacina	Moxifloxacin	Moxifloxacin	Моксифлоксацин
+Miconazole	FALSE	TRUE	TRUE	FALSE	米康唑	Miconazol	Miconazol	Miconazole	Miconazol	Miconazole	Miconazolo	ミオカマイシン	Mikonazol	Miconazole	Миконазол	Miconazol	Miconazol	Mikonazol	Міконазол
-Mupirocin	FALSE	TRUE	TRUE	FALSE	Mupirocin	Mupirocine	Mupirocina	Mupirocina	Mupirocine	Mupirocina	Mupirocin	Mupirocin	Мупироцин
+Midecamycin	FALSE	TRUE	TRUE	FALSE	咪康霉素	Midecamycin	Midecamycine	Midecamycine	Midecamycin	Μεδεκαμυκίνη	Midecamicina	モキシフロキサシン	Midecamycin	Midecamycin	Мидекамицин	Midecamicina	Midecamycin	Midecamycin	Мідекаміцин
-Nalidixic acid	FALSE	TRUE	TRUE	FALSE	Nalidixinsäure	Nalidixinezuur	Ácido nalidíxico	Acido nalidixico	Acide nalidixique	Ácido nalidíxico	Nalidixinsyre	Nalidixinsyra	Налидиксовая кислота
+Miocamycin	FALSE	TRUE	TRUE	FALSE	米卡霉素	Miocamycin	Miocamycine	Miocamycine	Miocamycin	Miocamycin	Miocamicina	ムピロシン	Miocamycin	Miocamicina	Миокамицин	Miocamycin	Miocamycin	Miocamycin	Міокаміцин
-Neomycin	FALSE	TRUE	TRUE	FALSE	Neomycin	Neomycine	Neomicina	Neomicina	Néomycine	Neomicina	Neomycin	Neomycin	Неомицин
+Moxifloxacin	FALSE	TRUE	TRUE	FALSE	莫西沙星	Moxifloxacin	Moxifloxacine	Moxifloxacine	Moxifloxacin	Moxifloxacin	Moxifloxacin	ナリディキシック酸	Moxifloxacin	Moxifloxacina	Моксифлоксацин	Moxifloxacina	Moxifloxacin	Moksifloksasin	Моксифлоксацин
-Netilmicin	FALSE	TRUE	TRUE	FALSE	Netilmicin	Netilmicine	Netilmicina	Netilmicin	Netilmicine	Netilmicin	Netilmicin	Netilmicin	Нетилмицин
+Mupirocin	FALSE	TRUE	TRUE	FALSE	莫匹罗星	Mupirocin	Mupirocine	Mupirocine	Mupirocin	Mupirocin	Mupirocina	ネオマイシン	Mupirocyna	Mupirocina	Мупироцин	Mupirocina	Mupirocin	Mupirosin	Мупіроцин
-Nitrofurantoin	FALSE	TRUE	TRUE	FALSE	Nitrofurantoin	Nitrofurantoine	Nitrofurantoína	Nitrofurantoina	Nitrofurantoïne	Nitrofurantoína	Nitrofurantoin	Nitrofurantoin	Нитрофурантоин
+Nalidixic acid	FALSE	TRUE	TRUE	FALSE	萘啶酸	Nalidixinsyre	Nalidixinezuur	Acide nalidixique	Nalidixinsäure	Ναλιδιξικό οξύ	Acido nalidixico	ネチルミシン	Kwas nalidyksowy	Ácido nalidíxico	Налидиксовая кислота	Ácido nalidíxico	Nalidixinsyra	Nalidiksik asit	Налідиксова кислота
-Norfloxacin	FALSE	TRUE	TRUE	FALSE	Norfloxacin	Norfloxacine	Norfloxacina	Norfloxacina	Norfloxacine	Norfloxacin	Norfloxacin	Norfloxacin	Норфлоксацин
+Neomycin	FALSE	TRUE	TRUE	FALSE	霉素	Neomycin	Neomycine	Néomycine	Neomycin	Νεομυκίνη	Neomicina	ニトロフラントイン	Neomycyna	Neomicina	Неомицин	Neomicina	Neomycin	Neomisin	Неоміцин
-Novobiocin	FALSE	TRUE	TRUE	FALSE	Novobiocin	Novobiocine	Novobiocina	Novobiocin	Novobiocine	Novobiocin	Novobiocin	Novobiocin	Новобиоцин
+Netilmicin	FALSE	TRUE	TRUE	FALSE	硝苯地平	Netilmicin	Netilmicine	Netilmicine	Netilmicin	Netilmicin	Netilmicin	ノルフロキサシン	Netilmicin	Netilmicin	Нетилмицин	Netilmicina	Netilmicin	Netilmisin	Нетилміцин
-Nystatin	FALSE	TRUE	TRUE	FALSE	Nystatin	Nystatine	Nistatina	Nystatin	Nystatine	Nystatin	Nystatin	Nystatin	Нистатин
+Nitrofurantoin	FALSE	TRUE	TRUE	FALSE	硝呋太尔	Nitrofurantoin	Nitrofurantoine	Nitrofurantoïne	Nitrofurantoin	Νιτροφουραντοΐνη	Nitrofurantoina	ノボビオシン	Nitrofurantoina	Nitrofurantoína	Нитрофурантоин	Nitrofurantoína	Nitrofurantoin	Nitrofurantoin	Нітрофурантоїн
-Ofloxacin	FALSE	TRUE	TRUE	FALSE	Ofloxacin	Ofloxacine	Ofloxacina	Ofloxacin	Ofloxacine	Ofloxacin	Ofloxacin	Ofloxacin	Офлоксацин
+Norfloxacin	FALSE	TRUE	TRUE	FALSE	诺氟沙星	Norfloxacin	Norfloxacine	Norfloxacine	Norfloxacin	Norfloxacin	Norfloxacina	ナイスタチン	Norfloxacin	Norfloxacin	Норфлоксацин	Norfloxacina	Norfloxacin	Norfloksasin	Норфлоксацин
-Oleandomycin	FALSE	TRUE	TRUE	FALSE	Oleandomycin	Oleandomycine	Oleandomicina	Oleandomicina	Oleandomycine	Oleandomicina	Oleandomycin	Oleandomycin	Олеандомицин
+Novobiocin	FALSE	TRUE	TRUE	FALSE	诺氟沙星	Novobiocin	Novobiocine	Novobiocine	Novobiocin	Novobiocin	Novobiocin	オフロキサシン	Nowobiocyna	Novobiocin	Новобиоцин	Novobiocina	Novobiocin	Novobiocin	Новобіоцин
-Ornidazole	FALSE	TRUE	TRUE	FALSE	Ornidazol	Ornidazol	Ornidazol	Ornidazolo	Ornidazole	Ornidazole	Ornidazol	Ornidazol	Орнидазол
+Nystatin	FALSE	TRUE	TRUE	FALSE	囊肿	Nystatin	Nystatine	Nystatine	Nystatin	Νυστατίνη	Nystatin	オレアンドマイシン	Nystatyna	Nystatin	Нистатин	Nistatina	Nystatin	Nistatin	Ністатин
-Oxacillin	FALSE	TRUE	TRUE	FALSE	Oxacillin	Oxacilline	Oxacilina	Oxacillina	Oxacilline	Oxacillin	Oxacillin	Oxacillin	Оксациллин
+Ofloxacin	FALSE	TRUE	TRUE	FALSE	氧氟沙星	Ofloxacin	Ofloxacine	Ofloxacine	Ofloxacin	Ofloxacin	Ofloxacin	オルニダゾール	Ofloxacin	Ofloxacin	Офлоксацин	Ofloxacina	Ofloxacin	Ofloksasin	Офлоксацин
-Oxolinic acid	FALSE	TRUE	TRUE	FALSE	Oxolinsäure	Oxolinezuur	Ácido oxolínico	Acido ossolinico	Acide oxolinique	Ácido oxolínico	Oxolinsyre	Oxolinsyra	Оксолиновая кислота
+Oleandomycin	FALSE	TRUE	TRUE	FALSE	奥兰多霉素	Oleandomycin	Oleandomycine	Oleandomycine	Oleandomycin	Oleandomycin	Oleandomicina	オキサシリン	Oleandomycin	Oleandomicina	Олеандомицин	Oleandomicina	Oleandomycin	Oleandomisin	Олеандоміцин
-Oxytetracycline	FALSE	TRUE	TRUE	FALSE	Oxytetracyclin	Oxytetracycline	Oxitetraciclina	Ossitetraciclina	Oxytétracycline	Oxitetraciclina	Oxytetracyclin	Oxytetracyklin	Окситетрациклин
+Ornidazole	FALSE	TRUE	TRUE	FALSE	奥硝唑	Ornidazol	Ornidazol	Ornidazole	Ornidazol	Ορνιδαζόλη	Ornidazolo	オキソリニック酸	Ornidazol	Ornidazole	Орнидазол	Ornidazol	Ornidazol	Ornidazol	Орнідазол
-Pazufloxacin	FALSE	TRUE	TRUE	FALSE	Pazufloxacin	Pazufloxacine	Pazufloxacina	Pazufloxacin	Pazufloxacine	Pazufloxacin	Pazufloxacin	Pazufloxacin	Пазуфлоксацин
+Oxacillin	FALSE	TRUE	TRUE	FALSE	奥沙西林	Oxacillin	Oxacilline	Oxacilline	Oxacillin	Οξακιλλίνη	Oxacillina	オキシテトラサイクリン	Oksacylina	Oxacillin	Оксациллин	Oxacilina	Oxacillin	Oksasilin	Оксацилін
-Pefloxacin	FALSE	TRUE	TRUE	FALSE	Pefloxacin	Pefloxacine	Pefloxacina	Pefloxacina	Péfloxacine	Pefloxacin	Pefloxacin	Pefloxacin	Пефлоксацин
+Oxolinic acid	FALSE	TRUE	TRUE	FALSE	氧氟沙星	Oxolinsyre	Oxolinezuur	Acide oxolinique	Oxolinsäure	Οξολινικό οξύ	Acido ossolinico	パズフロキサシン	Kwas oksolinowy	Ácido oxolínico	Оксолиновая кислота	Ácido oxolínico	Oxolinsyra	Oksolinik asit	Оксолінова кислота
-Penamecillin	FALSE	TRUE	TRUE	FALSE	Penamecillin	Penamecilline	Penamecilina	Penamecillina	Pénamécilline	Penamecilina	Penamecillin	Penamecillin	Пенамециллин
+Oxytetracycline	FALSE	TRUE	TRUE	FALSE	土四环素	Oxytetracyclin	Oxytetracycline	Oxytétracycline	Oxytetracyclin	Οξυτετρακυκλίνη	Ossitetraciclina	ペフロキサシン	Oksytetracyklina	Oxitetraciclina	Окситетрациклин	Oxitetraciclina	Oxytetracyklin	Oksitetrasiklin	Окситетрациклін
-Penicillin	FALSE	TRUE	TRUE	FALSE	Penicillin	Penicilline	Penicilina	Penicillina	Pénicilline	Penicilina	Penicillin	Penicillin	Пенициллин
+Pazufloxacin	FALSE	TRUE	TRUE	FALSE	帕唑沙星	Pazufloxacin	Pazufloxacine	Pazufloxacine	Pazufloxacin	Παζουφλοξασίνη	Pazufloxacin	ペナメシリン	Pazufloxacin	Pazufloxacin	Пазуфлоксацин	Pazufloxacina	Pazufloxacin	Pazufloksasin	Пазуфлоксацин
-Pheneticillin	FALSE	TRUE	TRUE	FALSE	Pheneticillin	Feneticilline	Feneticilina	Feneticillina	Phénéticilline	Pheneticillin	Pheneticillin	Feneticillin	Фенетициллин
+Pefloxacin	FALSE	TRUE	TRUE	FALSE	培氟沙星	Pefloxacin	Pefloxacine	Péfloxacine	Pefloxacin	Pefloxacin	Pefloxacina	ペニシリン	Pefloksacyna	Pefloxacin	Пефлоксацин	Pefloxacina	Pefloxacin	Pefloksasin	Пефлоксацин
-Phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Phenoxymethylpenicillin	Fenoxymethylpenicilline	Fenoximetilpenicilina	Fenossimetilpenicillina	Phénoxyméthylpénicilline	Fenoximetilpenicilina	Phenoxymethylpenicillin	Fenoximetylpenicillin	Феноксиметилпенициллин
+Penamecillin	FALSE	TRUE	TRUE	FALSE	青霉素	Penamecillin	Penamecilline	Pénamécilline	Penamecillin	Πεναμεσιλλίνη	Penamecillina	フェネチシリン	Penamecylina	Penamecilina	Пенамециллин	Penamecilina	Penamecillin	Penamecillin	Пенамецилін
-Pipemidic acid	FALSE	TRUE	TRUE	FALSE	Pipemidinsäure	Pipemidinezuur	Ácido pipemídico	Acido pipemidico	Acide pipémidique	Ácido pipemídico	Pipemidinsyre	Pipemidinsyra	Пипемидовая кислота
+Penicillin	FALSE	TRUE	TRUE	FALSE	青霉素	Penicillin	Penicilline	Pénicilline	Penicillin	Πενικιλλίνη	Penicillina	フェノキシメチルペニシリン	Penicylina	Penicilina	Пенициллин	Penicilina	Penicillin	Penisilin	Пеніцилін
-Piperacillin	FALSE	TRUE	TRUE	FALSE	Piperacillin	Piperacilline	Piperacilina	Piperacillina	Pipéracilline	Piperacilina	Piperacillin	Piperacillin	Пиперациллин
+Pheneticillin	FALSE	TRUE	TRUE	FALSE	菲尼克斯	Pheneticillin	Feneticilline	Phénéticilline	Pheneticillin	Φαινετικιλλίνη	Feneticillina	ピペミド酸	Fenicylina	Pheneticillin	Фенетициллин	Feneticilina	Feneticillin	Pheneticillin	Фенетіцилін
-Piperacillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Piperacillin/Beta-Lactamase-Hemmer	Piperacilline/enzymremmer	Piperacilina/inhib. de la beta-lactamasa	Piperacillina/inib. d. beta-lattamasi	Pipéracilline/inhib. de bêta-lactamase	Piperacilina/inibid. da beta-lactamase	Piperacillin/beta-lactamasehæmmer	Piperacillin/betalaktamashämmare	Пиперациллин/ингибитор бета-лактамазы
+Phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	苯氧甲基青霉素	Phenoxymethylpenicillin	Fenoxymethylpenicilline	Phénoxyméthylpénicilline	Phenoxymethylpenicillin	Φαινοξυμεθυλοπενικιλλίνη	Fenossimetilpenicillina	ピペラシリン	Fenoksymetylopenicylina	Fenoximetilpenicilina	Феноксиметилпенициллин	Fenoximetilpenicilina	Fenoximetylpenicillin	Fenoksimetilpenisilin	Феноксиметилпеніцилін
-Piromidic acid	FALSE	TRUE	TRUE	FALSE	Piromidinsäure	Piromidinezuur	Ácido piromídico	Acido piromidico	Acide piromidique	Ácido piromídico	Piromidinsyre	Piromidinsyra	Пиромидовая кислота
+Pipemidic acid	FALSE	TRUE	TRUE	FALSE	吡哌酸	Pipemidinsyre	Pipemidinezuur	Acide pipémidique	Pipemidinsäure	Πιπεμιδικό οξύ	Acido pipemidico	ピペラシリン／β-ラクタマーゼ阻害剤	Kwas pipemidowy	Ácido pipemídico	Пипемидовая кислота	Ácido pipemídico	Pipemidinsyra	Pipemidik asit	Піпемідова кислота
-Pivampicillin	FALSE	TRUE	TRUE	FALSE	Pivampicillin	Pivampicilline	Pivampicilina	Pivampicillina	Pivampicilline	Pivampicilina	Pivampicillin	Pivampicillin	Пивампициллин
+Piperacillin	FALSE	TRUE	TRUE	FALSE	哌拉西林	Piperacillin	Piperacilline	Pipéracilline	Piperacillin	Πιπερακιλλίνη	Piperacillina	ピロミジン酸	Piperacillin	Piperacilina	Пиперациллин	Piperacilina	Piperacillin	Piperasilin	Піперацилін
-Polymyxin B	FALSE	TRUE	TRUE	FALSE	Polymyxin B	Polymyxine B	Polimixina B	Polimixina B	Polymyxine B	Polimixina B	Polymyxin B	Polymyxin B	Полимиксин В
+Piperacillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	哌拉西林/β-内酰胺酶抑制剂	Piperacillin/beta-lactamasehæmmer	Piperacilline/enzymremmer	Pipéracilline/inhib. de bêta-lactamase	Piperacillin/Beta-Lactamase-Hemmer	Πιπερακιλλίνη/αναστολέας της β-λακταμάσης	Piperacillina/inib. d. beta-lattamasi	ピバンピシリン	Piperacylina/inhibitor beta-laktamazy	Piperacilina/inibid. da beta-lactamase	Пиперациллин/ингибитор бета-лактамазы	Piperacilina/inhib. de la beta-lactamasa	Piperacillin/betalaktamashämmare	Piperasilin/beta-laktamaz inhibitörü	Піперацилін/інгібітор бета-лактамаз
-Posaconazole	FALSE	TRUE	TRUE	FALSE	Posaconazol	Posaconazol	Posaconazol	Posaconazolo	Posaconazole	Posaconazole	Posaconazol	Posakonazol	Посаконазол
+Piromidic acid	FALSE	TRUE	TRUE	FALSE	吡罗米酸	Piromidinsyre	Piromidinezuur	Acide piromidique	Piromidinsäure	Πηρομιδικό οξύ	Acido piromidico	ポリミキシンB	Kwas piromidowy	Ácido piromídico	Пиромидовая кислота	Ácido piromídico	Piromidinsyra	Piromidik asit	Піромідова кислота
-Pristinamycin	FALSE	TRUE	TRUE	FALSE	Pristinamycin	Pristinamycine	Pristinamicina	Pristinamicina	Pristinamycine	Pristinamicina	Pristinamycin	Pristinamycin	Пристинамицин
+Pivampicillin	FALSE	TRUE	TRUE	FALSE	哌拉西林	Pivampicillin	Pivampicilline	Pivampicilline	Pivampicillin	Pivampicillin	Pivampicillina	ポサコナゾール	Pivampicillin	Pivampicilina	Пивампициллин	Pivampicilina	Pivampicillin	Pivampisilin	Півампіцилін
-Procaine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Procain-Benzylpenicillin	Benzylpenicillineprocaine	Bencilpenicilina procaína	Procaina benzilpenicillina	Procaïne benzylpénicilline	Procaína benzilpenicilina	Prokainbenzylpenicillin	Prokainbenzylpenicillin	Прокаин бензилпенициллин
+Polymyxin B	FALSE	TRUE	TRUE	FALSE	多粘菌素B	Polymyxin B	Polymyxine B	Polymyxine B	Polymyxin B	Πολυμυξίνη Β	Polimixina B	プリスチナマイシン	Polimyksyna B	Polimixina B	Полимиксин В	Polimixina B	Polymyxin B	Polimiksin B	Поліміксин B
-Propicillin	FALSE	TRUE	TRUE	FALSE	Propicillin	Propicilline	Propicilina	Propicillina	Propicilline	Propicilina	Propicillin	Propicillin	Пропициллин
+Posaconazole	FALSE	TRUE	TRUE	FALSE	泊沙康唑	Posaconazol	Posaconazol	Posaconazole	Posaconazol	Ποσακοναζόλη	Posaconazolo	プロカインベンジルペニシリン	Posaconazol	Posaconazole	Посаконазол	Posaconazol	Posakonazol	Posakonazol	Позаконазол
-Prulifloxacin	FALSE	TRUE	TRUE	FALSE	Prulifloxacin	Prulifloxacine	Prulifloxacina	Prulifloxacina	Prulifloxacine	Prulifloxacina	Prulifloxacin	Prulifloxacin	Прулифлоксацин
+Pristinamycin	FALSE	TRUE	TRUE	FALSE	普利司特霉素	Pristinamycin	Pristinamycine	Pristinamycine	Pristinamycin	Πριστιναμυκίνη	Pristinamicina	プロピシリン	Pristinamycin	Pristinamicina	Пристинамицин	Pristinamicina	Pristinamycin	Pristinamisin	Пристинаміцин
-Quinupristin/dalfopristin	FALSE	TRUE	TRUE	FALSE	Quinupristin/Dalfopristin	Quinupristine/dalfopristine	Quinupristina/dalfopristina	Quinupristina/dalfopristina	Quinupristine/dalfopristine	Quinupristin/dalfopristin	Quinupristin/dalfopristin	Quinupristin/dalfopristin	Квинупристин/дальфопристин
+Procaine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	普鲁卡因青霉素	Prokainbenzylpenicillin	Benzylpenicillineprocaine	Procaïne benzylpénicilline	Procain-Benzylpenicillin	Βενζυλοπενικιλλίνη προκαΐνης	Procaina benzilpenicillina	プルリフロキサシン	Benzylopenicylina prokainowa	Procaína benzilpenicilina	Прокаин бензилпенициллин	Bencilpenicilina procaína	Prokainbenzylpenicillin	Prokain benzilpenisilin	Прокаїну бензилпеніцилін
-Ribostamycin	FALSE	TRUE	TRUE	FALSE	Ribostamycin	Ribostamycine	Ribostamicina	Ribostamicina	Ribostamycine	Ribostamicina	Ribostamycin	Ribostamycin	Рибостамицин
+Propicillin	FALSE	TRUE	TRUE	FALSE	普利西林	Propicillin	Propicilline	Propicilline	Propicillin	Προπικιλλίνη	Propicillina	キヌプリスチン／ダルフォプリスチン	Propicylina	Propicilina	Пропициллин	Propicilina	Propicillin	Propisilin	Пропіцилін
-Rifabutin	FALSE	TRUE	TRUE	FALSE	Rifabutin	Rifabutine	Rifabutina	Rifabutina	Rifabutine	Rifabutin	Rifabutin	Rifabutin	Рифабутин
+Prulifloxacin	FALSE	TRUE	TRUE	FALSE	普利沙星	Prulifloxacin	Prulifloxacine	Prulifloxacine	Prulifloxacin	Προυλιφλοξασίνη	Prulifloxacina	リボスタマイシン	Prulifloksacyna	Prulifloxacina	Прулифлоксацин	Prulifloxacina	Prulifloxacin	Prulifloksasin	Пруліфлоксацин
-Rifampicin	FALSE	TRUE	TRUE	FALSE	Rifampicin	Rifampicine	Rifampicina	Rifampicina	Rifampicine	Rifampicina	Rifampicin	Rifampicin	Рифампицин
+Quinupristin/dalfopristin	FALSE	TRUE	TRUE	FALSE	奎宁斯丁/达夫普利斯丁	Quinupristin/dalfopristin	Quinupristine/dalfopristine	Quinupristine/dalfopristine	Quinupristin/Dalfopristin	Κινουπριστίνη/δαλφοπριστίνη	Quinupristina/dalfopristina	リファブチン	Quinupristin/dalfopristin	Quinupristin/dalfopristin	Квинупристин/дальфопристин	Quinupristina/dalfopristina	Quinupristin/dalfopristin	Quinupristin/dalfopristin	Хінупристин/дальфопристин
-Rifampicin/pyrazinamide/ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Pyrazinamid/Ethambutol/Isoniazid	Rifampicine/pyrazinamide/ethambutol/isoniazide	Rifampicina/pirazinamida/etambutol/isoniazida	Rifampicina/pirazinamide/etambutolo/isoniazide	Rifampicine/pyrazinamide/éthambutol/isoniazide	Rifampicina/pirazinamida/etambutol/isoniazida	Rifampicin/pyrazinamid/ethambutol/isoniazid	Rifampicin/pyrazinamid/ethambutol/isoniazid	Рифампицин/пиразинамид/этамбутол/исониазид
+Ribostamycin	FALSE	TRUE	TRUE	FALSE	利波霉素	Ribostamycin	Ribostamycine	Ribostamycine	Ribostamycin	Ριμποσταμυκίνη	Ribostamicina	リファンピシン	Ribostamycyna	Ribostamicina	Рибостамицин	Ribostamicina	Ribostamycin	Ribostamisin	Рибостаміцин
-Rifampicin/pyrazinamide/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Pyrazinamid/Isoniazid	Rifampicine/pyrazinamide/isoniazide	Rifampicina/pirazinamida/isoniazida	Rifampicina/pirazinamide/isoniazide	Rifampicine/pyrazinamide/isoniazide	Rifampicina/pirazinamida/isoniazida	Rifampicin/pyrazinamid/isoniazid	Rifampicin/pyrazinamid/isoniazid	Рифампицин/пиразинамид/изониазид
+Rifabutin	FALSE	TRUE	TRUE	FALSE	利福布汀	Rifabutin	Rifabutine	Rifabutine	Rifabutin	Rifabutin	Rifabutina	リファンピシン／ピラジナミド／エタンブトール／イソニアジド	Rifabutin	Rifabutin	Рифабутин	Rifabutina	Rifabutin	Rifabutin	Рифабутин
-Rifampicin/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Isoniazid	Rifampicine/isoniazide	Rifampicina/isoniazida	Rifampicina/isoniazide	Rifampicine/isoniazide	Rifampicina/isoniazida	Rifampicin/isoniazid	Rifampicin/isoniazid	Рифампицин/изониазид
+Rifampicin	FALSE	TRUE	TRUE	FALSE	利福平	Rifampicin	Rifampicine	Rifampicine	Rifampicin	Ριφαμπικίνη	Rifampicina	リファンピシン／ピラジナミド／イソニアジド	Rifampicyna	Rifampicina	Рифампицин	Rifampicina	Rifampicin	Rifampisin	Рифампіцин
-Rifamycin	FALSE	TRUE	TRUE	FALSE	Rifamycin	Rifamycine	Rifamicina	Rifamicina	Rifamycine	Rifamycin	Rifamycin	Rifamycin	Рифамицин
+Rifampicin/pyrazinamide/ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	利福平/吡嗪酰胺/乙胺丁醇/异烟肼	Rifampicin/pyrazinamid/ethambutol/isoniazid	Rifampicine/pyrazinamide/ethambutol/isoniazide	Rifampicine/pyrazinamide/éthambutol/isoniazide	Rifampicin/Pyrazinamid/Ethambutol/Isoniazid	Ριφαμπικίνη/πυραζιναμίδη/αιθαμβουτόλη/ισονιαζίδη	Rifampicina/pirazinamide/etambutolo/isoniazide	リファンピシン／イソニアジド	Rifampicyna/pirazinamid/etambutol/izoniazyd	Rifampicina/pirazinamida/etambutol/isoniazida	Рифампицин/пиразинамид/этамбутол/исониазид	Rifampicina/pirazinamida/etambutol/isoniazida	Rifampicin/pyrazinamid/ethambutol/isoniazid	Rifampisin/pirazinamid/etambutol/izoniazid	Рифампіцин/піразинамід/етамбутол/ізоніазид
-Rifaximin	FALSE	TRUE	TRUE	FALSE	Rifaximin	Rifaximine	Rifaximina	Rifaximina	Rifaximine	Rifaximin	Rifaximin	Rifaximin	Рифаксимин
+Rifampicin/pyrazinamide/isoniazid	FALSE	TRUE	TRUE	FALSE	利福平/吡嗪酰胺/异烟肼	Rifampicin/pyrazinamid/isoniazid	Rifampicine/pyrazinamide/isoniazide	Rifampicine/pyrazinamide/isoniazide	Rifampicin/Pyrazinamid/Isoniazid	Ριφαμπικίνη/πυραζιναμίδη/ισονιαζίδη	Rifampicina/pirazinamide/isoniazide	リファマイシン	Rifampicyna/pirazynamid/izoniazyd	Rifampicina/pirazinamida/isoniazida	Рифампицин/пиразинамид/изониазид	Rifampicina/pirazinamida/isoniazida	Rifampicin/pyrazinamid/isoniazid	Rifampisin/pirazinamid/izoniazid	Рифампіцин/піразинамід/ізоніазид
-Rokitamycin	FALSE	TRUE	TRUE	FALSE	Rokitamycin	Rokitamycine	Rokitamicina	Rokitamicina	Rokitamycine	Rokitamycin	Rokitamycin	Rokitamycin	Рокитамицин
+Rifampicin/isoniazid	FALSE	TRUE	TRUE	FALSE	利福平/异烟肼	Rifampicin/isoniazid	Rifampicine/isoniazide	Rifampicine/isoniazide	Rifampicin/Isoniazid	Ριφαμπικίνη/ισονιαζίδη	Rifampicina/isoniazide	リファキシミン	Rifampicyna/izoniazyd	Rifampicina/isoniazida	Рифампицин/изониазид	Rifampicina/isoniazida	Rifampicin/isoniazid	Rifampisin/izoniazid	Рифампіцин/ізоніазид
-Rosoxacin	FALSE	TRUE	TRUE	FALSE	Rosoxacin	Rosoxacine	Rosoxacina	Rosoxacina	Rosoxacine	Rosoxacina	Rosoxacin	Rosoxacin	Розоксацин
+Rifamycin	FALSE	TRUE	TRUE	FALSE	利福霉素	Rifamycin	Rifamycine	Rifamycine	Rifamycin	Ριφαμυκίνη	Rifamicina	ロキタマイシン	Rifamycyna	Rifamycin	Рифамицин	Rifamicina	Rifamycin	Rifamisin	Рифаміцин
-Roxithromycin	FALSE	TRUE	TRUE	FALSE	Roxithromycin	Roxitromycine	Roxitromicina	Roxitromicina	Roxithromycine	Roxitromicina	Roxithromycin	Roxitromycin	Рокситромицин
+Rifaximin	FALSE	TRUE	TRUE	FALSE	利福昔明	Rifaximin	Rifaximine	Rifaximine	Rifaximin	Rifaximin	Rifaximina	ロソキサシン	Rifaximin	Rifaximin	Рифаксимин	Rifaximina	Rifaximin	Rifaximin	Рифаксимін
-Rufloxacin	FALSE	TRUE	TRUE	FALSE	Rufloxacin	Rufloxacine	Rufloxacina	Rufloxacina	Rufloxacine	Rufloxacin	Rufloxacin	Rufloxacin	Руфлоксацин
+Rokitamycin	FALSE	TRUE	TRUE	FALSE	罗奇霉素	Rokitamycin	Rokitamycine	Rokitamycine	Rokitamycin	Ροκιταμυκίνη	Rokitamicina	ロキシスロマイシン	Rokitamycyna	Rokitamycin	Рокитамицин	Rokitamicina	Rokitamycin	Rokitamisin	Рокітаміцин
-Sisomicin	FALSE	TRUE	TRUE	FALSE	Sisomicin	Sisomicine	Sisomicina	Sisomicina	Sisomicine	Sisomicina	Sisomicin	Sisomicin	Сизомицин
+Rosoxacin	FALSE	TRUE	TRUE	FALSE	罗红霉素	Rosoxacin	Rosoxacine	Rosoxacine	Rosoxacin	Rosoxacin	Rosoxacina	ルフロキサシン	Rosoxacin	Rosoxacina	Розоксацин	Rosoxacina	Rosoxacin	Rosoxacin	Розоксацин
-Sodium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Natrium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de sodio	Sodio aminosalicilato	Aminosalicylate de sodium	Aminosalicilato de sódio	Natriumaminosalicylat	Natriumaminosalicylat	Аминосалицилат натрия
+Roxithromycin	FALSE	TRUE	TRUE	FALSE	罗红霉素	Roxithromycin	Roxitromycine	Roxithromycine	Roxithromycin	Roxithromycin	Roxitromicina	シソマイシン	Roksytromycyna	Roxitromicina	Рокситромицин	Roxitromicina	Roxitromycin	Roxithromycin	Рокситроміцин
-Sparfloxacin	FALSE	TRUE	TRUE	FALSE	Sparfloxacin	Sparfloxacine	Esparfloxacina	Sparfloxacina	Sparfloxacine	Sparfloxacin	Sparfloxacin	Sparfloxacin	Спарфлоксацин
+Rufloxacin	FALSE	TRUE	TRUE	FALSE	罗氟沙星	Rufloxacin	Rufloxacine	Rufloxacine	Rufloxacin	Rufloxacin	Rufloxacina	アミノサリチル酸ソーダ	Rufloxacin	Rufloxacin	Руфлоксацин	Rufloxacina	Rufloxacin	Rufloksasin	Руфлоксацин
-Spectinomycin	FALSE	TRUE	TRUE	FALSE	Spectinomycin	Spectinomycine	Espectinomicina	Spectinomycin	Spectinomycine	Spectinomycin	Spectinomycin	Spektinomycin	Спектиномицин
+Sisomicin	FALSE	TRUE	TRUE	FALSE	西索米星	Sisomicin	Sisomicine	Sisomicine	Sisomicin	Sisomicin	Sisomicina	スパルフロキサシン	Sisomicin	Sisomicina	Сизомицин	Sisomicina	Sisomicin	Sisomisin	Сизоміцин
-Spiramycin	FALSE	TRUE	TRUE	FALSE	Spiramycin	Spiramycine	Espiramicina	Spiramicina	Spiramycine	Spiramycin	Spiramycin	Spiramycin	Спирамицин
+Sodium aminosalicylate	FALSE	TRUE	TRUE	FALSE	氨基水杨酸钠	Natriumaminosalicylat	Aminosalicylzuur	Aminosalicylate de sodium	Natrium-Aminosalicylat	Αμινοσαλικυλικό νάτριο	Sodio aminosalicilato	スペクチノマイシン	Aminosalicylan sodu	Aminosalicilato de sódio	Аминосалицилат натрия	Aminosalicilato de sodio	Natriumaminosalicylat	Sodyum aminosalisilat	Натрію аміносаліцилат
-Spiramycin/metronidazole	FALSE	TRUE	TRUE	FALSE	Spiramycin/Metronidazol	Spiramycine/metronidazol	Espiramicina/metronidazol	Spiramicina/metronidazolo	Spiramycine/métronidazole	Spiramycin/metronidazol	Spiramycin/metronidazol	Spiramycin/metronidazol	Спирамицин/метронидазол
+Sparfloxacin	FALSE	TRUE	TRUE	FALSE	氨水杨酸钠	Sparfloxacin	Sparfloxacine	Sparfloxacine	Sparfloxacin	Sparfloxacin	Sparfloxacina	スピラマイシン	Sparfloxacin	Sparfloxacin	Спарфлоксацин	Esparfloxacina	Sparfloxacin	Sparfloksasin	Спарфлоксацин
-Staphylococcus immunoglobulin	FALSE	TRUE	TRUE	FALSE	Staphylococcus-Immunoglobulin	Stafylokokkenimmunoglobuline	Inmunoglobulina estafilocócica	Immunoglobulina per stafilococco	Immunoglobuline staphylococcique	Imunoglobulina de Staphylococcus	Stafylokok-immunglobulin	Immunoglobulin mot stafylokocker	Стафилококковый иммуноглобулин
+Spectinomycin	FALSE	TRUE	TRUE	FALSE	大观霉素	Spectinomycin	Spectinomycine	Spectinomycine	Spectinomycin	Spectinomycin	Spectinomycin	スピラマイシン／メトロニダゾール	Spektynomycyna	Spectinomycin	Спектиномицин	Espectinomicina	Spektinomycin	Spektinomisin	Спектиноміцин
-Streptoduocin	FALSE	TRUE	TRUE	FALSE	Streptoduocin	Streptoduocine	Estreptoduocina	Streptoduocin	Streptoduocine	Estreptoduocina	Streptoduocin	Streptoduocin	Стрептодуоцин
+Spiramycin	FALSE	TRUE	TRUE	FALSE	斯皮拉菌素	Spiramycin	Spiramycine	Spiramycine	Spiramycin	Σπιραμυκίνη	Spiramicina	ブドウ球菌免疫グロブリン	Spiramycyna	Spiramycin	Спирамицин	Espiramicina	Spiramycin	Spiramisin	Спіраміцин
-Streptomycin	FALSE	TRUE	TRUE	FALSE	Streptomycin	Streptomycine	Estreptomicina	Streptomicina	Streptomycine	Streptomycin	Streptomycin	Streptomycin	Стрептомицин
+Spiramycin/metronidazole	FALSE	TRUE	TRUE	FALSE	螺旋霉素/甲硝唑	Spiramycin/metronidazol	Spiramycine/metronidazol	Spiramycine/métronidazole	Spiramycin/Metronidazol	Σπιραμυκίνη/μετρονιδαζόλη	Spiramicina/metronidazolo	ストレプトデュオシン	Spiramycyna/metronidazol	Spiramycin/metronidazol	Спирамицин/метронидазол	Espiramicina/metronidazol	Spiramycin/metronidazol	Spiramisin/metronidazol	Спіраміцин/метронідазол
-Streptomycin/isoniazid	FALSE	TRUE	TRUE	FALSE	Streptomycin/Isoniazid	Streptomycine/isoniazide	Estreptomicina/isoniazida	Streptomicina/isoniazide	Streptomycine/isoniazide	Streptomicina/isoniazida	Streptomycin/isoniazid	Streptomycin/isoniazid	Стрептомицин/изониазид
+Staphylococcus immunoglobulin	FALSE	TRUE	TRUE	FALSE	葡萄球菌免疫球蛋白	Stafylokok-immunglobulin	Stafylokokkenimmunoglobuline	Immunoglobuline staphylococcique	Staphylococcus-Immunoglobulin	Σταφυλόκοκκος ανοσοσφαιρίνη	Immunoglobulina per stafilococco	ストレプトマイシン	Immunoglobulina gronkowcowa	Imunoglobulina de Staphylococcus	Стафилококковый иммуноглобулин	Inmunoglobulina estafilocócica	Immunoglobulin mot stafylokocker	Staphylococcus immünoglobulin	Стафілококовий імуноглобулін
-Sulbenicillin	FALSE	TRUE	TRUE	FALSE	Sulbenicillin	Sulbenicilline	Sulbenicilina	Sulbenicillina	Sulbenicilline	Sulbenicilina	Sulbenicillin	Sulbenicillin	Сульбенициллин
+Streptoduocin	FALSE	TRUE	TRUE	FALSE	链霉素	Streptoduocin	Streptoduocine	Streptoduocine	Streptoduocin	Streptoduocin	Streptoduocin	ストレプトマイシン／イソニアジド	Streptoduocin	Estreptoduocina	Стрептодуоцин	Estreptoduocina	Streptoduocin	Streptoduosin	Стрептодуоцин
-Sulfadiazine/tetroxoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Tetroxoprim	Sulfadiazine/tetroxoprim	Sulfadiazina/tetroxoprim	Sulfadiazina/tetroxoprim	Sulfadiazine/tetroxoprime	Sulfadiazina/tetroxoprim	Sulfadiazin/tetroxoprim	Sulfadiazin/tetroxoprim	Сульфадиазин/тетроксоприм
+Streptomycin	FALSE	TRUE	TRUE	FALSE	霉素	Streptomycin	Streptomycine	Streptomycine	Streptomycin	Στρεπτομυκίνη	Streptomicina	スルベニシリン	Streptomycyna	Streptomycin	Стрептомицин	Estreptomicina	Streptomycin	Streptomisin	Стрептоміцин
-Sulfadiazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Trimethoprim	Sulfadiazine/trimethoprim	Sulfadiazina/trimetoprima	Sulfadiazina/trimetoprim	Sulfadiazine/triméthoprime	Sulfadiazina/trimethoprim	Sulfadiazin/trimethoprim	Sulfadiazin/trimetoprim	Сульфадиазин/триметоприм
+Streptomycin/isoniazid	FALSE	TRUE	TRUE	FALSE	链霉素/异烟肼	Streptomycin/isoniazid	Streptomycine/isoniazide	Streptomycine/isoniazide	Streptomycin/Isoniazid	Στρεπτομυκίνη/ισονιαζίδη	Streptomicina/isoniazide	スルファダイアジン／テトロキソプリム	Streptomycyna/izoniazyd	Streptomicina/isoniazida	Стрептомицин/изониазид	Estreptomicina/isoniazida	Streptomycin/isoniazid	Streptomisin/izoniazid	Стрептоміцин/ізоніазид
-Sulfadimidine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadimidin/Trimethoprim	Sulfadimidine/trimethoprim	Sulfadimidina/trimetoprima	Sulfadimidina/trimetoprim	Sulfadimidine/triméthoprime	Sulfadimidina/trimethoprim	Sulfadimidin/trimethoprim	Sulfadimidin/trimetoprim	Сульфадимидин/триметоприм
+Sulbenicillin	FALSE	TRUE	TRUE	FALSE	磺苄西林	Sulbenicillin	Sulbenicilline	Sulbenicilline	Sulbenicillin	Sulbenicillin	Sulbenicillina	スルファジアジン／トリメトプリム	Sulbenicylina	Sulbenicilina	Сульбенициллин	Sulbenicilina	Sulbenicillin	Sulbenisilin	Сульбеніцилін
-Sulfafurazole	FALSE	TRUE	TRUE	FALSE	Sulfafurazol	Sulfafurazol	Sulfafurazol	Sulfafurazolo	Sulfafurazole	Sulfafurazole	Sulfafurazol	Sulfafurazol	Сульфафуразол
+Sulfadiazine/tetroxoprim	FALSE	TRUE	TRUE	FALSE	磺胺嘧啶/四氧嘧啶	Sulfadiazin/tetroxoprim	Sulfadiazine/tetroxoprim	Sulfadiazine/tetroxoprime	Sulfadiazin/Tetroxoprim	Σουλφαδιαζίνη/τετροξοπρίμη	Sulfadiazina/tetroxoprim	スルファジミジン／トリメトプリム	Sulfadiazyna/tetroksoprim	Sulfadiazina/tetroxoprim	Сульфадиазин/тетроксоприм	Sulfadiazina/tetroxoprim	Sulfadiazin/tetroxoprim	Sülfadiazin/tetroksoprim	Сульфадіазин/тетроксоприм
-Sulfaisodimidine	FALSE	TRUE	TRUE	FALSE	Sulfaisodimidin	Sulfisomidine	Sulfaisodimidina	Sulfaisodimidina	Sulfaisodimidine	Sulfaisodimidina	Sulfaisodimidin	Sulfaisodimidin	Сульфаизодимидин
+Sulfadiazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺嘧啶/三甲氧苄啶	Sulfadiazin/trimethoprim	Sulfadiazine/trimethoprim	Sulfadiazine/triméthoprime	Sulfadiazin/Trimethoprim	Σουλφαδιαζίνη/τριμεθοπρίμη	Sulfadiazina/trimetoprim	スルファフラゾール	Sulfadiazyna/trimetoprim	Sulfadiazina/trimethoprim	Сульфадиазин/триметоприм	Sulfadiazina/trimetoprima	Sulfadiazin/trimetoprim	Sülfadiazin/trimetoprim	Сульфадіазин/триметоприм
-Sulfalene	FALSE	TRUE	TRUE	FALSE	Sulfalene	Sulfaleen	Sulfaleno	Sulfalene	Sulfalène	Sulfaleno	Sulfalen	Sulfen	Сульфален
+Sulfadimidine/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺嘧啶/三甲氧苄啶	Sulfadimidin/trimethoprim	Sulfadimidine/trimethoprim	Sulfadimidine/triméthoprime	Sulfadimidin/Trimethoprim	Σουλφαδιμιδίνη/τριμεθοπρίμη	Sulfadimidina/trimetoprim	スルファイソジミジン	Sulfadimidyna/trimetoprim	Sulfadimidina/trimethoprim	Сульфадимидин/триметоприм	Sulfadimidina/trimetoprima	Sulfadimidin/trimetoprim	Sülfadimidin/trimetoprim	Сульфадимідин/триметоприм
-Sulfamazone	FALSE	TRUE	TRUE	FALSE	Sulfamazon	Sulfamazon	Sulfamazona	Sulfamazone	Sulfamazone	Sulfamazona	Sulfamazon	Sulfamazon	Сульфамазон
+Sulfafurazole	FALSE	TRUE	TRUE	FALSE	磺胺呋喃唑	Sulfafurazol	Sulfafurazol	Sulfafurazole	Sulfafurazol	Σουλφαφουραζόλη	Sulfafurazolo	スルファレン	Sulfafurazol	Sulfafurazole	Сульфафуразол	Sulfafurazol	Sulfafurazol	Sülfafurazol	Сульфафуразол
-Sulfamerazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamerazin/Trimethoprim	Sulfamerazine/trimethoprim	Sulfamerazina/trimetoprima	Sulfamerazina/trimetoprim	Sulfamérazine/triméthoprime	Sulfamerazina/trimethoprim	Sulfamerazin/trimethoprim	Sulfamerazin/trimetoprim	Сульфамеразин/триметоприм
+Sulfaisodimidine	FALSE	TRUE	TRUE	FALSE	磺胺二甲嘧啶	Sulfaisodimidin	Sulfisomidine	Sulfaisodimidine	Sulfaisodimidin	Sulfaisodimidine	Sulfaisodimidina	スルファマゾン	Sulfaisodimidine	Sulfaisodimidina	Сульфаизодимидин	Sulfaisodimidina	Sulfaisodimidin	Sülfaizodimidin	Сульфаізодимідин
-Sulfamethizole	FALSE	TRUE	TRUE	FALSE	Sulfamethizol	Sulfamethizol	Sulfametozol	Sulfamethizolo	Sulfaméthizole	Sulfametizole	Sulfamethizol	Sulfamethizol	Сульфаметизол
+Sulfalene	FALSE	TRUE	TRUE	FALSE	磺胺类药物	Sulfalen	Sulfaleen	Sulfalène	Sulfalene	Sulfalene	Sulfalene	スルファメラジン／トリメトプリム	Sulfalen	Sulfaleno	Сульфален	Sulfaleno	Sulfen	Sülfalen	Сульфален
-Sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol	Sulfamethoxazol	Sulfametoxazol	Sulfametossazolo	Sulfaméthoxazole	Sulfamethoxazole	Sulfamethoxazol	Sulfametoxazol	Сульфаметоксазол
+Sulfamazone	FALSE	TRUE	TRUE	FALSE	磺胺脒	Sulfamazon	Sulfamazon	Sulfamazone	Sulfamazon	Sulfamazone	Sulfamazone	スルファメチゾール	Sulfamazon	Sulfamazona	Сульфамазон	Sulfamazona	Sulfamazon	Sülfamazon	Сульфамазон
-Sulfamethoxazole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol/Trimethoprim	Sulfamethoxazol/trimethoprim	Sulfametoxazol/trimetoprima	Sulfametossazolo/trimetoprim	Sulfaméthoxazole/triméthoprime	Sulfametoxazol/trimethoprim	Sulfamethoxazol/trimethoprim	Sulfametoxazol/trimetoprim	Сульфаметоксазол/триметоприм
+Sulfamerazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺脒/三甲氧苄氨嘧啶	Sulfamerazin/trimethoprim	Sulfamerazine/trimethoprim	Sulfamérazine/triméthoprime	Sulfamerazin/Trimethoprim	Σουλφαμεραζίνη/τριμεθοπρίμη	Sulfamerazina/trimetoprim	スルファメトキサゾール	Sulfamerazyna/trimetoprim	Sulfamerazina/trimethoprim	Сульфамеразин/триметоприм	Sulfamerazina/trimetoprima	Sulfamerazin/trimetoprim	Sülfamerazin/trimetoprim	Сульфамеразин/триметоприм
-Sulfametoxydiazine	FALSE	TRUE	TRUE	FALSE	Sulfametoxydiazin	Sulfamethoxydiazine	Sulfametoxidiazina	Sulfametoxydiazine	Sulfamétoxydiazine	Sulfametoxidiazina	Sulfametoxydiazin	Sulfametoxydiazin	Сульфаметоксидиазин
+Sulfamethizole	FALSE	TRUE	TRUE	FALSE	磺胺甲基咪唑	Sulfamethizol	Sulfamethizol	Sulfaméthizole	Sulfamethizol	Sulfamethizole	Sulfamethizolo	スルファメトキサゾール／トリメトプリム	Sulfamethizole	Sulfametizole	Сульфаметизол	Sulfametozol	Sulfamethizol	Sülfametizol	Сульфаметізол
-Sulfametrole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfametrole/Trimethoprim	Sulfametrol/trimethoprim	Sulfametrol/trimetoprima	Sulfametrole/trimetoprim	Sulfamétrole/triméthoprime	Sulfametrole/trimethoprim	Sulfametrol/trimethoprim	Sulfametrol/trimetoprim	Сульфаметрол/триметоприм
+Sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	磺胺甲噁唑	Sulfamethoxazol	Sulfamethoxazol	Sulfaméthoxazole	Sulfamethoxazol	Σουλφαμεθοξαζόλη	Sulfametossazolo	スルファメトキシジアジン	Sulfametoksazol	Sulfamethoxazole	Сульфаметоксазол	Sulfametoxazol	Sulfametoxazol	Sülfametoksazol	Сульфаметоксазол
-Sulfamoxole	FALSE	TRUE	TRUE	FALSE	Sulfamoxol	Sulfamoxol	Sulfamoxole	Sulfamoxolo	Sulfamoxole	Sulfamoxole	Sulfamoxol	Sulfamoxol	Сульфамоксол
+Sulfamethoxazole/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺甲噁唑/三甲氧苄啶	Sulfamethoxazol/trimethoprim	Sulfamethoxazol/trimethoprim	Sulfaméthoxazole/triméthoprime	Sulfamethoxazol/Trimethoprim	Σουλφαμεθοξαζόλη/τριμεθοπρίμη	Sulfametossazolo/trimetoprim	スルファメトロール／トリメトプリム	Sulfametoksazol/trimetoprim	Sulfametoxazol/trimethoprim	Сульфаметоксазол/триметоприм	Sulfametoxazol/trimetoprima	Sulfametoxazol/trimetoprim	Sülfametoksazol/trimetoprim	Сульфаметоксазол/триметоприм
-Sulfamoxole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamoxol/Trimethoprim	Sulfamoxol/trimethoprim	Sulfamoxol/trimetoprima	Sulfamoxolo/trimetoprim	Sulfamoxole/triméthoprime	Sulfamoxole/trimethoprim	Sulfamoxol/trimethoprim	Sulfamoxol/trimetoprim	Сульфамоксол/триметоприм
+Sulfametoxydiazine	FALSE	TRUE	TRUE	FALSE	磺胺甲噁唑	Sulfametoxydiazin	Sulfamethoxydiazine	Sulfamétoxydiazine	Sulfametoxydiazin	Sulfametoxydiazine	Sulfametoxydiazine	スルファモキソール	Sulfametoksydiazyna	Sulfametoxidiazina	Сульфаметоксидиазин	Sulfametoxidiazina	Sulfametoxydiazin	Sulfametoksidiyazin	Сульфаметоксидіазин
-Sulfaperin	FALSE	TRUE	TRUE	FALSE	Sulfaperin	Sulfaperine	Sulfametoxazol	Sulfaperin	Sulfapérine	Sulfaperin	Sulfaperin	Sulfaperin	Сульфаперин
+Sulfametrole/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺甲醚/三甲氧嘧啶	Sulfametrol/trimethoprim	Sulfametrol/trimethoprim	Sulfamétrole/triméthoprime	Sulfametrole/Trimethoprim	Σουλφαμετρόλη/τριμεθοπρίμη	Sulfametrole/trimetoprim	スルファモキソール／トリメトプリム	Sulfametrol/trimetoprim	Sulfametrole/trimethoprim	Сульфаметрол/триметоприм	Sulfametrol/trimetoprima	Sulfametrol/trimetoprim	Sülfametrol/trimetoprim	Сульфаметрол/триметоприм
-Sulfaphenazole	FALSE	TRUE	TRUE	FALSE	Sulfaphenazol	Sulfafenazol	Sulfafenazol	Sulfafenazolo	Sulfaphénazole	Sulfafenazol	Sulfaphenazol	Sulfafenazol	Сульфафеназол
+Sulfamoxole	FALSE	TRUE	TRUE	FALSE	磺胺甲噁唑	Sulfamoxol	Sulfamoxol	Sulfamoxole	Sulfamoxol	Sulfamoxole	Sulfamoxolo	スルファペリン	Sulfamoksol	Sulfamoxole	Сульфамоксол	Sulfamoxole	Sulfamoxol	Sülfamoksol	Сульфамоксол
-Sulfathiazole	FALSE	TRUE	TRUE	FALSE	Sulfathiazol	Sulfathiazol	Sulfatiazol	Sulfathiazole	Sulfathiazole	Sulfatazol	Sulfathiazol	Sulfathiazol	Сульфатиазол
+Sulfamoxole/trimethoprim	FALSE	TRUE	TRUE	FALSE	磺胺甲噁唑/三甲氧苄啶	Sulfamoxol/trimethoprim	Sulfamoxol/trimethoprim	Sulfamoxole/triméthoprime	Sulfamoxol/Trimethoprim	Σουλφαμοξόλη/τριμεθοπρίμη	Sulfamoxolo/trimetoprim	スルファフェナゾール	Sulfamoksol/trimetoprim	Sulfamoxole/trimethoprim	Сульфамоксол/триметоприм	Sulfamoxol/trimetoprima	Sulfamoxol/trimetoprim	Sülfamoksol/trimetoprim	Сульфамоксол/триметоприм
-Sulfathiourea	FALSE	TRUE	TRUE	FALSE	Sulfathioharnstoff	Sulfathioureum	Sulfathiourea	Sulfathiourea	Sulfathiourée	Sulfathiourea	Sulfathiourea	Sulfatiourea	Сульфатиомочевина
+Sulfaperin	FALSE	TRUE	TRUE	FALSE	磺胺类药物	Sulfaperin	Sulfaperine	Sulfapérine	Sulfaperin	Sulfaperin	Sulfaperin	スルファチアゾール	Sulfaperin	Sulfaperin	Сульфаперин	Sulfametoxazol	Sulfaperin	Sülfaperin	Сульфаперин
-Sultamicillin	FALSE	TRUE	TRUE	FALSE	Sultamicillin	Sultamicilline	Sultamicilina	Sultamicillina	Sultamicilline	Sultamicillin	Sultamicillin	Sultamicillin	Сультамициллин
+Sulfaphenazole	FALSE	TRUE	TRUE	FALSE	磺胺苯吡唑	Sulfaphenazol	Sulfafenazol	Sulfaphénazole	Sulfaphenazol	Σουλφαφαιναζόλη	Sulfafenazolo	スルファチオ尿素	Sulfafenazol	Sulfafenazol	Сульфафеназол	Sulfafenazol	Sulfafenazol	Sülfafenazol	Сульфафеназол
-Talampicillin	FALSE	TRUE	TRUE	FALSE	Talampicillin	Talampicilline	Talampicilina	Talampicillina	Talampicilline	Talampicilina	Talampicillin	Talampicillin	Талампициллин
+Sulfathiazole	FALSE	TRUE	TRUE	FALSE	磺胺噻唑	Sulfathiazol	Sulfathiazol	Sulfathiazole	Sulfathiazol	Sulfathiazole	Sulfathiazole	スルタミシリン	Sulfatiazol	Sulfatazol	Сульфатиазол	Sulfatiazol	Sulfathiazol	Sulfathiazole	Сульфатіазол
-Teicoplanin	FALSE	TRUE	TRUE	FALSE	Teicoplanin	Teicoplanine	Teicoplanina	Teicoplanina	Teicoplanine	Teicoplanin	Teicoplanin	Teicoplanin	Тейкопланин
+Sulfathiourea	FALSE	TRUE	TRUE	FALSE	磺胺硫脲	Sulfathiourea	Sulfathioureum	Sulfathiourée	Sulfathioharnstoff	Sulfathiourea	Sulfathiourea	タランピシリン	Sulfathiourea	Sulfathiourea	Сульфатиомочевина	Sulfathiourea	Sulfatiourea	Sulfathiourea	Сульфатіосечовина
-Telithromycin	FALSE	TRUE	TRUE	FALSE	Telithromycin	Telitromycine	Telitromicina	Telitromicina	Télithromycine	Telitromicina	Telithromycin	Telitromycin	Телитромицин
+Sultamicillin	FALSE	TRUE	TRUE	FALSE	苏打米林	Sultamicillin	Sultamicilline	Sultamicilline	Sultamicillin	Sultamicillin	Sultamicillina	テイコプラニン	Sultamicillin	Sultamicillin	Сультамициллин	Sultamicilina	Sultamicillin	Sultamicillin	Сультаміцилін
-Temafloxacin	FALSE	TRUE	TRUE	FALSE	Temafloxacin	Temafloxacine	Temafloxacina	Temafloxacina	Temafloxacine	Temafloxacin	Temafloxacin	Temafloxacin	Темафлоксацин
+Talampicillin	FALSE	TRUE	TRUE	FALSE	塔拉比西林	Talampicillin	Talampicilline	Talampicilline	Talampicillin	Talampicillin	Talampicillina	テリスロマイシン	Talampicylina	Talampicilina	Талампициллин	Talampicilina	Talampicillin	Talampisilin	Талампіцилін
-Temocillin	FALSE	TRUE	TRUE	FALSE	Temocillin	Temocilline	Temocilina	Temocillina	Temocillin	Temocillin	Temocillin	Temocillin	Темоциллин
+Teicoplanin	FALSE	TRUE	TRUE	FALSE	泰科普兰素	Teicoplanin	Teicoplanine	Teicoplanine	Teicoplanin	Teicoplanin	Teicoplanina	テマフロキサシン	Teicoplanin	Teicoplanin	Тейкопланин	Teicoplanina	Teicoplanin	Teikoplanin	Тейкопланін
-Tenofovir disoproxil	FALSE	TRUE	TRUE	FALSE	Tenofovir Disoproxil	Tenofovir	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Тенофовир дизопроксил
+Telithromycin	FALSE	TRUE	TRUE	FALSE	泰利霉素	Telithromycin	Telitromycine	Télithromycine	Telithromycin	Τελιθρομυκίνη	Telitromicina	テモシリン	Telitromycyna	Telitromicina	Телитромицин	Telitromicina	Telitromycin	Telitromisin	Телітроміцин
-Terizidone	FALSE	TRUE	TRUE	FALSE	Terizidon	Terizidon	Terizidona	Terizidone	Terizidone	Terizidone	Terizidon	Terizidon	Теризидон
+Temafloxacin	FALSE	TRUE	TRUE	FALSE	氨甲环酸	Temafloxacin	Temafloxacine	Temafloxacine	Temafloxacin	Temafloxacin	Temafloxacina	テノホビルジソプロキシル	Temafloksacyna	Temafloxacin	Темафлоксацин	Temafloxacina	Temafloxacin	Temafloksasin	Темафлоксацин
-Thiamphenicol	FALSE	TRUE	TRUE	FALSE	Thiamphenicol	Thiamfenicol	Tiamfenicol	Tiamfenicolo	Thiamphénicol	Tiamfenicol	Thiamphenicol	Tiamfenikol	Тиамфеникол
+Temocillin	FALSE	TRUE	TRUE	FALSE	氨甲蝶呤	Temocillin	Temocilline	Temocillin	Temocillin	Temocillin	Temocillina	テリジドン	Temocillin	Temocillin	Темоциллин	Temocilina	Temocillin	Temocillin	Темоцилін
-Thioacetazone/isoniazid	FALSE	TRUE	TRUE	FALSE	Thioacetazon/Isoniazid	Thioacetazon/isoniazide	Tioacetazona/isoniazida	Tioacetazone/isoniazide	Thioacétazone/isoniazide	Thioacetazone/isoniazid	Thioacetazon/isoniazid	Thioacetazon/isoniazid	Тиоацетазон/изониазид
+Tenofovir disoproxil	FALSE	TRUE	TRUE	FALSE	特诺福韦酯	Tenofovir disoproxil	Tenofovir	Tenofovir disoproxil	Tenofovir Disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	チアンフェニコール	Tenofovir disoproxil	Tenofovir disoproxil	Тенофовир дизопроксил	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproksil	Тенофовір дизопроксил
-Ticarcillin	FALSE	TRUE	TRUE	FALSE	Ticarcillin	Ticarcilline	Ticarcilina	Ticarcillina	Ticarcilline	Ticarcilina	Ticarcillin	Ticarcillin	Тикарциллин
+Terizidone	FALSE	TRUE	TRUE	FALSE	特立兹酮	Terizidon	Terizidon	Terizidone	Terizidon	Terizidone	Terizidone	チオアセタゾン／イソニアジド	Terizidon	Terizidone	Теризидон	Terizidona	Terizidon	Terizidon	Теризидон
-Ticarcillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Ticarcillin/Beta-Lactamase-Hemmer	Ticarcilline/enzymremmer	Ticarcilina/inhib. de la betalactamasa	Ticarcillina/inib. d. beta-lattamasi	Ticarcilline/inhib. de bêta-lactamase	Ticarcilina/inibid. da beta-lactamase	Ticarcillin/beta-lactamasehæmmer	Ticarcillin/beta-laktamashämmare	Тикарциллин/ингибитор бета-лактамазы
+Thiamphenicol	FALSE	TRUE	TRUE	FALSE	硫苯尼考	Thiamphenicol	Thiamfenicol	Thiamphénicol	Thiamphenicol	Thiamphenicol	Tiamfenicolo	チカルシリン	Tiamfenikol	Tiamfenicol	Тиамфеникол	Tiamfenicol	Tiamfenikol	Thiamphenicol	Тіамфенікол
-Ticarcillin/clavulanic acid	FALSE	TRUE	TRUE	FALSE	Ticarcillin/Clavulansäure	Ticarcilline/clavulaanzuur	Ticarcilina/ácido clavulánico	Ticarcillina/acido clavulanico	Ticarcilline/acide clavulanique	Ticarcilina/ácido clavulanico	Ticarcillin/clavulansyre	Ticarcillin/clavulansyra	Тикарциллин/клавулановая кислота
+Thioacetazone/isoniazid	FALSE	TRUE	TRUE	FALSE	硫乙酰唑酮/异烟肼	Thioacetazon/isoniazid	Thioacetazon/isoniazide	Thioacétazone/isoniazide	Thioacetazon/Isoniazid	Θειοακεταζόνη/ισονιαζίδη	Tioacetazone/isoniazide	チカルシリン／β-ラクタマーゼ阻害剤	Tioacetazon/izoniazyd	Thioacetazone/isoniazid	Тиоацетазон/изониазид	Tioacetazona/isoniazida	Thioacetazon/isoniazid	Tiyoasetazon/izoniazid	Тіоацетазон/ізоніазид
-Tinidazole	FALSE	TRUE	TRUE	FALSE	Tinidazol	Tinidazol	Tinidazol	Tinidazolo	Tinidazole	Tinidazole	Tinidazol	Tinidazol	Тинидазол
+Ticarcillin	FALSE	TRUE	TRUE	FALSE	替卡西林	Ticarcillin	Ticarcilline	Ticarcilline	Ticarcillin	Τικαρκιλλίνη	Ticarcillina	チカルシリン／クラブラン酸	Ticarcillin	Ticarcilina	Тикарциллин	Ticarcilina	Ticarcillin	Ticarcillin	Тикарцилін
-Tobramycin	FALSE	TRUE	TRUE	FALSE	Tobramycin	Tobramycine	Tobramicina	Tobramicina	Tobramycine	Tobramycin	Tobramycin	Tobramycin	Тобрамицин
+Ticarcillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	替卡西林/β-内酰胺酶抑制剂	Ticarcillin/beta-lactamasehæmmer	Ticarcilline/enzymremmer	Ticarcilline/inhib. de bêta-lactamase	Ticarcillin/Beta-Lactamase-Hemmer	Τικαρκιλλίνη/αναστολέας της β-λακταμάσης	Ticarcillina/inib. d. beta-lattamasi	チニダゾール	Tikarcylina/inhibitor beta-laktamazy	Ticarcilina/inibid. da beta-lactamase	Тикарциллин/ингибитор бета-лактамазы	Ticarcilina/inhib. de la betalactamasa	Ticarcillin/beta-laktamashämmare	Tikarsilin/beta-laktamaz inhibitörü	Тикарцилін/інгібітор бета-лактамаз
-Trimethoprim/sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Trimethoprim/Sulfamethoxazol	Cotrimoxazol	Trimetoprima/sulfametoxazol	Trimetoprim/sulfametossazolo	Triméthoprime/sulfaméthoxazole	Trimethoprim/sulfametoxazol	Trimethoprim/sulfamethoxazol	Trimetoprim/sulfametoxazol	Триметоприм/сульфаметоксазол
+Ticarcillin/clavulanic acid	FALSE	TRUE	TRUE	FALSE	替卡西林/克拉维酸	Ticarcillin/clavulansyre	Ticarcilline/clavulaanzuur	Ticarcilline/acide clavulanique	Ticarcillin/Clavulansäure	Τικαρκιλλίνη/κλαβουλανικό οξύ	Ticarcillina/acido clavulanico	トブラマイシン	Tikarcylina/kwas klawulanowy	Ticarcilina/ácido clavulanico	Тикарциллин/клавулановая кислота	Ticarcilina/ácido clavulánico	Ticarcillin/clavulansyra	Tikarsilin/klavulanik asit	Тикарцилін/клавуланова кислота
-Troleandomycin	FALSE	TRUE	TRUE	FALSE	Troleandomycin	Troleandomycine	Troleandomicina	Troleandomicina	Troleandomycine	Troleandomicina	Troleandomycin	Troleandomycin	Тролеандомицин
+Tinidazole	FALSE	TRUE	TRUE	FALSE	替尼唑	Tinidazol	Tinidazol	Tinidazole	Tinidazol	Τινιδαζόλη	Tinidazolo	トリメトプリム／スルファメトキサゾール	Tinidazol	Tinidazole	Тинидазол	Tinidazol	Tinidazol	Tinidazol	Тинідазол
-Trovafloxacin	FALSE	TRUE	TRUE	FALSE	Trovafloxacin	Trovafloxacine	Trovafloxacina	Trovafloxacin	Trovafloxacine	Trovafloxacin	Trovafloxacin	Trovafloxacin	Тровафлоксацин
+Tobramycin	FALSE	TRUE	TRUE	FALSE	妥布霉素	Tobramycin	Tobramycine	Tobramycine	Tobramycin	Τομπραμυκίνη	Tobramicina	トロレアンドマイシン	Tobramycyna	Tobramycin	Тобрамицин	Tobramicina	Tobramycin	Tobramisin	Тобраміцин
-Vancomycin	FALSE	TRUE	TRUE	FALSE	Vancomycin	Vancomycine	Vancomicina	Vancomicina	Vancomycine	Vancomycin	Vancomycin	Vancomycin	Ванкомицин
+Trimethoprim/sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	三甲氧嘧啶/磺胺甲恶唑	Trimethoprim/sulfamethoxazol	Cotrimoxazol	Triméthoprime/sulfaméthoxazole	Trimethoprim/Sulfamethoxazol	Τριμεθοπρίμη/σουλφαμεθοξαζόλη	Trimetoprim/sulfametossazolo	トロバフロキサシン	Trimetoprim/sulfametoksazol	Trimethoprim/sulfametoxazol	Триметоприм/сульфаметоксазол	Trimetoprima/sulfametoxazol	Trimetoprim/sulfametoxazol	Trimetoprim/sülfametoksazol	Триметоприм/сульфаметоксазол
-Voriconazole	FALSE	TRUE	TRUE	FALSE	Voriconazol	Voriconazol	Voriconazol	Voriconazolo	Voriconazole	Voriconazol	Voriconazol	Vorikonazol	Вориконазол
+Troleandomycin	FALSE	TRUE	TRUE	FALSE	托拉多霉素	Troleandomycin	Troleandomycine	Troleandomycine	Troleandomycin	Τρολεαντομυκίνη	Troleandomicina	バンコマイシン	Troleandomycyna	Troleandomicina	Тролеандомицин	Troleandomicina	Troleandomycin	Troleandomisin	Тролеандоміцин
-Aminoglycosides	FALSE	TRUE	TRUE	FALSE	Aminoglykoside	Aminoglycosiden	Aminoglucósidos	Aminoglicosidi	Aminoglycosides	Aminoglycosides	Aminoglykosider	Aminoglykosider	Аминогликозиды
+Trovafloxacin	FALSE	TRUE	TRUE	FALSE	特戊沙星	Trovafloxacin	Trovafloxacine	Trovafloxacine	Trovafloxacin	Τροβαφλοξασίνη	Trovafloxacin	ボリコナゾール	Trovafloxacin	Trovafloxacin	Тровафлоксацин	Trovafloxacina	Trovafloxacin	Trovafloksasin	Тровафлоксацин
-Amphenicols	FALSE	TRUE	TRUE	FALSE	Amphenicole	Amfenicolen	Anfenicoles	Amphenicols	Amphénicols	Anfenicóis	Amphenicoler	Amfenikoler	Амфениколы
+Vancomycin	FALSE	TRUE	TRUE	FALSE	唑啉酮	Vancomycin	Vancomycine	Vancomycine	Vancomycin	Βανκομυκίνη	Vancomicina	アミノグリコシド系抗生物質	Wankomycyna	Vancomycin	Ванкомицин	Vancomicina	Vancomycin	Vankomisin	Ванкоміцин
-Antifungals/antimycotics	FALSE	TRUE	TRUE	FALSE	Antimykotika/Antimykotika	Antifungica/antimycotica	Antifúngicos/antimicóticos	Antifungini/antimicotici	Antifongiques/antimycotiques	Antifúngicos/antimicóticos	Antimykotika/antimykotika	Antimykotika/antimykotika	Противогрибковые препараты/антимикотики
+Voriconazole	FALSE	TRUE	TRUE	FALSE	伏立康唑	Voriconazol	Voriconazol	Voriconazole	Voriconazol	Voriconazole	Voriconazolo	アンフェニコール	Worikonazol	Voriconazol	Вориконазол	Voriconazol	Vorikonazol	Vorikonazol	Вориконазол
-Antimycobacterials	FALSE	TRUE	TRUE	FALSE	Antimykobakterielle Mittel	Antimycobacteriele middelen	Antimicrobianos	Antimicobatterici	Antimycobactériens	Antimycobacterials	Antimycobakterier	Antimykobakterier	Антимикобактериальные препараты
+Aminoglycosides	FALSE	TRUE	TRUE	FALSE	氨基糖苷类	Aminoglykosider	Aminoglycosiden	Aminoglycosides	Aminoglykoside	Αμινογλυκοσίδες	Aminoglicosidi	抗真菌剤／抗真菌剤	Aminoglikozydy	Aminoglycosides	Аминогликозиды	Aminoglucósidos	Aminoglykosider	Aminoglikozidler	Аміноглікозиди
-Beta-lactams/penicillins	FALSE	TRUE	TRUE	FALSE	Beta-Lactame/Penicilline	Beta-lactams/penicillines	Beta-lactámicos/penicilinas	Beta-lattami/penicilline	Bêta-lactamines/pénicillines	Beta-lactâmicas/penicilinas	Beta-lactamer/penicilliner	Beta-laktamer/penicilliner	Бета-лактамы/пенициллины
+Amphenicols	FALSE	TRUE	TRUE	FALSE	安息香醇	Amphenicoler	Amfenicolen	Amphénicols	Amphenicole	Αμφενικόλες	Amphenicols	抗マイコバクテリア薬	Amfenikol	Anfenicóis	Амфениколы	Anfenicoles	Amfenikoler	Amphenicols	Амфеніколи
-Cephalosporins (1st gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (1. Gen.)	Cefalosporines (1e gen.)	Cefalosporinas (1er gen.)	Cefalosporine (1° gen.)	Céphalosporines (1ère génération)	Cefalosporinas (1º género)	Cefalosporiner (1. gen.)	Kefalosporiner (första gen.)	Цефалоспорины (1-го пок.)
+Antifungals/antimycotics	FALSE	TRUE	TRUE	FALSE	抗真菌药/抗真菌药	Antimykotika/antimykotika	Antifungica/antimycotica	Antifongiques/antimycotiques	Antimykotika/Antimykotika	Αντιμυκητιασικά/αντιμυκητιασικά	Antifungini/antimicotici	β-ラクタム系/ペニシリン系	Środki przeciwgrzybicze/przeciwmikotyczne	Antifúngicos/antimicóticos	Противогрибковые препараты/антимикотики	Antifúngicos/antimicóticos	Antimykotika/antimykotika	Antifungaller/antimikotikler	Протигрибкові засоби/антимікотики
-Cephalosporins (2nd gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (2. Gen.)	Cefalosporines (2e gen.)	Cefalosporinas (2do gen.)	Cefalosporine (2° gen.)	Céphalosporines (2ème génération)	Cefalosporinas (2ª gen.)	Cefalosporiner (2. gen.)	Kefalosporiner (andra gen.)	Цефалоспорины (2-го пок.)
+Antimycobacterials	FALSE	TRUE	TRUE	FALSE	抗霉菌素类	Antimycobakterier	Antimycobacteriele middelen	Antimycobactériens	Antimykobakterielle Mittel	Αντιμυκοβακτηριακά	Antimicobatterici	セファロスポリン系（第1世代）	Środki przeciwgrzybicze	Antimycobacterials	Антимикобактериальные препараты	Antimicrobianos	Antimykobakterier	Antimikobakteriyeller	Засоби, що діють на мікобактерії
-Cephalosporins (3rd gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (3. Gen.)	Cefalosporines (3e gen.)	Cefalosporinas (3er gen.)	Cefalosporine (3° gen.)	Céphalosporines (3ème génération)	Cefalosporinas (3ª gen.)	Cefalosporiner (3. gen.)	Kefalosporiner (tredje gen.)	Цефалоспорины (3-го пок.)
+Beta-lactams/penicillins	FALSE	TRUE	TRUE	FALSE	β-内酰胺类/青霉素类	Beta-lactamer/penicilliner	Beta-lactams/penicillines	Bêta-lactamines/pénicillines	Beta-Lactame/Penicilline	Β-λακτάμες/πενικιλλίνες	Beta-lattami/penicilline	セファロスポリン（第2世代）	Beta-laktamy/penicyliny	Beta-lactâmicas/penicilinas	Бета-лактамы/пенициллины	Beta-lactámicos/penicilinas	Beta-laktamer/penicilliner	Beta-laktamlar/penisilinler	Бета-лактами/пеніциліни
-Cephalosporins (4th gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (4. Gen.)	Cefalosporines (4e gen.)	Cefalosporinas (4ª gen.)	Cefalosporine (4° gen.)	Céphalosporines (4ème génération)	Cefalosporinas (4.ª gen.)	Cefalosporiner (4. gen.)	Kefalosporiner (4:e gen.)	Цефалоспорины (4-го пок.)
+Cephalosporins (1st gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素类（第一代）	Cefalosporiner (1. gen.)	Cefalosporines (1e gen.)	Céphalosporines (1ère génération)	Cephalosporine (1. Gen.)	Κεφαλοσπορίνες (1ης γενιάς)	Cefalosporine (1° gen.)	セファロスポリン（第3世代）	Cefalosporyny (1. gen.)	Cefalosporinas (1º género)	Цефалоспорины (1-го пок.)	Cefalosporinas (1er gen.)	Kefalosporiner (första gen.)	Sefalosporinler (1. kuşak)	Цефалоспорини (1 пок.)
-Cephalosporins (5th gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (5. Gen.)	Cefalosporines (5e gen.)	Cefalosporinas (5º gen.)	Cefalosporine (5° gen.)	Céphalosporines (5e gén.)	Cefalosporinas (5.ª gen.)	Cefalosporiner (5. gen.)	Kefalosporiner (5:e gen.)	Цефалоспорины (5-го пок.)
+Cephalosporins (2nd gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素类（第二代）	Cefalosporiner (2. gen.)	Cefalosporines (2e gen.)	Céphalosporines (2ème génération)	Cephalosporine (2. Gen.)	Κεφαλοσπορίνες (2ης γενιάς)	Cefalosporine (2° gen.)	セファロスポリン（第4世代）	Cefalosporyny (2. gen.)	Cefalosporinas (2ª gen.)	Цефалоспорины (2-го пок.)	Cefalosporinas (2do gen.)	Kefalosporiner (andra gen.)	Sefalosporinler (2. kuşak)	Цефалоспорини (2 пок.)
-Cephalosporins (unclassified gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (unklassifiziert)	Cefalosporines (ongeclassificeerd)	Cefalosporinas (gen. no clasificado)	Cefalosporine (gen. non classificato)	Céphalosporines (genre non classifié)	Cefalosporinas (não classificado gen.)	Cefalosporiner (uklassificeret gen.)	Kefalosporiner (oklassificerad gen.)	Цефалоспорины (неклассифицированный род)
+Cephalosporins (3rd gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素类（第三代）	Cefalosporiner (3. gen.)	Cefalosporines (3e gen.)	Céphalosporines (3ème génération)	Cephalosporine (3. Gen.)	Κεφαλοσπορίνες (3ης γενιάς)	Cefalosporine (3° gen.)	セファロスポリン（第5世代）	Cefalosporyny (3 gen.)	Cefalosporinas (3ª gen.)	Цефалоспорины (3-го пок.)	Cefalosporinas (3er gen.)	Kefalosporiner (tredje gen.)	Sefalosporinler (3. kuşak)	Цефалоспорини (3 пок.)
-Cephalosporins	FALSE	TRUE	TRUE	FALSE	Cephalosporine	Cefalosporines	Cefalosporinas	Cefalosporine	Céphalosporines	Cefalosporinas	Cefalosporiner	Kefalosporiner	Цефалоспорины
+Cephalosporins (4th gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素类（第四代）	Cefalosporiner (4. gen.)	Cefalosporines (4e gen.)	Céphalosporines (4ème génération)	Cephalosporine (4. Gen.)	Κεφαλοσπορίνες (4ης γενιάς)	Cefalosporine (4° gen.)	セファロスポリン（未分類の世代）	Cefalosporyny (4 gen.)	Cefalosporinas (4.ª gen.)	Цефалоспорины (4-го пок.)	Cefalosporinas (4ª gen.)	Kefalosporiner (4:e gen.)	Sefalosporinler (4. kuşak)	Цефалоспорини (4 пок.)
-Glycopeptides	FALSE	TRUE	TRUE	FALSE	Glykopeptide	Glycopeptiden	Glicopéptidos	Glicopeptidi	Glycopeptides	Glycopeptides	Glykopeptider	Glykopeptider	Гликопептиды
+Cephalosporins (5th gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素（第五代）	Cefalosporiner (5. gen.)	Cefalosporines (5e gen.)	Céphalosporines (5e gén.)	Cephalosporine (5. Gen.)	Κεφαλοσπορίνες (5ης γενιάς)	Cefalosporine (5° gen.)	セファロスポリン	Cefalosporyny (5. gen.)	Cefalosporinas (5.ª gen.)	Цефалоспорины (5-го пок.)	Cefalosporinas (5º gen.)	Kefalosporiner (5:e gen.)	Sefalosporinler (5. kuşak)	Цефалоспорини (5 пок.)
-Macrolides/lincosamides	FALSE	TRUE	TRUE	FALSE	Makrolide/Linkosamide	Macroliden/lincosamiden	Macrólidos/lincosamidas	Macrolidi/lincosamidi	Macrolides/lincosamides	Macrolides/lincosamidas	Makrolider/lincosamider	Makrolider/linkosamider	Макролиды/линкозамиды
+Cephalosporins (unclassified gen.)	FALSE	TRUE	TRUE	FALSE	头孢菌素类（未分类的一代）	Cefalosporiner (uklassificeret gen.)	Cefalosporines (ongeclassificeerd)	Céphalosporines (genre non classifié)	Cephalosporine (unklassifiziert)	Κεφαλοσπορίνες (μη ταξινομημένη γενιά)	Cefalosporine (gen. non classificato)	糖ペプチド系	Cefalosporyny (niesklasyfikowana gen.)	Cefalosporinas (não classificado gen.)	Цефалоспорины (неклассифицированный род)	Cefalosporinas (gen. no clasificado)	Kefalosporiner (oklassificerad gen.)	Sefalosporinler (sınıflandırılmamış nesil)	Цефалоспорини (некласифікованого пок.)
-Other antibacterials	FALSE	TRUE	TRUE	FALSE	Andere Antibiotika	Overige antibiotica	Otros antibacterianos	Altri antibatterici	Autres antibactériens	Outros antibacterianos	Andre antibakterielle stoffer	Andra antibakteriella medel	Другие антибактериальные препараты
+Cephalosporins	FALSE	TRUE	TRUE	FALSE	头孢菌素类	Cefalosporiner	Cefalosporines	Céphalosporines	Cephalosporine	Κεφαλοσπορίνες	Cefalosporine	マクロライド系／リンコサミド系	Cefalosporyny	Cefalosporinas	Цефалоспорины	Cefalosporinas	Kefalosporiner	Sefalosporinler	Цефалоспорини
-Polymyxins	FALSE	TRUE	TRUE	FALSE	Polymyxine	Polymyxines	Polimixinas	Polimixine	Polymyxines	Polimixinas	Polymyxiner	Polymyxiner	Полимиксины
+Glycopeptides	FALSE	TRUE	TRUE	FALSE	糖肽类药物	Glykopeptider	Glycopeptiden	Glycopeptides	Glykopeptide	Γλυκοπεπτίδια	Glicopeptidi	その他の抗菌薬	Glikopeptydy	Glycopeptides	Гликопептиды	Glicopéptidos	Glykopeptider	Glikopeptitler	Глікопептиди
-Quinolones	FALSE	TRUE	TRUE	FALSE	Quinolone	Quinolonen	Quinolonas	Chinoloni	Quinolones	Quinolones	Kinoloner	Kinoloner	Хинолоны
+Macrolides/lincosamides	FALSE	TRUE	TRUE	FALSE	大环内酯类/林可酰胺类	Makrolider/lincosamider	Macroliden/lincosamiden	Macrolides/lincosamides	Makrolide/Linkosamide	Μακρολίδια/λινκοσαμίδια	Macrolidi/lincosamidi	ポリミキシン	Makrolidy/linkozamidy	Macrolides/lincosamidas	Макролиды/линкозамиды	Macrólidos/lincosamidas	Makrolider/linkosamider	Makrolidler/linkozamidler	Макроліди/лінкозаміди
+Other antibacterials	FALSE	TRUE	TRUE	FALSE	其他抗菌剂	Andre antibakterielle stoffer	Overige antibiotica	Autres antibactériens	Andere Antibiotika	Άλλα αντιβακτηριακά	Altri antibatterici	キノロン	Inne środki przeciwbakteryjne	Outros antibacterianos	Другие антибактериальные препараты	Otros antibacterianos	Andra antibakteriella medel	Diğer antibakteriyeller	Інші антибактеріальні засоби
+Polymyxins	FALSE	TRUE	TRUE	FALSE	多粘菌素类	Polymyxiner	Polymyxines	Polymyxines	Polymyxine	Πολυμυξίνες	Polimixine	ポリミキシン	Polimyksyny	Polimixinas	Полимиксины	Polimixinas	Polymyxiner	Polimiksinler	Поліміксини
+Quinolones	FALSE	TRUE	TRUE	FALSE	喹诺酮类	Kinoloner	Quinolonen	Quinolones	Quinolone	Κινολόνες	Chinoloni	キノロン	Quinolony	Quinolones	Хинолоны	Quinolonas	Kinoloner	Kinolonlar	Хінолони

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-    b) You must cause any work that you distribute or publish, that in
-    whole or in part contains or is derived from the Program or any
-    part thereof, to be licensed as a whole at no charge to all third
-    parties under the terms of this License.
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-    c) If the modified program normally reads commands interactively
-    when run, you must cause it, when started running for such
-    interactive use in the most ordinary way, to print or display an
-    announcement including an appropriate copyright notice and a
-    notice that there is no warranty (or else, saying that you provide
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-    License.  (Exception: if the Program itself is interactive but
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-These requirements apply to the modified work as a whole. If
-identifiable sections of that work are not derived from the Program,
-and can be reasonably considered independent and separate works in
-themselves, then this License, and its terms, do not apply to those
-sections when you distribute them as separate works. But when you
-distribute the same sections as part of a whole which is a work based
-on the Program, the distribution of the whole must be on the terms of
-this License, whose permissions for other licensees extend to the
-entire whole, and thus to each and every part regardless of who wrote it.
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-Thus, it is not the intent of this section to claim rights or contest
-your rights to work written entirely by you; rather, the intent is to
-exercise the right to control the distribution of derivative or
-collective works based on the Program.
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-In addition, mere aggregation of another work not based on the Program
-with the Program (or with a work based on the Program) on a volume of
-a storage or distribution medium does not bring the other work under
-the scope of this License.
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-3. You may copy and distribute the Program (or a work based on it,
-under Section 2) in object code or executable form under the terms of
-Sections 1 and 2 above provided that you also do one of the following:
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-    a) Accompany it with the complete corresponding machine-readable
-    source code, which must be distributed under the terms of Sections
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-    years, to give any third party, for a charge no more than your
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-    c) Accompany it with the information you received as to the offer
-    to distribute corresponding source code.  (This alternative is
-    allowed only for noncommercial distribution and only if you
-    received the program in object code or executable form with such
-    an offer, in accord with Subsection b above.)
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-The source code for a work means the preferred form of the work for
-making modifications to it. For an executable work, complete source
-code means all the source code for all modules it contains, plus any
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-anything that is normally distributed (in either source or binary
-form) with the major components (compiler, kernel, and so on) of the
-operating system on which the executable runs, unless that component
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-distribution of the source code, even though third parties are not
-compelled to copy the source along with the object code.
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-4. You may not copy, modify, sublicense, or distribute the Program
-except as expressly provided under this License. Any attempt
-otherwise to copy, modify, sublicense or distribute the Program is
-void, and will automatically terminate your rights under this License.
-However, parties who have received copies, or rights, from you under
-this License will not have their licenses terminated so long as such
-parties remain in full compliance.
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-5. You are not required to accept this License, since you have not
-signed it. However, nothing else grants you permission to modify or
-distribute the Program or its derivative works. These actions are
-prohibited by law if you do not accept this License. Therefore, by
-modifying or distributing the Program (or any work based on the
-Program), you indicate your acceptance of this License to do so, and
-all its terms and conditions for copying, distributing or modifying
-the Program or works based on it.
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-6. Each time you redistribute the Program (or any work based on the
-Program), the recipient automatically receives a license from the
-original licensor to copy, distribute or modify the Program subject to
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-restrictions on the recipients' exercise of the rights granted herein.
-You are not responsible for enforcing compliance by third parties to
-this License.
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-7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
-otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License. If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all. For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
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-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
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-through that system in reliance on consistent application of that
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-impose that choice.
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-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
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-8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded. In such case, this License incorporates
-the limitation as if written in the body of this License.
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-9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time. Such new versions will
-be similar in spirit to the present version, but may differ in detail to
-address new problems or concerns.
-
-Each version is given a distinguishing version number. If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation. If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-
-10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission. For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this. Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
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-NO WARRANTY
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-11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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-12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-
-END OF TERMS AND CONDITIONS
-</pre>
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