(v1.7.1.9045) unit tests

.Rbuildignore

@@ -23,8 +23,11 @@
 ^data-raw$
 ^\.lintr$
 ^tests/testthat/_snaps$
+^vignettes/AMR.Rmd$
 ^vignettes/benchmarks.Rmd$
+^vignettes/datasets.Rmd$
 ^vignettes/EUCAST.Rmd$
+^vignettes/MDR.Rmd$
 ^vignettes/PCA.Rmd$
 ^vignettes/resistance_predict.Rmd$
 ^vignettes/SPSS.Rmd$

.github/workflows/check.yaml

@@ -26,15 +26,15 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
   schedule:
-    # run a schedule everyday at 3 AM.
+    # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
-    - cron:  '0 3 * * *'
+    - cron:  '0 1 * * *'
 
 name: R-code-check
 
@@ -50,22 +50,16 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # these are the developmental version of R - we allow those tests to fail
+          # test all systems against all released versions of R >= 3.0, we support them all!
           - {os: macOS-latest,   r: 'devel',   allowfail: true}
-          - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {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: macOS-latest,   r: '3.4',     allowfail: false}
+          - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          - {os: macOS-latest,   r: '3.2',     allowfail: false}
           - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
-          # these are the current release of R
-          - {os: macOS-latest,   r: 'release', allowfail: false}
-          - {os: windows-latest, r: 'release', allowfail: false}
-          - {os: ubuntu-20.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
-          # these are the previous release of R
-          - {os: macOS-latest,   r: 'oldrel',  allowfail: false}
-          - {os: windows-latest, r: 'oldrel',  allowfail: false}
-          - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
-          # test against all released versions of R >= 3.0, we support them all!
           - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -75,41 +69,43 @@ jobs:
           - {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: false}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       R_REPOSITORIES: "https://cran.rstudio.com"
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
       
     steps:
       - uses: actions/checkout@v2
 
+      - uses: r-lib/actions/setup-pandoc@v1
+
       - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
           
-      - name: Install Linux dependencies
+      - name: show file list
-        if: runner.os == 'Linux'
+        run: ls -lh
-        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
+        shell: bash
-        # 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
-        run: |
-          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
         
-      - name: Restore cached R packages
+      - name: Install dependencies
-        # this step will add the step 'Post Restore cached R packages' on a succesful run
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
-
-      - name: Unpack AMR and install R dependencies
         if: always()
         run: |
-          tar -xf data-raw/AMR_latest.tar.gz
+          install.packages("remotes", repos = c("https://cloud.r-project.org", "https://cran.rstudio.com"))
-          Rscript -e "source('data-raw/_install_deps.R')"
+          remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
-        shell: bash
+        shell: Rscript {0}
        
       - name: Show session info
         if: always()
@@ -119,42 +115,25 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      # - name: Only keep vignettes on release version
+      - uses: r-lib/actions/check-r-package@v1
-      - name: Remove vignettes
-        # if: matrix.config.r != 'release'
-        if: always()
-        # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
-        run: |
-          rm -rf AMR/vignettes
-          Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
-          rm AMR/DESCRIPTION
-          mv AMR/DESCRIPTION2 AMR/DESCRIPTION
-        shell: bash
-        
-      - name: Run R CMD check
-        if: always()
         env:
           _R_CHECK_CRAN_INCOMING_: false
           _R_CHECK_FORCE_SUGGESTS_: false
           _R_CHECK_DEPENDS_ONLY_: true
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          R_RUN_TINYTEST: true
           # during 'R CMD check', R_LIBS_USER will be overwritten, so:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
-          R_RUN_TINYTEST: true
-        run: |
-          R CMD check --no-manual --run-donttest --run-dontrun AMR
-        shell: bash
       
       - name: Show unit tests output
         if: always()
-        run: |
+        run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
-          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
-      - name: Upload artifacts
+      - name: Upload check results
         if: always()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@main
         with:
-          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
+          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
-          path: AMR.Rcheck
+          path: check

.github/workflows/check.yaml.old

@@ -0,0 +1,157 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 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/   #
+# ==================================================================== #
+
+# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
+
+on:
+  push:
+    branches:
+      - premaster
+      - master
+  pull_request:
+    branches:
+      - master
+  schedule:
+    # run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available (see R/zzz.R)
+    - cron:  '0 1 * * *'
+
+name: R-code-check
+
+jobs:
+  R-code-check:
+    runs-on: ${{ matrix.config.os }}
+    
+    continue-on-error: ${{ matrix.config.allowfail }}
+
+    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          # test all systems against all released versions of R >= 3.0, we support them all!
+          - {os: macOS-latest,   r: 'devel',   allowfail: true}
+          - {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: macOS-latest,   r: '3.4',     allowfail: false}
+          - {os: macOS-latest,   r: '3.3',     allowfail: false}
+          - {os: macOS-latest,   r: '3.2',     allowfail: false}
+          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/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: false}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      R_REPOSITORIES: "https://cran.rstudio.com"
+    
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
+        # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
+        # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
+        run: |
+          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
+
+      - name: Query dependencies
+        # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
+        run: |
+          writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle")
+        shell: Rscript {0}
+        
+      - name: Restore cached R packages
+        # this step will add the step 'Post Restore cached R packages' on a succesful run
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4
+
+      - name: Unpack AMR and install R dependencies
+        if: always()
+        run: |
+          tar -xf data-raw/AMR_latest.tar.gz
+          Rscript -e "source('data-raw/_install_deps.R')"
+        shell: bash
+        
+      - name: Show session info
+        if: always()
+        run: |
+          options(width = 100)
+          utils::sessionInfo()
+          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
+        shell: Rscript {0}
+        
+      - name: Run R CMD check
+        if: always()
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_DEPENDS_ONLY_: true
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true
+        run: |
+          R CMD check --no-manual --run-donttest --run-dontrun AMR
+        shell: bash
+
+      - name: Show unit tests output
+        if: always()
+        run: |
+          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload artifacts
+        if: always()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
+          path: AMR.Rcheck

.github/workflows/codecovr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: code-coverage
 
@@ -48,12 +48,18 @@ jobs:
           
       - uses: r-lib/actions/setup-pandoc@master
 
+      - name: Query dependencies
+        # this will change once a week, so it will cache dependency updates
+        run: |
+          writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
+        shell: Rscript {0}
+        
       - name: Restore cached R packages
         # this step will add the step 'Post Restore cached R packages' on a succesful run
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: macOS-latest-r-release-v5-codecovr
+          key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
 
       - name: Unpack AMR and install R dependencies
         run: |
@@ -68,26 +74,14 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
 
-      # - name: Test coverage
-      #   env:
-      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      #   run: |
-      #     library(AMR)
-      #     library(tinytest)
-      #     library(covr)
-      #     source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
-      #     test_files <- list.files("inst/tinytest", full.names = TRUE)
-      #     cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
-      #     attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
-      #     codecov(coverage = cov, quiet = FALSE)
-      #   shell: Rscript {0}
-      
       - name: Test coverage
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
           R_RUN_TINYTEST: true
         run: |
+          install.packages("covr", repos = "https://cran.rstudio.com/")
           library(AMR)
           library(tinytest)
-          covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
+          x <- covr::codecov(line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
+          print(x)
         shell: Rscript {0}

.github/workflows/lintr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: lintr
 
@@ -52,7 +52,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

DESCRIPTION

@@ -1,68 +1,92 @@
 Package: AMR
-Version: 1.7.1
+Version: 1.7.1.9045
-Date: 2021-06-03
+Date: 2021-09-29
 Title: Antimicrobial Resistance Data Analysis
-Authors@R: c(
-    person(role = c("aut", "cre"), 
-           family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")),
-    person(role = c("aut", "ctb"),
-           family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
-    person(role = c("aut", "ths"),
-           family = "Friedrich", given = c("Alexander", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
-    person(role = c("aut", "ths"),
-           family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
-    person(role = c("aut", "ths"),
-           family = "Albers", given = c("Casper", "J."), email = "c.j.albers@rug.nl", comment = c(ORCID = "0000-0002-9213-6743")),
-    person(role = c("aut", "ths"),
-           family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
-    person(role = "ctb",
-           family = "Fonville", given = c("Judith", "M."), email = "j.fonville@pamm.nl"),
-    person(role = "ctb",
-           family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"),
-    person(role = "ctb",
-           family = "Hazenberg", given = c("Eric", "H.", "L.", "C.", "M."), email = "e.hazenberg@jbz.nl"),
-    person(role = "ctb",
-           family = "Knight", given = "Gwen", email = "gwen.knight@lshtm.ac.uk"),
-    person(role = "ctb",
-           family = "Lenglet", given = "Annick", email = "annick.lenglet@amsterdam.msf.org"),
-    person(role = "ctb",
-           family = "Meijer", given = c("Bart", "C."), email = "b.meijerg@certe.nl"),
-    person(role = "ctb",
-           family = "Ny", given = "Sofia", email = "sofia.ny@folkhalsomyndigheten.se"),
-    person(role = "ctb",
-           family = "Schade", given = c("Rogier", "P."), email = "r.schade@amsterdamumc.nl"),
-    person(role = "ctb",
-           family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"),
-    person(role = "ctb",
-           family = "Underwood", given = "Anthony", email = "au3@sanger.ac.uk"))
 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>.
-Depends:
+Authors@R: c(
-    R (>= 3.0.0)
+  person(given = c("Matthijs", "S."),
+         family = "Berends", 
+         email = "m.s.berends@umcg.nl",
+         role = c("aut", "cre"), 
+         comment = c(ORCID = "0000-0001-7620-1800")),
+  person(given = c("Christian", "F."),
+         family = "Luz", 
+         role = c("aut", "ctb"),
+         comment = c(ORCID = "0000-0001-5809-5995")),
+  person(given = c("Alexander", "W."),
+         family = "Friedrich", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-4881-038X")),
+  person(given = c("Bhanu", "N.", "M."),
+         family = "Sinha", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-1634-0010")),
+  person(given = c("Casper", "J."),
+         family = "Albers", 
+         role = "ths",
+         comment = c(ORCID = "0000-0002-9213-6743")),
+  person(given = "Corinna",
+         family = "Glasner", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-1241-1328")),
+  person(given = c("Judith", "M."),
+         family = "Fonville", 
+         role = "ctb"),
+  person(given = c("Erwin", "E.", "A."),
+         family = "Hassing", 
+         role = "ctb"),
+  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 = "Dennis",
+         family = "Souverein", 
+         role = "ctb",
+         comment = c(ORCID = "0000-0003-0455-0336")),
+  person(given = "Anthony", 
+         family = "Underwood", 
+         role = "ctb",
+         comment = c(ORCID = "0000-0002-8547-427")))
+Depends: R (>= 3.0.0)
+Enhances:
+  cleaner,
+  skimr,
+  ggplot2
 Suggests: 
-    cleaner,
+  curl,
-    curl,
+  dplyr,
-    dplyr,
+  ggtext,
-    ggplot2,
+  knitr,
-    ggtext,
+  readxl,
-    knitr,
+  rmarkdown,
-    microbenchmark,
+  rvest,
-    pillar,
+  tinytest,
-    readxl,
+  xml2
-    rmarkdown,
-    rstudioapi,
-    rvest,
-    skimr,
-    tidyr,
-    tinytest,
-    xml2
 VignetteBuilder: knitr,rmarkdown
-URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
+URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
 BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,6 +5,7 @@ S3method("!=",ab_selector)
 S3method("!=",mic)
 S3method("%%",mic)
 S3method("%/%",mic)
+S3method("&",ab_selector)
 S3method("&",mic)
 S3method("*",mic)
 S3method("+",mic)
@@ -35,6 +36,7 @@ S3method("[[<-",mic)
 S3method("[[<-",mo)
 S3method("[[<-",rsi)
 S3method("^",mic)
+S3method("|",ab_selector)
 S3method("|",mic)
 S3method(abs,mic)
 S3method(acos,mic)
@@ -120,7 +122,11 @@ S3method(print,rsi)
 S3method(prod,mic)
 S3method(quantile,mic)
 S3method(range,mic)
+S3method(rep,ab)
+S3method(rep,disk)
+S3method(rep,mic)
 S3method(rep,mo)
+S3method(rep,rsi)
 S3method(round,mic)
 S3method(sign,mic)
 S3method(signif,mic)
@@ -157,27 +163,35 @@ export(ab_atc_group2)
 export(ab_cid)
 export(ab_class)
 export(ab_ddd)
+export(ab_ddd_units)
 export(ab_from_text)
 export(ab_group)
 export(ab_info)
 export(ab_loinc)
 export(ab_name)
 export(ab_property)
+export(ab_selector)
 export(ab_synonyms)
 export(ab_tradenames)
 export(ab_url)
+export(administrable_iv)
+export(administrable_per_os)
 export(age)
 export(age_groups)
 export(all_antimicrobials)
 export(aminoglycosides)
+export(aminopenicillins)
 export(anti_join_microorganisms)
+export(antifungals)
 export(antimicrobials_equal)
+export(antimycobacterials)
 export(as.ab)
 export(as.disk)
 export(as.mic)
 export(as.mo)
 export(as.rsi)
 export(atc_online_ddd)
+export(atc_online_ddd_units)
 export(atc_online_groups)
 export(atc_online_property)
 export(availability)
@@ -207,24 +221,7 @@ export(eucast_dosage)
 export(eucast_exceptional_phenotypes)
 export(eucast_rules)
 export(facet_rsi)
-export(filter_1st_cephalosporins)
-export(filter_2nd_cephalosporins)
-export(filter_3rd_cephalosporins)
-export(filter_4th_cephalosporins)
-export(filter_5th_cephalosporins)
-export(filter_ab_class)
-export(filter_aminoglycosides)
-export(filter_betalactams)
-export(filter_carbapenems)
-export(filter_cephalosporins)
 export(filter_first_isolate)
-export(filter_first_weighted_isolate)
-export(filter_fluoroquinolones)
-export(filter_glycopeptides)
-export(filter_macrolides)
-export(filter_oxazolidinones)
-export(filter_penicillins)
-export(filter_tetracyclines)
 export(first_isolate)
 export(fluoroquinolones)
 export(full_join_microorganisms)
@@ -248,13 +245,13 @@ export(is.rsi.eligible)
 export(is_new_episode)
 export(italicise_taxonomy)
 export(italicize_taxonomy)
-export(key_antibiotics)
-export(key_antibiotics_equal)
 export(key_antimicrobials)
 export(kurtosis)
 export(labels_rsi_count)
 export(left_join_microorganisms)
 export(like)
+export(lincosamides)
+export(lipoglycopeptides)
 export(macrolides)
 export(mdr_cmi2012)
 export(mdr_tb)
@@ -294,15 +291,16 @@ export(mo_year)
 export(mrgn)
 export(n_rsi)
 export(oxazolidinones)
-export(p_symbol)
 export(pca)
 export(penicillins)
+export(polymyxins)
 export(proportion_I)
 export(proportion_IR)
 export(proportion_R)
 export(proportion_S)
 export(proportion_SI)
 export(proportion_df)
+export(quinolones)
 export(random_disk)
 export(random_mic)
 export(random_rsi)
@@ -314,11 +312,15 @@ export(rsi_predict)
 export(scale_rsi_colours)
 export(scale_y_percent)
 export(semi_join_microorganisms)
+export(set_ab_names)
 export(set_mo_source)
 export(skewness)
+export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
 export(theme_rsi)
+export(trimethoprims)
+export(ureidopenicillins)
 importFrom(graphics,arrows)
 importFrom(graphics,axis)
 importFrom(graphics,barplot)

NEWS.md

@@ -1,7 +1,56 @@
-# `AMR` 1.7.1
+# `AMR` 1.7.1.9045
+## <small>Last updated: 29 September 2021</small>
+
+### Breaking changes
+* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
+* Removed the `key_antibiotics()` and `key_antibiotics_equal()` functions, which were deprecated and superseded by `key_antimicrobials()` and `antimicrobials_equal()`
+* Removed all previously implemented `ggplot2::ggplot()` generics for classes `<mic>`, `<disk>`, `<rsi>` and `<resistance_predict>` as they did not follow the `ggplot2` logic. They were replaced with `ggplot2::autoplot()` generics.
+
+### New
+* Function `set_ab_names()` to rename data set columns that resemble antimicrobial drugs. This allows for quickly renaming columns to official names, ATC codes, etc.
+* Support for Danish, and also added missing translations of all antimicrobial drugs in Italian, French and Portuguese
+
+### Changed
+* The `antibiotics` data set now contains **all ATC codes** that are available through the [WHOCC website](https://www.whocc.no), regardless of drugs being present in more than one ATC group. This means that:
+  * Some drugs now contain multiple ATC codes (e.g., metronidazole contains 5)
+  * `antibiotics$atc` is now a `list` containing `character` vectors, and this `atc` column was moved to the 5th position of the `antibiotics` data set
+  * `ab_atc()` does not always return a character vector of length 1, and returns a `list` if the input is larger than length 1
+  * `ab_info()` has a slightly different output
+  * Some DDDs (daily defined doses) were added or updated according to newly included ATC codes
+* Antibiotic selectors
+  * They now also work in R-3.0 and R-3.1, supporting every version of R since 2013 like the rest of the package
+  * Added more selectors for antibiotic classes: `aminopenicillins()`, `antifungals()`, `antimycobacterials()`, `lincosamides()`, `lipoglycopeptides()`, `polymyxins()`, `quinolones()`, `streptogramins()`, `trimethoprims()` and `ureidopenicillins()`
+  * Added specific selectors for certain types for treatment: `administrable_per_os()` and `administrable_iv()`, which are based on available Defined Daily Doses (DDDs), as defined by the WHOCC. These are ideal for e.g. analysing pathogens in primary care where IV treatment is not an option. They can be combined with other AB selectors, e.g. to select penicillins that are only administrable per os (i.e., orally):
+    ```r
+    example_isolates[, penicillins() & administrable_per_os()]          # base R
+    example_isolates %>% select(penicillins() & administrable_per_os()) # dplyr
+    ```
+  * Added the selector `ab_selector()`, which accepts a filter to be used internally on the `antibiotics` data set, yielding great flexibility on drug properties, such as selecting antibiotic columns with an oral DDD of at least 1 gram:
+    ```r
+    example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]          # base R
+    example_isolates %>% select(ab_selector(oral_ddd > 1 & oral_units == "g")) # dplyr
+    ```
+  * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
+  * Added argument `only_treatable`, which defaults to `TRUE` and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)
+* Fixed the Gram stain (`mo_gramstain()`) determination of the taxonomic class Negativicutes within the phylum of Firmicutes - they were considered Gram-positives because of their phylum but are actually Gram-negative. This impacts 137 taxonomic species, genera and families, such as *Negativicoccus* and *Veillonella*.
+* Fix to prevent introducing `NA`s for old MO codes when running `as.mo()` on them
+* Added more informative error messages when any of the `proportion_*()` and `count_*()` functions fail
+* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
+* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
+* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
+* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
+* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
+* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
+* Fix for minor translation errors
+* Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline
+* Improved algorithm for generating random MICs with `random_mic()`
+* Improved plot legends for MICs and disk diffusion values
+* Improved speed of `as.ab()` and all `ab_*()` functions
+
+
+# AMR 1.7.1
 
 ### Breaking change
-* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release. Examples of how the selectors can be used for filtering:
   ```r
   # select columns with results for carbapenems
@@ -21,6 +70,7 @@
   ```
 
 ### New
+* Support for CLSI 2020 guideline for interpreting MICs and disk diffusion values (using `as.rsi()`)
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
 * Function `italicise_taxonomy()` to make taxonomic names within a string italic, with support for markdown and ANSI
 * Support for all four methods to determine first isolates as summarised by Hindler *et al.* (doi: [10.1086/511864](https://doi.org/10.1086/511864)): isolate-based, patient-based, episode-based and phenotype-based. The last method is now the default.
@@ -72,7 +122,7 @@
 * All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.
 
 
-# `AMR` 1.6.0
+# AMR 1.6.0
 
 ### New
 * Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@@ -166,7 +216,7 @@
 * Loading the package (i.e., `library(AMR)`) now is ~50 times faster than before, in costs of package size (which increased by ~3 MB)
 
 
-# `AMR` 1.5.0
+# AMR 1.5.0
 
 ### New
 * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. 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. They also support `dplyr`s grouping (i.e. using `group_by()`):
@@ -243,7 +293,7 @@
 * Added CodeFactor as a continuous code review to this package: <https://www.codefactor.io/repository/github/msberends/amr/>
 * Added Dr. Rogier Schade as contributor
 
-# `AMR` 1.4.0
+# AMR 1.4.0
 
 ### New
 * Support for 'EUCAST Expert Rules' / 'EUCAST Intrinsic Resistance and Unusual Phenotypes' version 3.2 of May 2020. With this addition to the previously implemented version 3.1 of 2016, the `eucast_rules()` function can now correct for more than 180 different antibiotics and the `mdro()` function can determine multidrug resistance based on more than 150 different antibiotics. All previously implemented versions of the EUCAST rules are now maintained and kept available in this package. The `eucast_rules()` function consequently gained the arguments `version_breakpoints` (at the moment defaults to v10.0, 2020) and `version_expertrules` (at the moment defaults to v3.2, 2020). The `example_isolates` data set now also reflects the change from v3.1 to v3.2. The `mdro()` function now accepts `guideline == "EUCAST3.1"` and `guideline == "EUCAST3.2"`.
@@ -315,7 +365,7 @@
 * Removed unnecessary references to the `base` package
 * Added packages that could be useful for some functions to the `Suggests` field of the `DESCRIPTION` file
 
-# `AMR` 1.3.0
+# AMR 1.3.0
 
 ### New
 * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@@ -368,7 +418,7 @@
 ### Other
 * Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
 
-# `AMR` 1.2.0
+# AMR 1.2.0
 
 ### Breaking 
 * Removed code dependency on all other R packages, making this package fully independent of the development process of others. This is a major code change, but will probably not be noticeable by most users.
@@ -406,7 +456,7 @@
 * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
 * Removed function `read.4d()`, that was only useful for reading data from an old test database.
 
-# `AMR` 1.1.0
+# AMR 1.1.0
 
 ### New
 * Support for easy principal component analysis for AMR, using the new `pca()` function 
@@ -428,7 +478,7 @@
 * Support for the upcoming `dplyr` version 1.0.0
 * More robust assigning for classes `rsi` and `mic`
 
-# `AMR` 1.0.1
+# AMR 1.0.1
 
 ### Changed
 * Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline
@@ -444,7 +494,7 @@
 * Added `uti` (as abbreviation of urinary tract infections) as argument to `as.rsi()`, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs
 * Info printing in functions `eucast_rules()`, `first_isolate()`, `mdro()` and `resistance_predict()` will now at default only print when R is in an interactive mode (i.e. not in RMarkdown)
 
-# `AMR` 1.0.0
+# AMR 1.0.0
 
 This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.
 
@@ -492,7 +542,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Full support for the upcoming R 4.0
 * Removed unnecessary `AMR::` calls
 
-# `AMR` 0.9.0
+# AMR 0.9.0
 
 ### Breaking
 * Adopted Adeolu *et al.* (2016), [PMID 27620848](https:/pubmed.ncbi.nlm.nih.gov/27620848/) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.
@@ -558,7 +608,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
 * Added Dr. Sofia Ny as contributor
 
-# `AMR` 0.8.0
+# AMR 0.8.0
 
 ### Breaking
 * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new argument `include_unknown`:
@@ -687,7 +737,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 * Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors
 * Cleaned the coding style of every single syntax line in this package with the help of the `lintr` package
 
-# `AMR` 0.7.1
+# AMR 0.7.1
 
 #### New
 * Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
@@ -748,7 +798,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 #### Other
 * Fixed a note thrown by CRAN tests
 
-# `AMR` 0.7.0
+# AMR 0.7.0
 
 #### New
 * Support for translation of disk diffusion and MIC values to RSI values (i.e. antimicrobial interpretations). Supported guidelines are EUCAST (2011 to 2019) and CLSI (2011 to 2019). Use `as.rsi()` on an MIC value (created with `as.mic()`), a disk diffusion value (created with the new `as.disk()`) or on a complete date set containing columns with MIC or disk diffusion values.
@@ -806,13 +856,13 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 #### Other
 * Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)
 
-# `AMR` 0.6.1
+# AMR 0.6.1
 
 #### Changed
 * Fixed a critical bug when using `eucast_rules()` with `verbose = TRUE`
 * Coercion of microbial IDs are now written to the package namespace instead of the user's home folder, to comply with the CRAN policy
 
-# `AMR` 0.6.0
+# AMR 0.6.0
 
 **New website!**
 
@@ -1005,7 +1055,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 #### Other
 * Updated licence text to emphasise GPL 2.0 and that this is an R package.
 
-# `AMR` 0.5.0
+# AMR 0.5.0
 
 #### New
 * Repository moved to GitLab
@@ -1088,7 +1138,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Updated vignettes to comply with README
 
 
-# `AMR` 0.4.0
+# AMR 0.4.0
 
 #### New
 * The data set `microorganisms` now contains **all microbial taxonomic data from ITIS** (kingdoms Bacteria, Fungi and Protozoa), the Integrated Taxonomy Information System, available via https://itis.gov. The data set now contains more than 18,000 microorganisms with all known bacteria, fungi and protozoa according ITIS with genus, species, subspecies, family, order, class, phylum and subkingdom. The new data set `microorganisms.old` contains all previously known taxonomic names from those kingdoms.
@@ -1199,7 +1249,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 #### Other
 * More unit tests to ensure better integrity of functions
 
-# `AMR` 0.3.0
+# AMR 0.3.0
 
 #### New
 * **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
@@ -1269,7 +1319,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
   * Windows: https://ci.appveyor.com/project/msberends/amr
 * Added thesis advisors to DESCRIPTION file
 
-# `AMR` 0.2.0
+# AMR 0.2.0
 
 #### New
 * Full support for Windows, Linux and macOS
@@ -1304,7 +1354,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
 * Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
 
-# `AMR` 0.1.1
+# AMR 0.1.1
 
 * `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
 * Edited column names to comply with GLIMS, the laboratory information system
@@ -1312,6 +1362,6 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Renamed 'Daily Defined Dose' to 'Defined Daily Dose'
 * Added barplots for `rsi` and `mic` classes
 
-# `AMR` 0.1.0
+# AMR 0.1.0
 
 * First submission to CRAN.

R/aa_helper_functions.R

@@ -135,7 +135,6 @@ check_dataset_integrity <- function() {
                " the AMR package from working correctly: ",
                vector_and(overwritten, quotes = "'"),
                ".\nPlease rename your object", plural[3], ".", call = FALSE)
-      remember_thrown_message("dataset_overwritten")
     }
   }
   # check if other packages did not overwrite our data sets
@@ -170,65 +169,73 @@ search_type_in_df <- function(x, type, info = TRUE) {
 
   # remove attributes from other packages
   x <- as.data.frame(x, stringsAsFactors = FALSE)
-  colnames(x) <- trimws(colnames(x))
+  colnames_formatted <- tolower(generalise_antibiotic_name(colnames(x)))
 
   # -- mo
   if (type == "mo") {
     if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) {
-      found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)])[1]
+      # take first <mo> column
-    } else if ("mo" %in% colnames(x) &
+      found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
-               suppressWarnings(
+    } else if ("mo" %in% colnames_formatted &
-                 all(x$mo %in% c(NA, microorganisms$mo)))) {
+               suppressWarnings(all(x$mo %in% c(NA, microorganisms$mo)))) {
       found <- "mo"
-    } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
+    } else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])
-    } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
+    } else if (any(colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|ba[ck]terie)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(microorganism|organism|bacteria|ba[ck]terie)"])
-    } else if (any(colnames(x) %like% "species")) {
+    } else if (any(colnames_formatted %like_case% "species")) {
-      found <- sort(colnames(x)[colnames(x) %like% "species"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
     }
 
   }
   # -- key antibiotics
   if (type %in% c("keyantibiotics", "keyantimicrobials")) {
-    if (any(colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)")) {
+    if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics|antimicrobials)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
     }
   }
   # -- date
   if (type == "date") {
-    if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) {
+    if (any(colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)")) {
       # WHONET support
-      found <- sort(colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen date|specimen_date|spec_date)"])
       if (!any(class(pm_pull(x, found)) %in% c("Date", "POSIXct"))) {
         stop(font_red(paste0("Found column '", font_bold(found), "' to be used as input for `col_", type,
                              "`, but this column contains no valid dates. Transform its values to valid dates first.")),
              call. = FALSE)
       }
+      
     } else if (any(vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct"))))) {
-      found <- sort(colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))])[1]
+      # take first <Date> column
+      found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(x) inherits(x, c("Date", "POSIXct")))]
     }
   }
   # -- patient id
   if (type == "patient_id") {
-    if (any(colnames(x) %like% "^(identification |patient|patid)")) {
+    crit1 <- colnames_formatted %like_case% "^(patient|patid)"
-      found <- sort(colnames(x)[colnames(x) %like% "^(identification |patient|patid)"])[1]
+    if (any(crit1)) {
+      found <- colnames(x)[crit1]
+    } else {
+      crit2 <- colnames_formatted %like_case% "(identification |patient|pat.*id)"
+      if (any(crit2)) {
+        found <- colnames(x)[crit2]
+      }
     }
   }
   # -- specimen
   if (type == "specimen") {
-    if (any(colnames(x) %like% "(specimen type|spec_type)")) {
+    if (any(colnames_formatted %like_case% "(specimen type|spec_type)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "(specimen type|spec_type)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "(specimen type|spec_type)"])
-    } else if (any(colnames(x) %like% "^(specimen)")) {
+    } else if (any(colnames_formatted %like_case% "^(specimen)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "^(specimen)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
     }
   }
   # -- UTI (urinary tract infection)
   if (type == "uti") {
-    if (any(colnames(x) == "uti")) {
+    if (any(colnames_formatted == "uti")) {
-      found <- colnames(x)[colnames(x) == "uti"][1]
+      found <- colnames(x)[colnames_formatted == "uti"]
-    } else if (any(colnames(x) %like% "(urine|urinary)")) {
+    } else if (any(colnames_formatted %like_case% "(urine|urinary)")) {
-      found <- sort(colnames(x)[colnames(x) %like% "(urine|urinary)"])[1]
+      found <- sort(colnames(x)[colnames_formatted %like_case% "(urine|urinary)"])
     }
     if (!is.null(found)) {
       # this column should contain logicals
@@ -241,14 +248,15 @@ search_type_in_df <- function(x, type, info = TRUE) {
     }
   }
   
+  found <- found[1]
+  
   if (!is.null(found) & info == TRUE) {
     if (message_not_thrown_before(fn = paste0("search_", type))) {
       msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
-      if (type %in% c("keyantibiotics", "specimen")) {
+      if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
         msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
       }
       message_(msg)
-      remember_thrown_message(fn = paste0("search_", type))
     }
   }
   found
@@ -290,7 +298,7 @@ stop_ifnot_installed <- function(package) {
 
 pkg_is_available <- function(pkg, also_load = TRUE) {
   if (also_load == TRUE) {
-    out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE, quietly = TRUE))
+    out <- suppressWarnings(require(pkg, character.only = TRUE, warn.conflicts = FALSE))
   } else {
     out <- requireNamespace(pkg, quietly = TRUE)
   }
@@ -390,6 +398,9 @@ word_wrap <- function(...,
   # format backticks
   msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg)
   
+  # clean introduced whitespace between fullstops
+  msg <- gsub("[.] +[.]", "..", msg)
+  
   msg
 }
 
@@ -506,12 +517,12 @@ dataset_UTF8_to_ASCII <- function(df) {
 
 # for eucast_rules() and mdro(), creates markdown output with URLs and names
 create_eucast_ab_documentation <- function() {
-  x <- trimws(unique(toupper(unlist(strsplit(eucast_rules_file$then_change_these_antibiotics, ",")))))
+  x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",")))))
   ab <- character()
   for (val in x) {
-    if (val %in% ls(envir = asNamespace("AMR"))) {
+    if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
       # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
-      val <- eval(parse(text = val), envir = asNamespace("AMR"))
+      val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AB_lookup$ab) {
       # separate drugs, such as `AMX`
       val <- as.ab(val)
@@ -521,7 +532,7 @@ create_eucast_ab_documentation <- function() {
     ab <- c(ab, val)
   }
   ab <- unique(ab)
-  atcs <- ab_atc(ab)
+  atcs <- ab_atc(ab, only_first = TRUE)
   # only keep ABx with an ATC code:
   ab <- ab[!is.na(atcs)]
   ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
@@ -533,7 +544,7 @@ create_eucast_ab_documentation <- function() {
   out
 }
 
-vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep = " or ") {
+vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
   # makes unique and sorts, and this also removed NAs
   v <- unique(v)
   if (isTRUE(sort)) {
@@ -549,6 +560,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep =
   } else {
     quotes <- quotes[1L]
   }
+  if (isTRUE(initial_captital)) {
+    v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
+  }
   if (length(v) == 1) {
     return(paste0(quotes, v, quotes))
   }
@@ -561,8 +575,9 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, last_sep =
          last_sep, paste0(quotes, v[length(v)], quotes))
 }
 
-vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE) {
+vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) {
-  vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort, last_sep = " and ")
+  vector_or(v = v, quotes = quotes, reverse = reverse, sort = sort,
+            initial_captital = initial_captital, last_sep = " and ")
 }
 
 format_class <- function(class, plural = FALSE) {
@@ -696,7 +711,7 @@ meet_criteria <- function(object,
             ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
                    "be a finite number",
                    "all be finite numbers"),
-            " (i.e., not be infinite)",
+            " (i.e. not be infinite)",
             call = call_depth)
   }
   if (!is.null(contains_column_class)) {
@@ -714,11 +729,6 @@ meet_criteria <- function(object,
 }
 
 get_current_data <- function(arg_name, call) {
-  # check if retrieved before, then get it from package environment
-  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
-    return(pkg_env$get_current_data.out)
-  }
-  
   # try dplyr::cur_data_all() first to support dplyr groups
   # only useful for e.g. dplyr::filter(), dplyr::mutate() and dplyr::summarise()
   # not useful (throws error) with e.g. dplyr::select() - but that will be caught later in this function
@@ -726,72 +736,32 @@ get_current_data <- function(arg_name, call) {
   if (!is.null(cur_data_all)) {
     out <- tryCatch(cur_data_all(), error = function(e) NULL)
     if (is.data.frame(out)) {
-      out <- structure(out, type = "dplyr_cur_data_all")
+      return(structure(out, type = "dplyr_cur_data_all"))
-      pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
-      pkg_env$get_current_data.out <- out
-      return(out)
     }
   }
   
-  if (getRversion() < "3.2") {
+  # try a manual (base R) method, by going over all underlying environments with sys.frames()
-    # R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
+  for (env in sys.frames()) {
-    if (is.na(arg_name)) {
+    if (!is.null(env$`.Generic`)) {
-      # like in carbapenems() etc.
+      # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
-      warning_("this function can only be used in R >= 3.2", call = call)
-      return(data.frame())
-    } else {
-      # mimic a default R error, e.g. for example_isolates[which(mo_name() %like% "^ent"), ] 
-      stop_("argument `", arg_name, "` is missing with no default", call = call)
-    }
-  }
       
-  # try a (base R) method, by going over the complete system call stack with sys.frames()
+      if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
-  not_set <- TRUE
+        # an element `.data` will be in the environment when using `dplyr::select()`
-  source <- "base_R"
+        # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
-  frms <- lapply(sys.frames(), function(el) {
+        return(structure(env$`.data`, type = "dplyr_selector"))
-    if (not_set == TRUE && ".Generic" %in% names(el)) {
+        
-      if (tryCatch(".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
+      } else if (!is.null(env$xx) && is.data.frame(env$xx)) {
-        # - - - -
+        # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
-        # dplyr
+        return(structure(env$xx, type = "base_R"))
-        # - - - -
+        
-        # an element `.data` will be in the system call stack when using dplyr::select()
+      } else if (!is.null(env$x) && is.data.frame(env$x)) {
-        # [but not when using dplyr::filter(), dplyr::mutate() or dplyr::summarise()]
+        # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
-        not_set <<- FALSE
+        return(structure(env$x, type = "base_R"))
-        source <<- "dplyr_selector"
-        el$`.data`
-      } else if (tryCatch(any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
-        # - - - -
-        # base R
-        # - - - -
-        # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
-        # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
-        if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
-          not_set <<- FALSE
-          el$xx
-        } else if (tryCatch(is.data.frame(el$x))) {
-          not_set <<- FALSE
-          el$x
-        } else {
-          NULL
-        }
-      } else {
-        NULL
       }
-    } else {
-      NULL
     }
-  })
-  
-  # lookup the matched frame and return its value: a data.frame
-  vars_df <- tryCatch(frms[[which(!vapply(FUN.VALUE = logical(1), frms, is.null))]], error = function(e) NULL)
-  if (is.data.frame(vars_df)) {
-    out <- structure(vars_df, type = source)
-    pkg_env$get_current_data.call <- unique_call_id(entire_session = FALSE)
-    pkg_env$get_current_data.out <- out
-    return(out)
   }
   
-  # nothing worked, so:
+  # no data.frame found, so an error  must be returned:
   if (is.na(arg_name)) {
     if (isTRUE(is.numeric(call))) {
       fn <- as.character(sys.call(call + 1)[1])
@@ -803,10 +773,11 @@ get_current_data <- function(arg_name, call) {
     } else {
       examples <- ""
     }
-    stop_("this function must be used inside valid dplyr selection verbs or inside a data.frame call",
+    stop_("this function must be used inside a `dplyr` verb or `data.frame` call",
           examples,
           call = call)
   } else {
+    # mimic a base R error that the argument is missing
     stop_("argument `", arg_name, "` is missing with no default", call = call)
   }
 }
@@ -821,19 +792,19 @@ get_current_column <- function() {
     }
   }
   
-  # cur_column() doesn't always work (only allowed for conditions set by dplyr), but it's probably still possible:
+  # cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
-  frms <- lapply(sys.frames(), function(el) {
+  frms <- lapply(sys.frames(), function(env) {
-    if ("i" %in% names(el)) {
+    if (!is.null(env$i)) {
-      if ("tibble_vars" %in% names(el)) {
+      if (!is.null(env$tibble_vars)) {
         # for mutate_if()
-        el$tibble_vars[el$i]
+        env$tibble_vars[env$i]
       } else {
         # for mutate(across())
         df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
         if (is.data.frame(df)) {
-          colnames(df)[el$i]
+          colnames(df)[env$i]
         } else {
-          el$i
+          env$i
         }
       }
     } else {
@@ -851,7 +822,7 @@ get_current_column <- function() {
 }
 
 is_null_or_grouped_tbl <- function(x) {
-  # attribute "grouped_df" might change at one point, so only set in one place; here.
+  # class "grouped_df" might change at one point, so only set in one place; here.
   is.null(x) || inherits(x, "grouped_df")
 }
 
@@ -860,7 +831,7 @@ unique_call_id <- function(entire_session = FALSE) {
     c(envir = "session",
       call = "session")
   } else {
-    # combination of environment ID (like "0x7fed4ee8c848")
+    # combination of environment ID (such as "0x7fed4ee8c848")
     # and highest system call
     call <- paste0(deparse(sys.calls()[[1]]), collapse = "")
     if (!interactive() || call %like% "run_test_dir|test_all|tinytest|test_package|testthat") {
@@ -872,16 +843,18 @@ unique_call_id <- function(entire_session = FALSE) {
   }
 }
 
-remember_thrown_message <- function(fn, entire_session = FALSE) {
-  # this is to prevent that messages/notes will be printed for every dplyr group
-  # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
-  assign(x = paste0("thrown_msg.", fn),
-         value = unique_call_id(entire_session = entire_session),
-         envir = pkg_env)
-}
-
 message_not_thrown_before <- function(fn, entire_session = FALSE) {
-  is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
+  # this is to prevent that messages/notes will be printed for every dplyr group or more than once per session
+  # e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
+  not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]],
+                                                                                   unique_call_id(entire_session = entire_session))
+  if (isTRUE(not_thrown_before)) {
+    # message was not thrown before - remember this so on the next run it will return FALSE:
+    assign(x = paste0("thrown_msg.", fn),
+           value = unique_call_id(entire_session = entire_session),
+           envir = pkg_env)
+  }
+  not_thrown_before
 }
 
 has_colour <- function() {
@@ -976,12 +949,12 @@ font_grey <- function(..., collapse = " ") {
   try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
 }
 font_grey_bg <- function(..., collapse = " ") {
-  if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) {
+  if (tryCatch(import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)()$dark, error = function(e) FALSE)) {
     # similar to HTML #444444
     try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)  
   } else {
-    # similar to HTML #eeeeee
+    # similar to HTML #f0f0f0
-    try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
+    try_colour(..., before = "\033[48;5;255m", after = "\033[49m", collapse = collapse)
   }
 }
 font_green_bg <- function(..., collapse = " ") {

R/ab.R

@@ -33,7 +33,7 @@
 #' @param ... arguments passed on to internal functions
 #' @rdname as.ab
 #' @inheritSection WHOCC WHOCC
-#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.
+#' @details All entries in the [antibiotics] data set have three different identifiers: a human readable EARS-Net code (column `ab`, used by ECDC and WHONET), an ATC code (column `atc`, used by WHO), and a CID code (column `cid`, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
 #' 
 #' All these properties will be searched for the user input. The [as.ab()] can correct for different forms of misspelling:
 #' 
@@ -101,6 +101,11 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   if (is.ab(x)) {
     return(x)
   }
+  if (all(x %in% c(AB_lookup$ab, NA))) {
+    # all valid AB codes, but not yet right class
+    return(set_clean_class(x,
+                           new_class = c("ab", "character")))
+  }
   
   initial_search <- is.null(list(...)$initial_search)
   already_regex <- isTRUE(list(...)$already_regex)
@@ -110,28 +115,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   x <- toupper(x)
   x_nonNA <- x[!is.na(x)]
   
-  if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
-    # all valid AB codes, but not yet right class
-    return(set_clean_class(x,
-                           new_class = c("ab", "character")))
-  }
-  if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
-    # all valid AB names
-    out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
-    out[is.na(x)] <- NA_character_
-    return(out)
-  }
-  if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
-    # all valid ATC codes
-    out <- antibiotics$ab[match(x, antibiotics$atc)]
-    out[is.na(x)] <- NA_character_
-    return(out)
-  }
-  
   # remove diacritics
   x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
   x <- gsub('"', "", x, fixed = TRUE)
-  x <- gsub("(specimen|specimen date|specimen_date|spec_date|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
+  x <- gsub("(specimen|specimen date|specimen_date|spec_date|gender|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
   x_bak_clean <- x
   if (already_regex == FALSE) {
     x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
@@ -155,12 +142,28 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     found[1L]
   }
   
-  if (initial_search == TRUE) {
+  # Fill in names, AB codes, CID codes and ATC codes directly (`x` is already clean and uppercase)
-    progress <- progress_ticker(n = length(x), n_min = 25, print = info) # start if n >= 25
+  known_names <- x %in% AB_lookup$generalised_name
+  x_new[known_names] <- AB_lookup$ab[match(x[known_names], AB_lookup$generalised_name)]
+  known_codes_ab <- x %in% AB_lookup$ab
+  known_codes_atc <- vapply(FUN.VALUE = logical(1), x, function(x_) x_ %in% unlist(AB_lookup$atc), USE.NAMES = FALSE)
+  known_codes_cid <- x %in% AB_lookup$cid
+  x_new[known_codes_ab] <- AB_lookup$ab[match(x[known_codes_ab], AB_lookup$ab)]
+  x_new[known_codes_atc] <- AB_lookup$ab[vapply(FUN.VALUE = integer(1),
+                                                x[known_codes_atc],
+                                                function(x_) which(vapply(FUN.VALUE = logical(1),
+                                                                          AB_lookup$atc,
+                                                                          function(atc) x_ %in% atc)),
+                                                USE.NAMES = FALSE)]
+  x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
+  already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid
+  
+  if (initial_search == TRUE & sum(already_known) < length(x)) {
+    progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
     on.exit(close(progress))
   }
   
-  for (i in seq_len(length(x))) {
+  for (i in which(!already_known)) {
     
     if (initial_search == TRUE) {
       progress$tick()
@@ -189,34 +192,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       next
     }
     
-    # exact name
-    found <- antibiotics[which(AB_lookup$generalised_name == x[i]), ]$ab
-    if (length(found) > 0) {
-      x_new[i] <- found[1L]
-      next
-    }
-    
-    # exact AB code
-    found <- antibiotics[which(antibiotics$ab == x[i]), ]$ab
-    if (length(found) > 0) {
-      x_new[i] <- note_if_more_than_one_found(found, i, from_text)
-      next
-    }
-    
-    # exact ATC code
-    found <- antibiotics[which(antibiotics$atc == x[i]), ]$ab
-    if (length(found) > 0) {
-      x_new[i] <- note_if_more_than_one_found(found, i, from_text)
-      next
-    }
-    
-    # exact CID code
-    found <- antibiotics[which(antibiotics$cid == x[i]), ]$ab
-    if (length(found) > 0) {
-      x_new[i] <- note_if_more_than_one_found(found, i, from_text)
-      next
-    }
-    
     # exact LOINC code
     loinc_found <- unlist(lapply(AB_lookup$generalised_loinc,
                                  function(s) x[i] %in% s))
@@ -325,9 +300,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
                                    function(y) {
                                      for (i in seq_len(length(y))) {
                                        for (lang in LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]) {
-                                         y[i] <- ifelse(tolower(y[i]) %in% tolower(translations_file[, lang, drop = TRUE]),
+                                         y[i] <- ifelse(tolower(y[i]) %in% tolower(TRANSLATIONS[, lang, drop = TRUE]),
-                                                        translations_file[which(tolower(translations_file[, lang, drop = TRUE]) == tolower(y[i]) &
+                                                        TRANSLATIONS[which(tolower(TRANSLATIONS[, lang, drop = TRUE]) == tolower(y[i]) &
-                                                                                  !isFALSE(translations_file$fixed)), "pattern"],
+                                                                                  !isFALSE(TRANSLATIONS$fixed)), "pattern"],
                                                         y[i])
                                        }
                                      }
@@ -461,14 +436,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }
   
-  if (initial_search == TRUE) {
+  if (initial_search == TRUE & sum(already_known) < length(x)) {
     close(progress)
   }
   
   # take failed ATC codes apart from rest
   x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
   x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
-  if (length(x_unknown_ATCs) > 0) {
+  if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
     warning_("These ATC codes are not (yet) in the antibiotics data set: ",
              vector_and(x_unknown_ATCs), ".",
              call = FALSE)
@@ -480,10 +455,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
              call = FALSE)
   }
 
-  x_result <- data.frame(x = x_bak_clean, stringsAsFactors = FALSE) %pm>%
+  x_result <- x_new[match(x_bak_clean, x)]
-    pm_left_join(data.frame(x = x, x_new = x_new, stringsAsFactors = FALSE), by = "x") %pm>%
-    pm_pull(x_new)
-  
   if (length(x_result) == 0) {
     x_result <- NA_character_
   }
@@ -580,6 +552,15 @@ unique.ab <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep ab
+#' @export
+#' @noRd
+rep.ab <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 generalise_antibiotic_name <- function(x) {
   x <- toupper(x)
   # remove suffices

R/ab_class_selectors.R

@@ -23,22 +23,32 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Antibiotic Class Selectors
+#' Antibiotic Selectors
 #' 
-#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
+#' 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, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
+#' @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()]
-#' @details \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
+#' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
+#' @param ... ignored, only in place to allow future extensions
+#' @details
+#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
 #' 
+#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. 
 #' 
-#' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
+#' The [ab_class()] function can be used to filter/select on a manually defined antibiotic class. It searches for results in the [antibiotics] data set within the columns `group`, `atc_group1` and `atc_group2`.
 #' 
-#' All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+#' The [ab_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
 #' 
-#' The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
+#' The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antibiotic columns will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
+#' 
+#' @section Full list of supported (antibiotic) classes:
+#' 
+#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
 #' @rdname antibiotic_class_selectors
 #' @name antibiotic_class_selectors
+#' @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!
@@ -46,7 +56,7 @@
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
 #' 
-#' # Base R ------------------------------------------------------------------
+#' # base R ------------------------------------------------------------------
 #' 
 #' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
 #' example_isolates[, carbapenems()]
@@ -54,6 +64,9 @@
 #' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
 #' example_isolates[, c("mo", aminoglycosides())]
 #' 
+#' # select only antibiotic columns with DDDs for oral treatment
+#' example_isolates[, administrable_per_os()]
+#' 
 #' # filter using any() or all()
 #' example_isolates[any(carbapenems() == "R"), ]
 #' subset(example_isolates, any(carbapenems() == "R"))
@@ -68,6 +81,17 @@
 #' # filter + select in one go: get penicillins in carbapenems-resistant strains
 #' example_isolates[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()]
+#' 
+#' # 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")]
 #' 
 #' # dplyr -------------------------------------------------------------------
 #' \donttest{
@@ -78,6 +102,16 @@
 #'     group_by(hospital_id) %>% 
 #'     summarise(across(aminoglycosides(), resistance))
 #'     
+#'   # You can combine selectors with '&' to be more specific:
+#'   example_isolates %>%
+#'     select(penicillins() & administrable_per_os())
+#'     
+#'   # get susceptibility for antibiotics whose name contains "trim":
+#'   example_isolates %>%
+#'     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 %>% 
 #'     select(carbapenems())
@@ -104,7 +138,6 @@
 #'   example_isolates %>% 
 #'     select(mo, ab_class("mycobact"))
 #'     
-#'     
 #'   # get bug/drug combinations for only macrolides in Gram-positives:
 #'   example_isolates %>% 
 #'     filter(mo_is_gram_positive()) %>% 
@@ -112,178 +145,379 @@
 #'     bug_drug_combinations() %>%
 #'     format()
 #'     
-#'     
 #'   data.frame(some_column = "some_value",
 #'              J01CA01 = "S") %>%   # ATC code of ampicillin
 #'     select(penicillins())         # only the 'J01CA01' column will be selected
 #'     
 #'     
 #'   # with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
-#'   # (though the row names on the first are more correct)
 #'   example_isolates[carbapenems() == "R", ]
 #'   example_isolates %>% filter(carbapenems() == "R")
 #'   example_isolates %>% filter(across(carbapenems(), ~.x == "R"))
 #' }
 #' }
 ab_class <- function(ab_class, 
-                     only_rsi_columns = FALSE) {
+                     only_rsi_columns = FALSE,
-  ab_selector(ab_class, function_name = "ab_class", only_rsi_columns = only_rsi_columns)
+                     only_treatable = TRUE,
+                     ...) {
+  meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec(NULL, only_rsi_columns = only_rsi_columns, ab_class_args = ab_class, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-aminoglycosides <- function(only_rsi_columns = FALSE) {
+ab_selector <- function(filter, 
-  ab_selector("aminoglycoside", function_name = "aminoglycosides", only_rsi_columns = only_rsi_columns)
+                        only_rsi_columns = FALSE,
+                        only_treatable = TRUE,
+                        ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+  # but it only takes a couple of milliseconds
+  vars_df <- get_current_data(arg_name = NA, call = -2)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
+  call <- substitute(filter)
+  agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE],
+                     error = function(e) stop_(e$message, call = -5))
+  agents <- ab_in_data[ab_in_data %in% agents]
+  message_agent_names(function_name = "ab_selector", 
+                      agents = agents,
+                      ab_group = NULL,
+                      examples = "",
+                      call = call)
+  structure(unname(agents),
+            class = c("ab_selector", "character"))
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-betalactams <- function(only_rsi_columns = FALSE) {
+administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("carbapenem|cephalosporin|penicillin", function_name = "betalactams", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
-}
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
-#' @rdname antibiotic_class_selectors
+  # but it only takes a couple of milliseconds
-#' @export
+  vars_df <- get_current_data(arg_name = NA, call = -2)
-carbapenems <- function(only_rsi_columns = FALSE) {
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
-  ab_selector("carbapenem", function_name = "carbapenems", only_rsi_columns = only_rsi_columns)
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
+  agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
+  agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
+  agents <- ab_in_data[ab_in_data %in% agents]
+  message_agent_names(function_name = "administrable_per_os", 
+                      agents = agents,
+                      ab_group = "administrable_per_os",
+                      examples = paste0(" (such as ", 
+                                        vector_or(ab_name(sample(agents_all,
+                                                                 size = min(5, length(agents_all)),
+                                                                 replace = FALSE),
+                                                          tolower = TRUE,
+                                                          language = NULL),
+                                                  quotes = FALSE), 
+                                        ")"))
+  structure(unname(agents),
+            class = c("ab_selector", "character"))
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins <- function(only_rsi_columns = FALSE) {
+administrable_iv <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("cephalosporin", function_name = "cephalosporins", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+  # but it only takes a couple of milliseconds
+  vars_df <- get_current_data(arg_name = NA, call = -2)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
+  agents_all <- antibiotics[which(!is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
+  agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$iv_ddd)), "ab", drop = TRUE]
+  agents <- ab_in_data[ab_in_data %in% agents]
+  message_agent_names(function_name = "administrable_iv", 
+                      agents = agents,
+                      ab_group = "administrable_iv",
+                      examples = "")
+  structure(unname(agents),
+            class = c("ab_selector", "character"))
+}
+
+# nolint start
+# #' @rdname antibiotic_class_selectors
+# #' @export
+# not_intrinsic_resistant <- function(mo, ..., only_rsi_columns = FALSE, ...) {
+#   meet_criteria(mo, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), has_length = 1, allow_NA = FALSE)
+#   meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+# 
+#   x <- as.mo(mo, ...)
+#   wont_work <- intrinsic_resistant[which(intrinsic_resistant$microorganism == mo_name(x, language = NULL)),
+#                                    "antibiotic",
+#                                    drop = TRUE]
+# 
+#   # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+#   # but it only takes a couple of milliseconds
+#   vars_df <- get_current_data(arg_name = NA, call = -2)
+#   # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
+#   ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
+# 
+#   agents <- ab_in_data[!names(ab_in_data) %in% as.character(as.ab(wont_work))]
+# 
+#   # show used version number once per session (pkg_env will reload every session)
+#   if (message_not_thrown_before("intrinsic_resistant_version.ab", entire_session = TRUE)) {
+#     message_("Determining intrinsic resistance based on ",
+#              format_eucast_version_nr(3.2, markdown = FALSE), ". ",
+#              font_red("This note will be shown once per session."))
+#   }
+# 
+#   message_agent_names(function_name = "not_intrinsic_resistant", 
+#                       agents = ab_in_data,
+#                       ab_group = NULL,
+#                       examples = "",
+#                       call = mo_name(x, language = NULL))
+# 
+#   agents
+# }
+# nolint end
+
+#' @rdname antibiotic_class_selectors
+#' @export
+aminoglycosides <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec("aminoglycosides", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins_1st <- function(only_rsi_columns = FALSE) {
+aminopenicillins <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("aminopenicillins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins_2nd <- function(only_rsi_columns = FALSE) {
+antifungals <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("antifungals", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins_3rd <- function(only_rsi_columns = FALSE) {
+antimycobacterials <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("antimycobacterials", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins_4th <- function(only_rsi_columns = FALSE) {
+betalactams <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
-  ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec("betalactams", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-cephalosporins_5th <- function(only_rsi_columns = FALSE) {
+carbapenems <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
-  ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec("carbapenems", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-fluoroquinolones <- function(only_rsi_columns = FALSE) {
+cephalosporins <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("fluoroquinolone", function_name = "fluoroquinolones", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-glycopeptides <- function(only_rsi_columns = FALSE) {
+cephalosporins_1st <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("glycopeptide", function_name = "glycopeptides", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins_1st", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-macrolides <- function(only_rsi_columns = FALSE) {
+cephalosporins_2nd <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("macrolide", function_name = "macrolides", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins_2nd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-oxazolidinones <- function(only_rsi_columns = FALSE) {
+cephalosporins_3rd <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("oxazolidinone", function_name = "oxazolidinones", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins_3rd", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-penicillins <- function(only_rsi_columns = FALSE) {
+cephalosporins_4th <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("penicillin", function_name = "penicillins", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins_4th", only_rsi_columns = only_rsi_columns)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-tetracyclines <- function(only_rsi_columns = FALSE) {
+cephalosporins_5th <- function(only_rsi_columns = FALSE, ...) {
-  ab_selector("tetracycline", function_name = "tetracyclines", only_rsi_columns = only_rsi_columns)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("cephalosporins_5th", only_rsi_columns = only_rsi_columns)
 }
 
-ab_selector <- function(ab_class,
+#' @rdname antibiotic_class_selectors
-                        function_name,
+#' @export
-                        only_rsi_columns) {
+fluoroquinolones <- function(only_rsi_columns = FALSE, ...) {
-  meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
-  meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
+  ab_select_exec("fluoroquinolones", only_rsi_columns = only_rsi_columns)
-  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
+}
 
-  if (getRversion() < "3.2") {
+#' @rdname antibiotic_class_selectors
-    warning_("antibiotic class selectors such as ", function_name, 
+#' @export
-             "() require R version 3.2 or later - you have ", R.version.string,
+glycopeptides <- function(only_rsi_columns = FALSE, ...) {
-             call = FALSE)
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
-    return(NULL)
+  ab_select_exec("glycopeptides", only_rsi_columns = only_rsi_columns)
-  }
+}
 
-  # to improve speed, get_current_data() and get_column_abx() only run once when e.g. in a select or group call
+#' @rdname antibiotic_class_selectors
+#' @export
+lincosamides <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("lincosamides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+lipoglycopeptides <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("lipoglycopeptides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+macrolides <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("macrolides", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+oxazolidinones <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("oxazolidinones", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+penicillins <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("penicillins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+polymyxins <- function(only_rsi_columns = FALSE, only_treatable = TRUE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec("polymyxins", only_rsi_columns = only_rsi_columns, only_treatable = only_treatable)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+streptogramins <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("streptogramins", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+quinolones <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("quinolones", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+tetracyclines <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("tetracyclines", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+trimethoprims <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("trimethoprims", only_rsi_columns = only_rsi_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+ureidopenicillins <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns)
+}
+
+ab_select_exec <- function(function_name,
+                           only_rsi_columns = FALSE,
+                           only_treatable = FALSE,
+                           ab_class_args = NULL) {
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+  # but it only takes a couple of milliseconds
   vars_df <- get_current_data(arg_name = NA, call = -3)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
   ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
   
+  # untreatable drugs
+  untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate"), "ab", drop = TRUE]
+  if (only_treatable == TRUE & any(untreatable %in% names(ab_in_data))) {
+    if (message_not_thrown_before(paste0("ab_class.untreatable.", function_name), entire_session = TRUE)) {
+      warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
+               vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
+                                  language = NULL,
+                                  tolower = TRUE),
+                          quotes = FALSE,
+                          sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
+               "This warning will be shown once per session.",
+               call = FALSE)
+    }
+    ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
+  }
+  
   if (length(ab_in_data) == 0) {
-    message_("No antimicrobial agents found.")
+    message_("No antimicrobial agents found in the data.")
     return(NULL)
   }
   
-  ab_reference <- subset(antibiotics,
+  if (is.null(ab_class_args)) {
-                         group %like% ab_class | 
+    # their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
-                           atc_group1 %like% ab_class | 
+    # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
-                           atc_group2 %like% ab_class)
+    abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))  
-  ab_group <- find_ab_group(ab_class)
+    ab_group <- function_name
-  if (ab_group == "") {
+    examples <- paste0(" (such as ", vector_or(ab_name(sample(abx, size = min(2, length(abx)), replace = FALSE),
-    ab_group <- paste0("'", ab_class, "'")
+                                                       tolower = TRUE,
-    examples <- ""
+                                                       language = NULL),
+                                               quotes = FALSE), ")")
   } else {
-    examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
+    # this for the 'manual' ab_class() function
+    abx <- subset(AB_lookup,
+                  group %like% ab_class_args |
+                    atc_group1 %like% ab_class_args |
+                    atc_group2 %like% ab_class_args)$ab
+    ab_group <- find_ab_group(ab_class_args)
+    function_name <- "ab_class"
+    examples <- paste0(" (such as ", find_ab_names(ab_class_args, 2), ")")
   }
+  
   # get the columns with a group names in the chosen ab class
-  agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
+  agents <- ab_in_data[names(ab_in_data) %in% abx]
   
-  if (message_not_thrown_before(function_name)) {
+  message_agent_names(function_name = function_name, 
-    if (length(agents) == 0) {
+                      agents = agents,
-      message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
+                      ab_group = ab_group,
-    } else {
+                      examples = examples,
-      agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+                      ab_class_args = ab_class_args)
-      agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
-      need_name <- tolower(gsub("[^a-zA-Z]", "", agents)) != tolower(gsub("[^a-zA-Z]", "", agents_names))
-      agents_formatted[need_name] <- paste0(agents_formatted[need_name],
-                                            " (", agents_names[need_name], ")")
-      message_("For `", function_name, "(", ifelse(function_name == "ab_class", paste0("\"", ab_class, "\""), ""), ")` using ",
-               ifelse(length(agents) == 1, "column: ", "columns: "),
-               vector_and(agents_formatted, quotes = FALSE))
-    }
-    remember_thrown_message(function_name)
-  }
   
-  if (!is.null(attributes(vars_df)$type) &&
+  structure(unname(agents),
-      attributes(vars_df)$type %in% c("dplyr_cur_data_all", "base_R") &&
+            class = c("ab_selector", "character"))
-      !any(as.character(sys.calls()) %like% paste0("(across|if_any|if_all)\\((c\\()?[a-z(), ]*", function_name))) {
-    structure(unname(agents),
-              class = c("ab_selector", "character"))
-  } else {
-    # don't return with "ab_selector" class if method is a dplyr selector,
-    # dplyr::select() will complain:
-    # > Subscript has the wrong type `ab_selector`.
-    # > It must be numeric or character.
-    unname(agents)
-  }
 }
 
 #' @method c ab_selector
@@ -321,7 +555,6 @@ all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
 #' @export
 #' @noRd
 all.ab_selector <- function(..., na.rm = FALSE) {
-  # this is all() for 
   all_any_ab_selector("all", ..., na.rm = na.rm)
 }
 
@@ -367,7 +600,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
 `==.ab_selector` <- function(e1, e2) {
   calls <- as.character(match.call())
   fn_name <- calls[2]
-  # keep only the ... in c(...)
   fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
   if (is_any(fn_name)) {
     type <- "any"
@@ -390,7 +622,6 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
 `!=.ab_selector` <- function(e1, e2) {
   calls <- as.character(match.call())
   fn_name <- calls[2]
-  # keep only the ... in c(...)
   fn_name <- gsub("^(c\\()(.*)(\\))$", "\\2", fn_name)
   if (is_any(fn_name)) {
     type <- "any"
@@ -410,6 +641,25 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
             class = c("ab_selector_any_all", "logical"))
 }
 
+#' @method & ab_selector
+#' @export
+#' @noRd
+`&.ab_selector` <- function(e1, e2) {
+  # this is only required for base R, since tidyselect has already implemented this
+  # e.g., for: example_isolates[, penicillins() & administrable_per_os()]
+  structure(intersect(unclass(e1), unclass(e2)),
+            class = c("ab_selector", "character"))
+}
+#' @method | ab_selector
+#' @export
+#' @noRd
+`|.ab_selector` <- function(e1, e2) {
+  # this is only required for base R, since tidyselect has already implemented this
+  # e.g., for: example_isolates[, penicillins() | administrable_per_os()]
+  structure(union(unclass(e1), unclass(e2)),
+            class = c("ab_selector", "character"))
+}
+
 is_any <- function(el1) {
   syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
   el1 <- gsub("(.*),.*", "\\1", el1)
@@ -421,30 +671,17 @@ is_all <- function(el1) {
   syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
 }
 
-
+find_ab_group <- function(ab_class_args) {
-find_ab_group <- function(ab_class) {
+  ab_class_args <- gsub("[^a-zA-Z0-9]", ".*", ab_class_args)
-  ab_class[ab_class == "carbapenem|cephalosporin|penicillin"] <- "betalactam"
+  AB_lookup %pm>%
-  ab_class <- gsub("[^a-zA-Z0-9]", ".*", ab_class)
+    subset(group %like% ab_class_args | 
-  ifelse(ab_class %in% c("aminoglycoside",
+             atc_group1 %like% ab_class_args | 
-                         "betalactam",
+             atc_group2 %like% ab_class_args) %pm>%
-                         "carbapenem",
+    pm_pull(group) %pm>%
-                         "cephalosporin",
+    unique() %pm>%
-                         "fluoroquinolone",
+    tolower() %pm>%
-                         "glycopeptide",
+    sort() %pm>% 
-                         "macrolide",
+    paste(collapse = "/")
-                         "oxazolidinone",
-                         "tetracycline"),
-         paste0(ab_class, "s"),
-         antibiotics %pm>%
-           subset(group %like% ab_class | 
-                    atc_group1 %like% ab_class | 
-                    atc_group2 %like% ab_class) %pm>%
-           pm_pull(group) %pm>%
-           unique() %pm>%
-           tolower() %pm>%
-           sort() %pm>% 
-           paste(collapse = "/")
-  )
 }
 
 find_ab_names <- function(ab_group, n = 3) {
@@ -462,8 +699,41 @@ find_ab_names <- function(ab_group, n = 3) {
                                   antibiotics$atc_group2 %like% ab_group) &
                                  antibiotics$ab %unlike% "[0-9]$"), ]$name
   }
+  if (length(drugs) == 0) {
+    return("??")
+  }
   vector_or(ab_name(sample(drugs, size = min(n, length(drugs)), replace = FALSE),
                     tolower = TRUE,
                     language = NULL),
             quotes = FALSE)
 }
+
+message_agent_names <- function(function_name, agents, ab_group = NULL, examples = "", ab_class_args = NULL, call = NULL) {
+  if (message_not_thrown_before(paste0(function_name, ".", paste(sort(agents), collapse = "|")))) {
+    if (length(agents) == 0) {
+      if (is.null(ab_group)) {
+        message_("For `", function_name, "()` no antimicrobial agents found", examples, ".")
+      } else if (ab_group == "administrable_per_os") {
+        message_("No orally administrable agents found", examples, ".")
+      } else if (ab_group == "administrable_iv") {
+        message_("No IV administrable agents found", examples, ".")
+      } else {
+        message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
+      }
+    } else {
+      agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+      agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
+      need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
+      agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
+      message_("For `", function_name, "(",
+               ifelse(function_name == "ab_class", 
+                      paste0("\"", ab_class_args, "\""),
+                      ifelse(!is.null(call),
+                             paste0(deparse(call), collapse = " "),
+                             "")),
+               ")` using ",
+               ifelse(length(agents) == 1, "column ", "columns "),
+               vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
+    }
+  }
+}

R/ab_property.R

@@ -29,22 +29,27 @@
 #' @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
+#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
 #' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param administration way of administration, either `"oral"` or `"iv"`
-#' @param units a [logical] to indicate whether the units instead of the DDDs itself must be returned, see *Examples*
 #' @param open browse the URL using [utils::browseURL()]
 #' @param ... other arguments passed on to [as.ab()]
+#' @param data a [data.frame] of which the columns need to be renamed, or a [character] vector of column names
+#' @param snake_case a [logical] to indicate whether the names should be in so-called [snake case](https://en.wikipedia.org/wiki/Snake_case): in lower case and all spaces/slashes replaced with an underscore (`_`)
+#' @param only_first a [logical] to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)
 #' @details All output [will be translated][translate] where possible.
 #' 
 #' The function [ab_url()] will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
+#' 
+#' The function [set_ab_names()] is a special column renaming function for [data.frame]s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If `property = "atc"` is set, preference is given to ATC codes from the J-group.
 #' @inheritSection as.ab Source
 #' @rdname ab_property
 #' @name ab_property
 #' @return 
 #' - An [integer] in case of [ab_cid()]
-#' - A named [list] in case of [ab_info()] and multiple [ab_synonyms()]/[ab_tradenames()]
+#' - A named [list] in case of [ab_info()] and multiple [ab_atc()]/[ab_synonyms()]/[ab_tradenames()]
 #' - A [double] in case of [ab_ddd()]
+#' - A [data.frame] in case of [set_ab_names()]
 #' - A [character] in all other cases
 #' @export
 #' @seealso [antibiotics]
@@ -53,7 +58,7 @@
 #' @examples
 #' # all properties:
 #' ab_name("AMX")       # "Amoxicillin"
-#' ab_atc("AMX")        # J01CA04 (ATC code from the WHO)
+#' ab_atc("AMX")        # "J01CA04" (ATC code from the WHO)
 #' ab_cid("AMX")        # 33613 (Compound ID from PubChem)
 #' ab_synonyms("AMX")   # a list with brand names of amoxicillin
 #' ab_tradenames("AMX") # same
@@ -68,10 +73,10 @@
 #'         tolower = TRUE)       # "amoxicillin/clavulanic acid" "polymyxin B"
 #'
 #' # defined daily doses (DDD)
-#' ab_ddd("AMX", "oral")               #  1
+#' ab_ddd("AMX", "oral")       #  1.5
-#' ab_ddd("AMX", "oral", units = TRUE) # "g"
+#' ab_ddd_units("AMX", "oral") # "g"
-#' ab_ddd("AMX", "iv")                 #  1
+#' ab_ddd("AMX", "iv")         #  3
-#' ab_ddd("AMX", "iv", units = TRUE)   # "g"
+#' ab_ddd_units("AMX", "iv")   # "g"
 #'
 #' ab_info("AMX")       # all properties as a list
 #'
@@ -88,6 +93,24 @@
 #' ab_atc("cephtriaxone")
 #' ab_atc("cephthriaxone")
 #' ab_atc("seephthriaaksone")
+#' 
+#' # use set_ab_names() for renaming columns
+#' colnames(example_isolates)
+#' colnames(set_ab_names(example_isolates))
+#' \donttest{
+#' if (require("dplyr")) {
+#'   example_isolates %>%
+#'     set_ab_names()
+#'     
+#'   # this does the same:
+#'   example_isolates %>%
+#'     rename_with(set_ab_names)
+#'   
+#'   # set_ab_names() works with any AB property:
+#'   example_isolates %>%
+#'     set_ab_names("atc")
+#' }
+#' }
 ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@@ -102,14 +125,6 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
   x
 }
 
-#' @rdname ab_property
-#' @aliases ATC
-#' @export
-ab_atc <- function(x, ...) {
-  meet_criteria(x, allow_NA = TRUE)
-  ab_validate(x = x, property = "atc", ...)
-}
-
 #' @rdname ab_property
 #' @export
 ab_cid <- function(x, ...) {
@@ -145,6 +160,36 @@ ab_group <- function(x, language = get_locale(), ...) {
   translate_AMR(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
 }
 
+#' @rdname ab_property
+#' @aliases ATC
+#' @export
+ab_atc <- function(x, only_first = FALSE, ...) {
+  meet_criteria(x, allow_NA = TRUE)
+  meet_criteria(only_first, allow_class = "logical", has_length = 1)
+  
+  atcs <- ab_validate(x = x, property = "atc", ...)
+  
+  if (only_first == TRUE) {
+    atcs <- vapply(FUN.VALUE = character(1),
+                   # get only the first ATC code
+                   atcs,
+                   function(x) {
+                     # try to get the J-group
+                     if (any(x %like% "^J")) {
+                       x[x %like% "^J"][1L]
+                     } else {
+                       as.character(x[1L])
+                     }
+                   })
+  } else if (length(atcs) == 1) {
+    atcs <- unname(unlist(atcs))
+  } else {
+    names(atcs) <- x
+  }
+  
+  atcs
+}
+
 #' @rdname ab_property
 #' @export
 ab_atc_group1 <- function(x, language = get_locale(), ...) {
@@ -176,18 +221,48 @@ ab_loinc <- function(x, ...) {
 
 #' @rdname ab_property
 #' @export
-ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
+ab_ddd <- function(x, administration = "oral", ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
-  meet_criteria(units, allow_class = "logical", has_length = 1)
   
+  x <- as.ab(x, ...)
   ddd_prop <- administration
-  if (units == TRUE) {
+  # old behaviour
+  units <- list(...)$units
+  if (!is.null(units) && isTRUE(units)) {
+    if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
+      warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
+               "This warning will be shown once per session.", call = FALSE)
+    }
     ddd_prop <- paste0(ddd_prop, "_units")
   } else {
     ddd_prop <- paste0(ddd_prop, "_ddd")
   }
-  ab_validate(x = x, property = ddd_prop, ...)
+  out <- ab_validate(x = x, property = ddd_prop)
+  
+  if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
+    warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
+             "Please refer to the WHOCC website:\n",
+             "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
+  }
+  out
+}
+
+#' @rdname ab_property
+#' @export
+ab_ddd_units <- function(x, administration = "oral", ...) {
+  meet_criteria(x, allow_NA = TRUE)
+  meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
+  
+  x <- as.ab(x, ...)
+  if (any(ab_name(x, language = NULL) %like% "/")) {
+    warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
+             "Please refer to the WHOCC website:\n",
+             "www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
+  }
+  
+  ddd_prop <- paste0(administration, "_units")
+  ab_validate(x = x, property = ddd_prop)
 }
 
 #' @rdname ab_property
@@ -198,17 +273,18 @@ ab_info <- function(x, language = get_locale(), ...) {
   
   x <- as.ab(x, ...)
   list(ab = as.character(x),
-             atc = ab_atc(x),
+       cid = ab_cid(x),
-             cid = ab_cid(x),
+       name = ab_name(x, language = language),
-             name = ab_name(x, language = language),
+       group = ab_group(x, language = language),
-             group = ab_group(x, language = language),
+       atc = ab_atc(x),
-             atc_group1 = ab_atc_group1(x, language = language),
+       atc_group1 = ab_atc_group1(x, language = language),
-             atc_group2 = ab_atc_group2(x, language = language),
+       atc_group2 = ab_atc_group2(x, language = language),
-             tradenames = ab_tradenames(x),
+       tradenames = ab_tradenames(x),
-             ddd = list(oral = list(amount = ab_ddd(x, administration = "oral", units = FALSE),
+       loinc = ab_loinc(x),
-                                    units = ab_ddd(x, administration = "oral", units = TRUE)),
+       ddd = list(oral = list(amount = ab_ddd(x, administration = "oral"),
-                        iv = list(amount = ab_ddd(x, administration = "iv", units = FALSE),
+                              units = ab_ddd_units(x, administration = "oral")),
-                                  units = ab_ddd(x, administration = "iv", units = TRUE))))
+                  iv = list(amount = ab_ddd(x, administration = "iv"),
+                            units = ab_ddd_units(x, administration = "iv"))))
 }
 
 
@@ -218,12 +294,13 @@ ab_url <- function(x, open = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(open, allow_class = "logical", has_length = 1)
   
-  ab <- as.ab(x = x, ... = ...)
+  ab <- as.ab(x = x, ...)
-  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", ab_atc(ab), "&showdescription=no")
+  atcs <- ab_atc(ab, only_first = TRUE)
-  u[is.na(ab_atc(ab))] <- NA_character_
+  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
+  u[is.na(atcs)] <- NA_character_
   names(u) <- ab_name(ab)
   
-  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(ab_atc(ab))]
+  NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
   if (length(NAs) > 0) {
     warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
   }
@@ -248,20 +325,103 @@ ab_property <- function(x, property = "name", language = get_locale(), ...) {
   translate_AMR(ab_validate(x = x, property = property, ...), language = language)
 }
 
+#' @rdname ab_property
+#' @aliases ATC
+#' @export
+set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = NULL) {
+  meet_criteria(data, allow_class = c("data.frame", "character"))
+  meet_criteria(property, is_in = colnames(antibiotics), has_length = 1, ignore.case = TRUE)
+  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
+  meet_criteria(snake_case, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
+  
+  x_deparsed <- deparse(substitute(data))
+  if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
+    x_deparsed <- "your_data"
+  }
+  
+  property <- tolower(property)
+  if (is.null(snake_case)) {
+    snake_case <- property == "name"
+  }
+  
+  if (is.data.frame(data)) {
+    vars <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
+    if (length(vars) == 0) {
+      message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
+      return(data)
+    }
+  } else {
+    # quickly get antibiotic codes
+    vars_ab <- as.ab(data, fast_mode = TRUE)
+    vars <- data[!is.na(vars_ab)]
+  }
+  x <- vapply(FUN.VALUE = character(1),
+              ab_property(vars, property = property, language = language),
+              function(x) {
+                if (property == "atc") {
+                  # try to get the J-group
+                  if (any(x %like% "^J")) {
+                    x[x %like% "^J"][1L]
+                  } else {
+                    as.character(x[1L])
+                  }
+                } else {
+                  as.character(x[1L])
+                }
+              },
+              USE.NAMES = FALSE)
+  if (any(x %in% c("", NA))) {
+    warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
+    x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
+  }
+  
+  if (snake_case == TRUE) {
+    x <- tolower(gsub("[^a-zA-Z0-9]+", "_", x))
+  }
+  
+  if (any(duplicated(x))) {
+    # very hacky way of adding the index to each duplicate
+    # so      "Amoxicillin", "Amoxicillin",   "Amoxicillin"
+    # will be "Amoxicillin", "Amoxicillin_2", "Amoxicillin_3"
+    invisible(lapply(unique(x),
+                     function(u) {
+                       dups <- which(x == u)
+                       if (length(dups) > 1) {
+                         # there are duplicates
+                         dup_add_int <- dups[2:length(dups)]
+                         x[dup_add_int] <<- paste0(x[dup_add_int], "_", c(2:length(dups)))
+                       }
+                     }))
+  }
+  if (is.data.frame(data)) {
+    colnames(data)[colnames(data) %in% vars] <- x
+    data
+  } else {
+    data[which(!is.na(vars_ab))] <- x
+    data
+  }
+}
+
 ab_validate <- function(x, property, ...) {
   
   check_dataset_integrity()
   
-  # try to catch an error when inputting an invalid argument
+  if (tryCatch(all(x[!is.na(x)] %in% AB_lookup$ab), error = function(e) FALSE)) {
-  # so the 'call.' can be set to FALSE
+    # special case for ab_* functions where class is already <ab>
-  tryCatch(x[1L] %in% antibiotics[1, property],
+    x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
-           error = function(e) stop(e$message, call. = FALSE))
+    
-  x_bak <- x
+  } else {
-  if (!all(x %in% antibiotics[, property])) {
+    # try to catch an error when inputting an invalid argument
-    x <- data.frame(ab = as.ab(x, ...), stringsAsFactors = FALSE) %pm>%
+    # so the 'call.' can be set to FALSE
-      pm_left_join(antibiotics, by = "ab") %pm>%
+    tryCatch(x[1L] %in% antibiotics[1, property],
-      pm_pull(property)
+             error = function(e) stop(e$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]
+    }
   }
+  
   if (property == "ab") {
     return(set_clean_class(x, new_class = c("ab", "character")))
   } else if (property == "cid") {
@@ -269,7 +429,7 @@ ab_validate <- function(x, property, ...) {
   } else if (property %like% "ddd") {
     return(as.double(x))
   } else {
-    x[is.na(x) & !is.na(x_bak)] <- NA
+    x[is.na(x)] <- NA
     return(x)
   }
 }

R/amr.R

@@ -61,7 +61,7 @@
 #' Matthijs S. Berends \cr
 #' m.s.berends \[at\] umcg \[dot\] nl \cr
 #' University of Groningen
-#' Department of Medical Microbiology and Infection Prevention
+#' Department of Medical Microbiology and Infection Prevention \cr
 #' University Medical Center Groningen \cr
 #' Post Office Box 30001 \cr
 #' 9700 RB Groningen \cr

R/atc_online.R

@@ -25,9 +25,9 @@
 
 #' Get ATC Properties from WHOCC Website
 #'
-#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
+#' 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] or [character] vector with ATC code(s) of antibiotic(s)
+#' @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*
 #' @param url url of website of the WHOCC. The sign `%s` can be used as a placeholder for ATC codes.
@@ -68,6 +68,7 @@
 #' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) { 
 #'   # oral DDD (Defined Daily Dose) of amoxicillin
 #'   atc_online_property("J01CA04", "DDD", "O")
+#'   atc_online_ddd(ab_atc("amox"))
 #' 
 #'   # parenteral DDD (Defined Daily Dose) of amoxicillin
 #'   atc_online_property("J01CA04", "DDD", "P")
@@ -81,7 +82,7 @@ atc_online_property <- function(atc_code,
                                 url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
                                 url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
   meet_criteria(atc_code, allow_class = "character")
-  meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups"), ignore.case = TRUE)
+  meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "unit", "Adm.R", "Note", "groups"), ignore.case = TRUE)
   meet_criteria(administration, allow_class = "character", has_length = 1)
   meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
   meet_criteria(url_vet, allow_class = "character", has_length = 1, looks_like = "https?://")
@@ -97,8 +98,8 @@ atc_online_property <- function(atc_code,
   
   check_dataset_integrity()
   
-  if (!all(atc_code %in% antibiotics)) {
+  if (!all(atc_code %in% unlist(antibiotics$atc))) {
-    atc_code <- as.character(ab_atc(atc_code))
+    atc_code <- as.character(ab_atc(atc_code, only_first = TRUE))
   }
   
   if (!has_internet()) {
@@ -108,12 +109,11 @@ atc_online_property <- function(atc_code,
     return(rep(NA, length(atc_code)))
   }
   
-  # also allow unit as property
-  if (property %like% "unit") {
-    property <- "U"
-  }
-  
   property <- tolower(property)
+  # also allow unit as property
+  if (property == "unit") {
+    property <- "u"
+  }
   if (property == "ddd") {
     returnvalue <- rep(NA_real_, length(atc_code))
   } else if (property == "groups") {
@@ -206,3 +206,10 @@ atc_online_ddd <- function(atc_code, ...) {
   meet_criteria(atc_code, allow_class = "character")
   atc_online_property(atc_code = atc_code, property = "ddd", ...)
 }
+
+#' @rdname atc_online
+#' @export
+atc_online_ddd_units <- function(atc_code, ...) {
+  meet_criteria(atc_code, allow_class = "character")
+  atc_online_property(atc_code = atc_code, property = "unit", ...)
+}

R/bug_drug_combinations.R

@@ -25,7 +25,7 @@
 
 #' 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 publicable/printable format, see *Examples*.
+#' 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
@@ -81,7 +81,7 @@ bug_drug_combinations <- function(x,
   unique_mo <- sort(unique(x[, col_mo, drop = TRUE]))
   
   # select only groups and antibiotics
-  if (inherits(x.bak, "grouped_df")) {
+  if (is_null_or_grouped_tbl(x.bak)) {
     data_has_groups <- TRUE
     groups <- setdiff(names(attributes(x.bak)$groups), ".rows")
     x <- x[, c(groups, col_mo, colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]), drop = FALSE]
@@ -113,7 +113,7 @@ bug_drug_combinations <- function(x,
         data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
       })
       merged <- do.call(rbind, pivot)
-      out_group <- data.frame(mo = unique_mo[i],
+      out_group <- data.frame(mo = rep(unique_mo[i], NROW(merged)),
                               ab = rownames(merged),
                               S = merged$S,
                               I = merged$I,
@@ -218,7 +218,7 @@ format.bug_drug_combinations <- function(x,
       ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i])
       ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i])
       ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i])
-      ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i])
+      ab_txt[i] <- gsub("atc", ab_atc(ab[i], only_first = TRUE), ab_txt[i])
       ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i])
       ab_txt[i]
     }

R/count.R

@@ -83,6 +83,12 @@
 #'               n2 = n_rsi(CIP),      # same - analogous to n_distinct
 #'               total = n())          # NOT the number of tested isolates!
 #'               
+#'   # Number of available isolates for a whole antibiotic class
+#'   # (i.e., in this data set columns GEN, TOB, AMK, KAN)
+#'   example_isolates %>%
+#'     group_by(hospital_id) %>%
+#'     summarise(across(aminoglycosides(), n_rsi))
+#'  
 #'   # Count co-resistance between amoxicillin/clav acid and gentamicin,
 #'   # so we can see that combination therapy does a lot more than mono therapy.
 #'   # Please mind that `susceptibility()` calculates percentages right away instead.
@@ -108,81 +114,95 @@
 #' }
 #' }
 count_resistant <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "R",
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = "R",
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_susceptible <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("S", "I"),
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = c("S", "I"),
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_R <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "R",
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = "R",
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_IR <- function(..., only_all_tested = FALSE) {
-  if (message_not_thrown_before("count_IR")) {
+  if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
-    warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
+    message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
-    remember_thrown_message("count_IR")
   }
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("I", "R"),
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = c("I", "R"),
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_I <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "I",
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = "I",
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_SI <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("S", "I"),
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = c("S", "I"),
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_S <- function(..., only_all_tested = FALSE) {
-  if (message_not_thrown_before("count_S")) {
+  if (message_not_thrown_before("count_S", entire_session = TRUE)) {
-    warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
+    message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
-    remember_thrown_message("count_S")
   }
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "S",
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = "S",
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
 #' @export
 count_all <- function(..., only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("S", "I", "R"),
+    rsi_calc(...,
-           only_all_tested = only_all_tested,
+             ab_result = c("S", "I", "R"),
-           only_count = TRUE)
+             only_all_tested = only_all_tested,
+             only_count = TRUE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname count
@@ -196,11 +216,13 @@ count_df <- function(data,
                      language = get_locale(),
                      combine_SI = TRUE,
                      combine_IR = FALSE) {
-  rsi_calc_df(type = "count",
+  tryCatch(
-              data = data,
+    rsi_calc_df(type = "count",
-              translate_ab = translate_ab,
+                data = data,
-              language = language,
+                translate_ab = translate_ab,
-              combine_SI = combine_SI,
+                language = language,
-              combine_IR = combine_IR,
+                combine_SI = combine_SI,
-              combine_SI_missing = missing(combine_SI))
+                combine_IR = combine_IR,
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/custom_eucast_rules.R

@@ -89,9 +89,9 @@
 #' 
 #' ### 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 antibiotic agents that will be matched when running the rule.
+#' 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(x), "``\\cr(", paste0(sort(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE)), collapse = ", "), ")"), 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
@@ -140,12 +140,12 @@ custom_eucast_rules <- function(...) {
     stop_ifnot(deparse(result) %like% "==", 
                "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`")
     result_group <- as.character(result)[[2]]
-    if (paste0(toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
+    if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
       # support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
       result_group <- paste0(result_group, "s")
     }
-    if (toupper(result_group) %in% DEFINED_AB_GROUPS) {
+    if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) {
-      result_group <- eval(parse(text = toupper(result_group)), envir = asNamespace("AMR"))
+      result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR"))
     } else {
       result_group <- tryCatch(
         suppressWarnings(as.ab(result_group,
@@ -157,7 +157,7 @@ custom_eucast_rules <- function(...) {
     stop_if(any(is.na(result_group)),
             "this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"", 
             as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ", 
-            vector_or(tolower(DEFINED_AB_GROUPS), quotes = FALSE), ".")
+            vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), ".")
     result_value <- as.character(result)[[3]]
     result_value[result_value == "NA"] <- NA
     stop_ifnot(result_value %in% c("R", "S", "I", NA),

R/data.R

@@ -23,28 +23,28 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobials
+#' Data Sets with `r format(nrow(antibiotics) + nrow(antivirals), big.mark = ",")` Antimicrobial Drugs
 #'
-#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
+#' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
 #' @format
 #' ## For the [antibiotics] data set: a [data.frame] with `r nrow(antibiotics)` observations and `r ncol(antibiotics)` variables:
 #' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
-#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
 #' - `cid`\cr Compound ID as found in PubChem
 #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
 #' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
+#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
 #' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
 #' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
 #' - `abbr`\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
 #' - `synonyms`\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
-#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment
+#' - `oral_ddd`\cr Defined Daily Dose (DDD), oral treatment, currently available for `r sum(!is.na(antibiotics$oral_ddd))` drugs
 #' - `oral_units`\cr Units of `oral_ddd`
-#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
+#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs
 #' - `iv_units`\cr Units of `iv_ddd`
 #' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
 #' 
 #' ## For the [antivirals] data set: a [data.frame] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
-#' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
+#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
 #' - `cid`\cr Compound ID as found in PubChem
 #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO
 #' - `atc_group`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
@@ -55,7 +55,7 @@
 #' - `iv_units`\cr Units of `iv_ddd`
 #' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
 #'
-#' Synonyms (i.e. trade names) are derived from the Compound ID (`cid`) and consequently only available where a CID is available.
+#' Synonyms (i.e. trade names) were derived from the Compound ID (`cid`) and consequently only available where a CID is available.
 #' 
 #' ## Direct download
 #' These data sets are available as 'flat files' for use even without \R - you can find the files here:

R/deprecated.R

@@ -26,477 +26,9 @@
 #' 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).
-#' @details All antibiotic class selectors (such as [carbapenems()], [aminoglycosides()]) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as [filter_carbapenems()], [filter_aminoglycosides()]).
 #' @inheritSection lifecycle Retired Lifecycle
 #' @inheritSection AMR Read more on Our Website!
 #' @keywords internal
 #' @name AMR-deprecated
-#' @export
+# @export
-p_symbol <- function(p, emptychar = " ") {
+NULL
-  .Deprecated(package = "AMR", new = "cleaner::p_symbol")
-  
-  p <- as.double(p)
-  s <- rep(NA_character_, length(p))
-  
-  s[p <= 1] <- emptychar
-  s[p <= 0.100] <- "."
-  s[p <= 0.050] <- "*"
-  s[p <= 0.010] <- "**"
-  s[p <= 0.001] <- "***"
-  
-  s
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_first_weighted_isolate <- function(x = NULL,
-                                          col_date = NULL,
-                                          col_patient_id = NULL,
-                                          col_mo = NULL,
-                                          ...) {
-  
-  .Deprecated(old = "filter_first_weighted_isolate()",
-              new = "filter_first_isolate()",
-              package = "AMR")
-  
-  if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
-    # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
-  }
-  meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
-  meet_criteria(col_date, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(col_patient_id, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
-  
-  filter_first_isolate(x = x, col_date = col_date, col_patient_id = col_patient_id, col_mo = col_mo, ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-key_antibiotics <- function(x = NULL,
-                            col_mo = NULL,
-                            universal_1 = guess_ab_col(x, "amoxicillin"),
-                            universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
-                            universal_3 = guess_ab_col(x, "cefuroxime"),
-                            universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
-                            universal_5 = guess_ab_col(x, "ciprofloxacin"),
-                            universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
-                            GramPos_1 = guess_ab_col(x, "vancomycin"),
-                            GramPos_2 = guess_ab_col(x, "teicoplanin"),
-                            GramPos_3 = guess_ab_col(x, "tetracycline"),
-                            GramPos_4 = guess_ab_col(x, "erythromycin"),
-                            GramPos_5 = guess_ab_col(x, "oxacillin"),
-                            GramPos_6 = guess_ab_col(x, "rifampin"),
-                            GramNeg_1 = guess_ab_col(x, "gentamicin"),
-                            GramNeg_2 = guess_ab_col(x, "tobramycin"),
-                            GramNeg_3 = guess_ab_col(x, "colistin"),
-                            GramNeg_4 = guess_ab_col(x, "cefotaxime"),
-                            GramNeg_5 = guess_ab_col(x, "ceftazidime"),
-                            GramNeg_6 = guess_ab_col(x, "meropenem"),
-                            warnings = TRUE,
-                            ...) {
-  
-  .Deprecated(old = "key_antibiotics()",
-              new = "key_antimicrobials()",
-              package = "AMR")
-  
-  if (is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
-    # is also fix for using a grouped df as input (a dot as first argument)
-    x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
-  }
-
-  key_antimicrobials(x = x, 
-                     col_mo = col_mo, 
-                     universal = c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6),
-                     gram_negative = c(GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6),
-                     gram_positive = c(GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6),
-                     antifungal = NULL,
-                     only_rsi_columns = FALSE,
-                     ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-key_antibiotics_equal <- function(y,
-                                  z,
-                                  type = "keyantimicrobials",
-                                  ignore_I = TRUE,
-                                  points_threshold = 2,
-                                  info = FALSE,
-                                  na.rm = TRUE,
-                                  ...) {
-  
-  .Deprecated(old = "key_antibiotics_equal()",
-              new = "antimicrobials_equal()",
-              package = "AMR")
-  
-  antimicrobials_equal(y = y,
-                       z = z,
-                       type = type,
-                       ignore_I = ignore_I,
-                       points_threshold = points_threshold,
-                       info = info)
-}
-
-
-#' @name AMR-deprecated
-#' @export
-filter_ab_class <- function(x,
-                            ab_class,
-                            result = NULL,
-                            scope = "any",
-                            only_rsi_columns = FALSE,
-                            ...) {
-  
-  .call_depth <- list(...)$`.call_depth`
-  if (is.null(.call_depth)) {
-    .call_depth <- 0
-  }
-  .x_name <- list(...)$`.x_name`
-  if (is.null(.x_name)) {
-    .x_name <- deparse(substitute(x))
-  }
-  .fn <- list(...)$`.fn`
-  if (is.null(.fn)) {
-    .fn <- "filter_ab_class"
-  }
-  .fn_old <- .fn
-  # new way: using the ab selectors
-  .fn <- gsub("filter_", "", .fn, fixed = TRUE)
-  .fn <- gsub("^([1-5][a-z]+)_cephalosporins", "cephalosporins_\\1", .fn)
-  
-  if (missing(x) || is_null_or_grouped_tbl(x)) {
-    # when `x` is left blank, auto determine it (get_current_data() also contains dplyr::cur_data_all())
-    # is also fix for using a grouped df as input (a dot as first argument)
-    x <- get_current_data(arg_name = "x", call = -2 - .call_depth)
-    .x_name <- "your_data"
-  }
-  meet_criteria(x, allow_class = "data.frame", .call_depth = .call_depth)
-  meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = .call_depth)
-  if (!is.null(result)) {
-    # make result = "SI" works too:
-    result <- toupper(unlist(strsplit(result, "")))
-  }
-  meet_criteria(result, allow_class = "character", has_length = c(1, 2, 3), is_in = c("S", "I", "R"), allow_NULL = TRUE, .call_depth = .call_depth)
-  meet_criteria(scope, allow_class = "character", has_length = 1, is_in = c("all", "any"), .call_depth = .call_depth)
-  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = .call_depth)
-  
-  if (is.null(result)) {
-    result <- c("S", "I", "R")
-  }
-  
-  # get e.g. carbapenems() from filter_carbapenems()
-  fn <- get(.fn, envir = asNamespace("AMR"))
-  if (scope == "any") {
-    scope_fn <- any
-  } else {
-    scope_fn <- all
-  }
-  
-  # be nice here, be VERY extensive about how the AB selectors have taken over this function
-  deprecated_fn <- paste0(.fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ")",
-                          ifelse(length(result) > 1,
-                                 paste0(", c(", paste0("\"", result, "\"", collapse = ", "), ")"),
-                                 ifelse(is.null(result),
-                                        "",
-                                        paste0(" == \"", result, "\""))))
-  if (.x_name == ".") {
-    .x_name <- "your_data"
-  }
-  warning_(paste0("`", .fn_old, "()` is deprecated. Use the antibiotic selector `", .fn, "()` instead.\n",
-                  "In dplyr:\n",
-                  "  - ", .x_name, " %>% filter(", scope, "(", deprecated_fn, "))\n",
-                  ifelse(length(result) > 1, 
-                         paste0("  - ", .x_name, " %>% filter(", scope, "(", 
-                                .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))\n"),
-                         ""),
-                  "In base R:\n",
-                  "  - ", .x_name, "[", scope, "(", deprecated_fn, "), ]\n",
-                  ifelse(length(result) > 1, 
-                         paste0("  - ", .x_name, "[", scope, "(", 
-                                .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"), ]\n"),
-                         ""),
-                  "  - subset(", .x_name, ", ", scope, "(", deprecated_fn, "))",
-                  ifelse(length(result) > 1, 
-                         paste0("\n  - subset(", .x_name, ", ", scope, "(", 
-                                .fn, "(", ifelse(.fn == "ab_class", paste0("\"", ab_class, "\""), ""), ") == \"R\"))"),
-                         "")),
-           call = FALSE)
-  
-  if (.fn == "ab_class") {
-    subset(x, scope_fn(fn(ab_class = ab_class), result))
-  } else {
-    subset(x, scope_fn(fn(), result))
-  }
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_aminoglycosides <- function(x,
-                                   result = NULL,
-                                   scope = "any",
-                                   only_rsi_columns = FALSE,
-                                   ...) {
-  filter_ab_class(x = x,
-                  ab_class = "aminoglycoside",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_aminoglycosides",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_betalactams <- function(x,
-                               result = NULL,
-                               scope = "any",
-                               only_rsi_columns = FALSE,
-                               ...) {
-  filter_ab_class(x = x,
-                  ab_class = "carbapenem|cephalosporin|penicillin",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_betalactams",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-#' @name AMR-deprecated
-#' @export
-filter_carbapenems <- function(x,
-                               result = NULL,
-                               scope = "any",
-                               only_rsi_columns = FALSE,
-                               ...) {
-  filter_ab_class(x = x,
-                  ab_class = "carbapenem",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_carbapenems",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_cephalosporins <- function(x,
-                                  result = NULL,
-                                  scope = "any",
-                                  only_rsi_columns = FALSE,
-                                  ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporin",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_1st_cephalosporins <- function(x,
-                                      result = NULL,
-                                      scope = "any",
-                                      only_rsi_columns = FALSE,
-                                      ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporins (1st gen.)",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_1st_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_2nd_cephalosporins <- function(x,
-                                      result = NULL,
-                                      scope = "any",
-                                      only_rsi_columns = FALSE,
-                                      ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporins (2nd gen.)",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_2nd_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_3rd_cephalosporins <- function(x,
-                                      result = NULL,
-                                      scope = "any",
-                                      only_rsi_columns = FALSE,
-                                      ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporins (3rd gen.)",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_3rd_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_4th_cephalosporins <- function(x,
-                                      result = NULL,
-                                      scope = "any",
-                                      only_rsi_columns = FALSE,
-                                      ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporins (4th gen.)",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_4th_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_5th_cephalosporins <- function(x,
-                                      result = NULL,
-                                      scope = "any",
-                                      only_rsi_columns = FALSE,
-                                      ...) {
-  filter_ab_class(x = x,
-                  ab_class = "cephalosporins (5th gen.)",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_5th_cephalosporins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_fluoroquinolones <- function(x,
-                                    result = NULL,
-                                    scope = "any",
-                                    only_rsi_columns = FALSE,
-                                    ...) {
-  filter_ab_class(x = x,
-                  ab_class = "fluoroquinolone",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_fluoroquinolones",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_glycopeptides <- function(x,
-                                 result = NULL,
-                                 scope = "any",
-                                 only_rsi_columns = FALSE,
-                                 ...) {
-  filter_ab_class(x = x,
-                  ab_class = "glycopeptide",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_glycopeptides",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_macrolides <- function(x,
-                              result = NULL,
-                              scope = "any",
-                              only_rsi_columns = FALSE,
-                              ...) {
-  filter_ab_class(x = x,
-                  ab_class = "macrolide",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_macrolides",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_oxazolidinones <- function(x,
-                                  result = NULL,
-                                  scope = "any",
-                                  only_rsi_columns = FALSE,
-                                  ...) {
-  filter_ab_class(x = x,
-                  ab_class = "oxazolidinone",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_oxazolidinones",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_penicillins <- function(x,
-                               result = NULL,
-                               scope = "any",
-                               only_rsi_columns = FALSE,
-                               ...) {
-  filter_ab_class(x = x,
-                  ab_class = "penicillin",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_penicillins",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}
-
-#' @name AMR-deprecated
-#' @export
-filter_tetracyclines <- function(x,
-                                 result = NULL,
-                                 scope = "any",
-                                 only_rsi_columns = FALSE,
-                                 ...) {
-  filter_ab_class(x = x,
-                  ab_class = "tetracycline",
-                  result = result,
-                  scope = scope,
-                  only_rsi_columns = only_rsi_columns,
-                  .call_depth = 1,
-                  .fn = "filter_tetracyclines",
-                  .x_name = deparse(substitute(x)),
-                  ...)
-}

R/disk.R

@@ -195,6 +195,15 @@ unique.disk <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep disk
+#' @export
+#' @noRd
+rep.disk <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 # will be exported using s3_register() in R/zzz.R
 get_skimmers.disk <- function(column) {
   skimr::sfl(

R/eucast_rules.R

@@ -55,7 +55,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
 #' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
 #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
-#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(eucast_rules_file[which(eucast_rules_file$reference.version == 3.2 & eucast_rules_file$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
+#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version == 3.2 & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
 #' @param ... column name of an antibiotic, see section *Antibiotics* below
 #' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
 #' @param administration route of administration, either `r vector_or(dosage$administration)`
@@ -320,9 +320,9 @@ eucast_rules <- function(x,
     x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
     x_new <- character()
     for (val in x) {
-      if (val %in% ls(envir = asNamespace("AMR"))) {
+      if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-        # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
+        # antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
-        val <- eval(parse(text = val), envir = asNamespace("AMR"))
+        val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
       } else if (val %in% AB_lookup$ab) {
         # separate drugs, such as `AMX`
         val <- as.ab(val)
@@ -561,11 +561,11 @@ eucast_rules <- function(x,
   # Official EUCAST rules ---------------------------------------------------
   eucast_notification_shown <- FALSE
   if (!is.null(list(...)$eucast_rules_df)) {
-    # this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %>% filter(is.na(have_these_values)))
+    # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
     eucast_rules_df <- list(...)$eucast_rules_df
   } else {
     # otherwise internal data file, created in data-raw/_internals.R
-    eucast_rules_df <- eucast_rules_file
+    eucast_rules_df <- EUCAST_RULES_DF
   }
   
   # filter on user-set guideline versions ----
@@ -1072,7 +1072,6 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
     message_("Dosages for antimicrobial drugs, as meant for ",
              format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
              font_red("This note will be shown once per session."))
-    remember_thrown_message(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)
   }
   
   ab <- as.ab(ab)

R/first_isolate.R

@@ -23,9 +23,9 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Determine First (Weighted) Isolates
+#' Determine First Isolates
 #'
-#' Determine first (weighted) 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.
+#' 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
@@ -34,7 +34,7 @@
 #' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (such as test codes for screening). In that case `testcodes_exclude` will be ignored.
 #' @param col_specimen column name of the specimen type or group
 #' @param col_icu column name of the logicals (`TRUE`/`FALSE`) whether a ward or department is an Intensive Care Unit (ICU)
-#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first (weighted) isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
+#' @param col_keyantimicrobials (only useful when `method = "phenotype-based"`) column name of the key antimicrobials to determine first isolates, see [key_antimicrobials()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' or 'antimicrobials' (case insensitive). Use `col_keyantimicrobials = FALSE` to prevent this. Can also be the output of [key_antimicrobials()].
 #' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again. The default of 365 days is based on the guideline by CLSI, see *Source*. 
 #' @param testcodes_exclude a [character] vector with test codes that should be excluded (case-insensitive)
 #' @param icu_exclude a [logical] to indicate whether ICU isolates should be excluded (rows with value `TRUE` in the column set with `col_icu`)
@@ -102,9 +102,9 @@
 #' 
 #' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
 #' 
-#' 1. Using `type = "points"` and argument `points_threshold`
+#' 1. Using `type = "points"` and argument `points_threshold` (default)
 #' 
-#'    This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as 0.5 points, a difference from S to R (or vice versa) counts as 1 point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
+#'    This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as `0.5` points, a difference from S to R (or vice versa) counts as `1` point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
 #'    
 #'    All antimicrobials are internally selected using the [all_antimicrobials()] function. The output of this function does not need to be passed to the [first_isolate()] function.
 #' 
@@ -131,11 +131,8 @@
 #' # `example_isolates` is a data set available in the AMR package.
 #' # See ?example_isolates.
 #' 
-#' example_isolates[first_isolate(example_isolates), ]
-#' \donttest{
-#' # faster way, only works in R 3.2 and later:
 #' example_isolates[first_isolate(), ]
-#' 
+#' \donttest{
 #' # get all first Gram-negatives
 #' example_isolates[which(first_isolate() & mo_is_gram_negative()), ]
 #'
@@ -221,7 +218,7 @@ first_isolate <- function(x = NULL,
   meet_criteria(col_icu, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
   # method
   method <- coerce_method(method)
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
+  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
   # key antimicrobials
   if (length(col_keyantimicrobials) > 1) {
     meet_criteria(col_keyantimicrobials, allow_class = "character", has_length = nrow(x))
@@ -259,15 +256,14 @@ first_isolate <- function(x = NULL,
     method <- "episode-based"
   }
   if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
-    message_(paste0("Determining first isolates using the '", font_bold(method), "' method",
+    message_(paste0("Determining first isolates ",
                     ifelse(method %in% c("episode-based", "phenotype-based"),
                            ifelse(is.infinite(episode_days),
-                                  " without a specified episode length",
+                                  "without a specified episode length",
-                                  paste(" and an episode length of", episode_days, "days")),
+                                  paste("using an episode length of", episode_days, "days")),
                            "")),
              as_note = FALSE,
              add_fn = font_black)
-    remember_thrown_message("first_isolate.method")
   }
   
   # try to find columns based on type
@@ -364,10 +360,9 @@ first_isolate <- function(x = NULL,
   }
   # remove testcodes
   if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate.excludingtestcodes")) {
-    message_("Excluding test codes: ", toString(paste0("'", testcodes_exclude, "'")),
+    message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
              add_fn = font_black,
              as_note = FALSE)
-    remember_thrown_message("first_isolate.excludingtestcodes")
   }
   
   if (is.null(col_specimen)) {
@@ -381,7 +376,6 @@ first_isolate <- function(x = NULL,
       message_("Excluding other than specimen group '", specimen_group, "'",
                add_fn = font_black,
                as_note = FALSE)
-      remember_thrown_message("first_isolate.excludingspecimen")
     }
   }
   if (!is.null(col_keyantimicrobials)) {
@@ -460,9 +454,7 @@ first_isolate <- function(x = NULL,
                                            episode_days = episode_days),
                                     use.names = FALSE)
   
-  weighted.notice <- ""
   if (!is.null(col_keyantimicrobials)) {
-    weighted.notice <- "weighted "
     if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
       if (type == "keyantimicrobials") {
         message_("Basing inclusion on key antimicrobials, ",
@@ -477,7 +469,6 @@ first_isolate <- function(x = NULL,
                  add_fn = font_black,
                  as_note = FALSE)
       }
-      remember_thrown_message("first_isolate.type")
     }
     type_param <- type
     
@@ -590,16 +581,16 @@ first_isolate <- function(x = NULL,
     }
     # mark up number of found
     n_found <- format(n_found, big.mark = big.mark, decimal.mark = decimal.mark)
-    if (p_found_total != p_found_scope) {
+    message_(paste0("=> Found ",
-      msg_txt <- paste0("=> Found ",
+                    font_bold(paste0(n_found,
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
+                                     ifelse(method == "isolate-based", "", paste0(" '", method, "'")),
-                        " (", method, ", ", p_found_scope, " within scope and ", p_found_total, " of total where a microbial ID was available)")
+                                     " first isolates")),
-    } else {
+                    " (",
-      msg_txt <- paste0("=> Found ",
+                    ifelse(p_found_total != p_found_scope,
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
+                           paste0(p_found_scope, " within scope and "),
-                        " (", method, ", ", p_found_total, " of total where a microbial ID was available)")
+                           ""),
-    }
+                    p_found_total, " of total where a microbial ID was available)"),
-    message_(msg_txt, add_fn = font_black, as_note = FALSE)
+             add_fn = font_black, as_note = FALSE)
   }
   
   x$newvar_first_isolate
@@ -626,7 +617,7 @@ filter_first_isolate <- function(x = NULL,
   meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
   meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
   method <- coerce_method(method)
-  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based", "p", "e", "i"))
+  meet_criteria(method, allow_class = "character", has_length = 1, is_in = c("phenotype-based", "episode-based", "patient-based", "isolate-based"))
   
   subset(x, first_isolate(x = x,
                           col_date = col_date,
@@ -644,7 +635,7 @@ coerce_method <- function(method) {
   method <- tolower(as.character(method[1L]))
   method[method %like% "^(p$|pheno)"] <- "phenotype-based"
   method[method %like% "^(e$|episode)"] <- "episode-based"
-  method[method %like% "^patient"] <- "patient-based"
+  method[method %like% "^pat"] <- "patient-based"
   method[method %like% "^(i$|iso)"] <- "isolate-based"
   method
 }

R/ggplot_rsi.R

@@ -123,8 +123,7 @@
 #'            mo == as.mo("E. coli")) %>%
 #'     # age_groups() is also a function in this AMR package:
 #'     group_by(age_group = age_groups(age)) %>%
-#'     select(age_group,
+#'     select(age_group, CIP) %>%
-#'            CIP) %>%
 #'     ggplot_rsi(x = "age_group")
 #'   
 #'   # a shorter version which also adjusts data label colours:
@@ -135,6 +134,8 @@
 #'
 #'   # it also supports groups (don't forget to use the group var on `x` or `facet`):
 #'   example_isolates %>%
+#'     filter(mo_is_gram_negative()) %>% 
+#'     # select only UTI-specific drugs
 #'     select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
 #'     group_by(hospital_id) %>%
 #'     ggplot_rsi(x = "hospital_id",
@@ -370,7 +371,6 @@ scale_rsi_colours <- function(...,
                               aesthetics = "fill") {
   stop_ifnot_installed("ggplot2")
   meet_criteria(aesthetics, allow_class = "character", is_in = c("alpha", "colour", "color", "fill", "linetype", "shape", "size"))
-  
   # behaviour until AMR pkg v1.5.0 and also when coming from ggplot_rsi()
   if ("colours" %in% names(list(...))) {
     original_cols <- c(S = "#3CAEA3",
@@ -379,22 +379,25 @@ scale_rsi_colours <- function(...,
                        IR = "#ED553B",
                        R = "#ED553B")
     colours <- replace(original_cols, names(list(...)$colours), list(...)$colours)
-    return(ggplot2::scale_fill_manual(values = colours))
+    # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
+    # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
+    return(ggplot2::scale_fill_manual(values = colours, limits = force))
   }
   if (identical(unlist(list(...)), FALSE)) {
     return(invisible())
   }
   
   names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
-                         unique(translations_file[which(translations_file$pattern == "Susceptible"),
+                         unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
                                                   "replacement", drop = TRUE]))
-  names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure", "Increased exposure", "Incr. exposure",
+  names_incr_exposure <- c("I", "intermediate", "increased exposure", "incr. exposure",
-                           unique(translations_file[which(translations_file$pattern == "Intermediate"),
+                           "Increased exposure", "Incr. exposure", "Susceptible, incr. exp.",
+                           unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
                                                     "replacement", drop = TRUE]),
-                           unique(translations_file[which(translations_file$pattern == "Incr. exposure"),
+                           unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible, incr. exp."),
                                                     "replacement", drop = TRUE]))
   names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
-                       unique(translations_file[which(translations_file$pattern == "Resistant"), 
+                       unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"), 
                                                 "replacement", drop = TRUE]))
   
   susceptible <- rep("#3CAEA3", length(names_susceptible))
@@ -411,7 +414,9 @@ scale_rsi_colours <- function(...,
   dots[dots == "I"] <- "#F6D55C"
   dots[dots == "R"] <- "#ED553B"
   cols <- replace(original_cols, names(dots), dots)
-  ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols)
+  # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
+  # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
+  ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols, limits = force)
 }
 
 #' @rdname ggplot_rsi

R/guess_ab_col.R

@@ -97,16 +97,39 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
 }
 
 get_column_abx <- function(x,
+                           ...,
                            soft_dependencies = NULL,
                            hard_dependencies = NULL,
                            verbose = FALSE,
                            info = TRUE,
                            only_rsi_columns = FALSE,
                            sort = TRUE,
-                           ...) {
+                           reuse_previous_result = TRUE) {
   
   # check if retrieved before, then get it from package environment
-  if (identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+  if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+    # so within the same call, within the same environment, we got here again.
+    # but we could've come from another function within the same call, so now only check the columns that changed
+    
+    # first remove the columns that are not existing anymore
+    previous <- pkg_env$get_column_abx.out
+    current <- previous[previous %in% colnames(x)]
+    
+    # then compare columns in current call with columns in original call
+    new_cols <- colnames(x)[!colnames(x) %in% pkg_env$get_column_abx.checked_cols]
+    if (length(new_cols) > 0) {
+      # these columns did not exist in the last call, so add them
+      new_cols_rsi <- get_column_abx(x[, new_cols, drop = FALSE], reuse_previous_result = FALSE, info = FALSE, sort = FALSE)
+      current <- c(current, new_cols_rsi)
+      # order according to columns in current call
+      current <- current[match(colnames(x)[colnames(x) %in% current], current)]
+    }
+    
+    # update pkg environment to improve speed on next run
+    pkg_env$get_column_abx.out <- current
+    pkg_env$get_column_abx.checked_cols <- colnames(x)
+
+    # and return right values
     return(pkg_env$get_column_abx.out)
   }
   
@@ -123,6 +146,7 @@ get_column_abx <- function(x,
   }
   
   x <- as.data.frame(x, stringsAsFactors = FALSE)
+  x.bak <- x
   if (only_rsi_columns == TRUE) {
     x <- x[, which(is.rsi(x)), drop = FALSE]
   }
@@ -155,7 +179,7 @@ get_column_abx <- function(x,
                         } else {
                           return(NA_character_)
                         }
-                      })
+                      }, USE.NAMES = FALSE)
   
   x_columns <- x_columns[!is.na(x_columns)]
   x <- x[, x_columns, drop = FALSE] # without drop = FALSE, x will become a vector when x_columns is length 1
@@ -163,62 +187,77 @@ get_column_abx <- function(x,
                          abcode = suppressWarnings(as.ab(colnames(x), info = FALSE)),
                          stringsAsFactors = FALSE)
   df_trans <- df_trans[!is.na(df_trans$abcode), , drop = FALSE]
-  x <- as.character(df_trans$colnames)
+  out <- as.character(df_trans$colnames)
-  names(x) <- df_trans$abcode
+  names(out) <- df_trans$abcode
   
   # add from self-defined dots (...):
   # such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
+  all_okay <- TRUE
   dots <- list(...)
   if (length(dots) > 0) {
     newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
     if (any(is.na(newnames))) {
-      warning_("Invalid antibiotic reference(s): ", toString(names(dots)[is.na(newnames)]),
+      if (info == TRUE) {
+        message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+      }
+      warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
                call = FALSE,
                immediate = TRUE)
+      all_okay <- FALSE
+    }
+    unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
+    if (length(unexisting_cols) > 0) {
+      if (info == TRUE) {
+        message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
+      }
+      stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
+            call = FALSE)
+      all_okay <- FALSE
     }
     # turn all NULLs to NAs
-    dots <- unlist(lapply(dots, function(x) if (is.null(x)) NA else x))
+    dots <- unlist(lapply(dots, function(dot) if (is.null(dot)) NA else dot))
     names(dots) <- newnames
     dots <- dots[!is.na(names(dots))]
     # merge, but overwrite automatically determined ones by 'dots'
-    x <- c(x[!x %in% dots & !names(x) %in% names(dots)], dots)
+    out <- c(out[!out %in% dots & !names(out) %in% names(dots)], dots)
     # delete NAs, this will make e.g. eucast_rules(... TMP = NULL) work to prevent TMP from being used
-    x <- x[!is.na(x)]
+    out <- out[!is.na(out)]
   }
   
-  if (length(x) == 0) {
+  if (length(out) == 0) {
-    if (info == TRUE) {
+    if (info == TRUE & all_okay == TRUE) {
       message_("No columns found.")
     }
     pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
-    pkg_env$get_column_abx.out <- x
+    pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
-    return(x)
+    pkg_env$get_column_abx.out <- out
+    return(out)
   }
   
   # sort on name
   if (sort == TRUE) {
-    x <- x[order(names(x), x)]
+    out <- out[order(names(out), out)]
   }
-  duplicates <- c(x[duplicated(x)], x[duplicated(names(x))]) 
+  duplicates <- c(out[duplicated(out)], out[duplicated(names(out))]) 
   duplicates <- duplicates[unique(names(duplicates))]
-  x <- c(x[!names(x) %in% names(duplicates)], duplicates)
+  out <- c(out[!names(out) %in% names(duplicates)], duplicates)
   if (sort == TRUE) {
-    x <- x[order(names(x), x)]
+    out <- out[order(names(out), out)]
   }
   
   # succeeded with auto-guessing
-  if (info == TRUE) {
+  if (info == TRUE & all_okay == TRUE) {
     message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
   }
   
-  for (i in seq_len(length(x))) {
+  for (i in seq_len(length(out))) {
-    if (info == TRUE & verbose == TRUE & !names(x[i]) %in% names(duplicates)) {
+    if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
-      message_("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
+      message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
-               " (", ab_name(names(x)[i], tolower = TRUE, language = NULL), ").")
+               " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
     }
-    if (info == TRUE & names(x[i]) %in% names(duplicates)) {
+    if (info == TRUE & names(out[i]) %in% names(duplicates)) {
-      warning_(paste0("Using column '", font_bold(x[i]), "' as input for ", names(x)[i],
+      warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
-                      " (", ab_name(names(x)[i], tolower = TRUE, language = NULL),
+                      " (", ab_name(names(out)[i], tolower = TRUE, language = NULL),
                       "), although it was matched for multiple antibiotics or columns."),
                add_fn = font_red,
                call = FALSE, 
@@ -228,18 +267,18 @@ get_column_abx <- function(x,
   
   if (!is.null(hard_dependencies)) {
     hard_dependencies <- unique(hard_dependencies)
-    if (!all(hard_dependencies %in% names(x))) {
+    if (!all(hard_dependencies %in% names(out))) {
       # missing a hard dependency will return NA and consequently the data will not be analysed
-      missing <- hard_dependencies[!hard_dependencies %in% names(x)]
+      missing <- hard_dependencies[!hard_dependencies %in% names(out)]
       generate_warning_abs_missing(missing, any = FALSE)
       return(NA)
     }
   }
   if (!is.null(soft_dependencies)) {
     soft_dependencies <- unique(soft_dependencies)
-    if (info == TRUE & !all(soft_dependencies %in% names(x))) {
+    if (info == TRUE & !all(soft_dependencies %in% names(out))) {
       # missing a soft dependency may lower the reliability
-      missing <- soft_dependencies[!soft_dependencies %in% names(x)]
+      missing <- soft_dependencies[!soft_dependencies %in% names(out)]
       missing_msg <- vector_and(paste0(ab_name(missing, tolower = TRUE, language = NULL), 
                                        " (", font_bold(missing, collapse = NULL), ")"), 
                                 quotes = FALSE)
@@ -249,8 +288,9 @@ get_column_abx <- function(x,
   }
   
   pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
-  pkg_env$get_column_abx.out <- x
+  pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
-  x
+  pkg_env$get_column_abx.out <- out
+  out
 }
 
 generate_warning_abs_missing <- function(missing, any = FALSE) {

R/italicise_taxonomy.R

@@ -44,11 +44,11 @@
 #' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
 #' 
 #' # since ggplot2 supports no markdown (yet), use
-#' # italicise_taxonomy() and the `ggtext` pkg for titles:
+#' # italicise_taxonomy() and the `ggtext` package for titles:
 #' \donttest{
 #' if (require("ggplot2") && require("ggtext")) {
-#'   ggplot(example_isolates$AMC,
+#'   autoplot(example_isolates$AMC,
-#'          title = italicise_taxonomy("Amoxi/clav in E. coli")) +
+#'            title = italicise_taxonomy("Amoxi/clav in E. coli")) +
 #'     theme(plot.title = ggtext::element_markdown())
 #' }
 #' }

R/join_microorganisms.R

@@ -36,7 +36,7 @@
 #' @param ... ignored, only in place to allow future extensions
 #' @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.
+#' 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

R/key_antimicrobials.R

@@ -177,7 +177,6 @@ key_antimicrobials <- function(x = NULL,
                       paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
                "as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
                call = FALSE)
-      remember_thrown_message(paste0("key_antimicrobials.", name))
     }
     
     generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])

R/mdro.R

@@ -187,12 +187,8 @@ mdro <- function(x = NULL,
   check_dataset_integrity()
   
   info.bak <- info
-  if (message_not_thrown_before("mdro")) {
+  # don't thrown info's more than once per call
-    remember_thrown_message("mdro")
+  info <- message_not_thrown_before("mdro")
-  } else {
-    # don't thrown info's more than once per call
-    info <- FALSE
-  }
 
   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.",
@@ -252,7 +248,7 @@ mdro <- function(x = NULL,
     if (info == TRUE) {
       txt <- paste0("Determining MDROs based on custom rules",
                     ifelse(isTRUE(attributes(guideline)$as_factor),
-                           paste0(", resulting in [factor] levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
+                           paste0(", resulting in factor levels: ", paste0(attributes(guideline)$values, collapse = " < ")),
                            ""),
                     ".")
       txt <- word_wrap(txt)
@@ -1416,7 +1412,6 @@ mdro <- function(x = NULL,
       if (message_not_thrown_before("mdro.availability")) {
         warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
                  percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
-        remember_thrown_message("mdro.availability")
       }
       # set these -1s to NA
       x[which(x$MDRO == -1), "MDRO"] <- NA_integer_

R/mic.R

@@ -320,6 +320,15 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep mic
+#' @export
+#' @noRd
+rep.mic <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 #' @method sort mic
 #' @export
 #' @noRd
@@ -337,7 +346,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
 #' @export
 #' @noRd
 hist.mic <- function(x, ...) {
-  warning_("Use `plot()` or `ggplot()` for optimal plotting of MIC values", call = FALSE)
+  warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
   hist(log2(x))
 }
 

R/mo.R

@@ -469,7 +469,7 @@ exec_as.mo <- function(x,
     x <- strip_whitespace(x, dyslexia_mode)
     # translate 'unknown' names back to English
     if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
-      trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
+      trns <- subset(TRANSLATIONS, pattern %like% "unknown")
       langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
       for (l in langs) {
         for (i in seq_len(nrow(trns))) {
@@ -492,7 +492,7 @@ exec_as.mo <- function(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 at once
+    # 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 <- toupper(x_backup) %in% MO_lookup$mo
@@ -1551,16 +1551,7 @@ exec_as.mo <- function(x,
                                             & !identical(x_input, "")
                                             & !identical(x_input, "xxx")])
 
-  # left join the found results to the original input values (x_input)
+  x <- x[match(x_input, x_input_unique_nonempty)]
-  df_found <- data.frame(input = as.character(x_input_unique_nonempty),
-                         found = as.character(x),
-                         stringsAsFactors = FALSE)
-  df_input <- data.frame(input = as.character(x_input),
-                         stringsAsFactors = FALSE)
-
-  # super fast using match() which is a lot faster than merge()
-  x <- df_found$found[match(df_input$input, df_found$input)]
-
   if (property == "mo") {
     x <- set_clean_class(x, new_class = c("mo", "character"))
   }
@@ -1664,16 +1655,23 @@ pillar_shaft.mo <- function(x, ...) {
   out[is.na(x)] <- font_na("  NA")
   out[x == "UNKNOWN"] <- font_na("  UNKNOWN")
   
-  if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
+  df <- tryCatch(get_current_data(arg_name = "x", call = 0),
+                 error = function(e) NULL)
+  if (!is.null(df)) {
+    mo_cols <- vapply(FUN.VALUE = logical(1), df, is.mo)
+  } else {
+    mo_cols <- NULL
+  }
+  
+  if (!all(x[!is.na(x)] %in% MO_lookup$mo) | 
+      (!is.null(df) && !all(unlist(df[, which(mo_cols), drop = FALSE]) %in% MO_lookup$mo))) {
     # markup old mo codes
     out[!x %in% MO_lookup$mo] <- font_italic(font_na(x[!x %in% MO_lookup$mo], 
                                                      collapse = NULL),
                                              collapse = NULL)
-    # throw a warning with the affected column name
+    # throw a warning with the affected column name(s)
-    mo <- tryCatch(search_type_in_df(get_current_data(arg_name = "x", call = 0), type = "mo", info = FALSE),
+    if (!is.null(mo_cols)) {
-                   error = function(e) NULL)
+      col <- paste0("Column ", vector_or(colnames(df)[mo_cols], quotes = TRUE, sort = FALSE))
-    if (!is.null(mo)) {
-      col <- paste0("Column '", mo, "'")
     } else {
       col <- "The data"
     }
@@ -1880,36 +1878,30 @@ print.mo_uncertainties <- function(x, ...) {
   if (NROW(x) == 0) {
     return(NULL)
   }
-  message_("Matching scores are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.", as_note = FALSE)
+  cat(word_wrap("Matching scores", ifelse(has_colour(), " (in blue)", ""), " are based on human pathogenic prevalence and the resemblance between the input and the full taxonomic name. See `?mo_matching_score`.\n\n", add_fn = font_blue))
   
-  msg <- ""
+  txt <- ""
   for (i in seq_len(nrow(x))) {
     if (x[i, ]$candidates != "") {
       candidates <- unlist(strsplit(x[i, ]$candidates, ", ", fixed = TRUE))
       scores <- mo_matching_score(x = x[i, ]$input, n = candidates)
-      # sort on descending scores
-      candidates <- candidates[order(1 - scores)]
-      scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
       n_candidates <- length(candidates)
-      candidates <- vector_and(paste0(candidates, " (", scores_formatted[order(1 - scores)], ")"),
+      
-                               quotes = FALSE, 
+      candidates_formatted <- font_italic(candidates, collapse = NULL)
-                               sort = FALSE)
+      scores_formatted <- trimws(formatC(round(scores, 3), format = "f", digits = 3))
-      # align with input after arrow
+      
-      candidates <- paste0("\n",
+      # sort on descending scores
-                           strwrap(paste0("Also matched",
+      candidates_formatted <- candidates_formatted[order(1 - scores)]
-                                          ifelse(n_candidates >= 25, " (max 25)", ""), ": ",
+      scores_formatted <- scores_formatted[order(1 - scores)]
-                                          candidates), # this is already max 25 due to format_uncertainty_as_df()
+      
-                                   indent = nchar(x[i, ]$input) + 6,
+      candidates <- word_wrap(paste0("Also matched: ",
-                                   exdent = nchar(x[i, ]$input) + 6,
+                                     vector_and(paste0(candidates_formatted,
-                                   width = 0.98 * getOption("width")),
+                                                       font_blue(paste0(" (", scores_formatted, ")"), collapse = NULL)), 
-                           collapse = "")
+                                                quotes = FALSE, sort = FALSE),
-      # after strwrap, make taxonomic names italic
+                                     ifelse(n_candidates > 25,
-      candidates <- gsub("([A-Za-z]+)", font_italic("\\1"), candidates, perl = TRUE)
+                                            paste0(" [showing first 25 of ", n_candidates, "]"),
-      candidates <- gsub(font_italic("and"), "and", candidates, fixed = TRUE)
+                                            "")), 
-      candidates <- gsub(paste(font_italic(c("Also", "matched"), collapse = NULL), collapse = " "),
+                              extra_indent = nchar("Also matched: "))
-                         "Also matched",
-                         candidates, fixed = TRUE)
-      candidates <- gsub(font_italic("max"), "max", candidates, fixed = TRUE)
     } else {
       candidates <- ""
     }
@@ -1917,23 +1909,24 @@ print.mo_uncertainties <- function(x, ...) {
                                                     n = x[i, ]$fullname),
                                   3),
                             format = "f", digits = 3))
-    msg <- paste(msg,
+    txt <- paste(txt,
                  paste0(
                    strwrap(
-                     paste0('"', x[i, ]$input, '" -> ',
+                     paste0(font_red('"', x[i, ]$input, '"', collapse = ""),
+                            " -> ",
                             paste0(font_bold(font_italic(x[i, ]$fullname)),
                                    ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
                                    " (", x[i, ]$mo,
-                                   ", matching score = ", score,
+                                   ", ", font_blue(score),
                                    ") ")),
                      width = 0.98 * getOption("width"),
                      exdent = nchar(x[i, ]$input) + 6),
                    collapse = "\n"),
                  candidates,
                  sep = "\n")
-    msg <- paste0(gsub("\n\n", "\n", msg), "\n\n")
+    txt <- paste0(gsub("\n\n", "\n", txt), "\n\n")
   }
-  cat(msg)
+  cat(txt)
 }
 
 #' @rdname as.mo
@@ -2039,12 +2032,12 @@ parse_and_convert <- function(x) {
         x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
       }
     }
-    x[is.null(x)] <- NA
+    parsed <- iconv(as.character(x), to = "UTF-8")
-    parsed <- iconv(x, to = "UTF-8")
     parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
     parsed <- gsub('"', "", parsed, fixed = TRUE)
     parsed <- gsub(" +", " ", parsed, perl = TRUE)
     parsed <- trimws(parsed)
+    parsed
   }, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
   parsed
 }

R/mo_matching_score.R

@@ -46,6 +46,8 @@
 #' 
 #' The grouping into human pathogenic prevalence (\eqn{p}) is based on experience from several microbiological laboratories in the Netherlands in conjunction with international reports on pathogen prevalence. **Group 1** (most prevalent microorganisms) consists of all microorganisms where the taxonomic class is Gammaproteobacteria or where the taxonomic genus is *Enterococcus*, *Staphylococcus* or *Streptococcus*. This group consequently contains all common Gram-negative bacteria, such as *Pseudomonas* and *Legionella* and all species within the order Enterobacterales. **Group 2** consists of all microorganisms where the taxonomic phylum is Proteobacteria, Firmicutes, Actinobacteria or Sarcomastigophora, or where the taxonomic genus is *Absidia*, *Acremonium*, *Actinotignum*, *Alternaria*, *Anaerosalibacter*, *Apophysomyces*, *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* or *Ureaplasma*. **Group 3** consists of all other microorganisms.
 #' 
+#' All characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
+#' 
 #' All matches are sorted descending on their matching score and for all user input values, the top match will be returned. This will lead to the effect that e.g., `"E. coli"` will return the microbial ID of *Escherichia coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Escherichia coli"), 3)`}, a highly prevalent microorganism found in humans) and not *Entamoeba coli* (\eqn{m = `r round(mo_matching_score("E. coli", "Entamoeba coli"), 3)`}, a less prevalent microorganism in humans), although the latter would alphabetically come first. 
 #' @export
 #' @inheritSection AMR Reference Data Publicly Available

R/mo_property.R

@@ -42,7 +42,7 @@
 #'
 #' Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions [mo_kingdom()] and [mo_domain()] return the exact same results.
 #'
-#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
+#' The Gram stain - [mo_gramstain()] - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, [PMID 11837318](https://pubmed.ncbi.nlm.nih.gov/11837318)), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive, except for members of the class Negativicutes which are Gram-negative. Members of other bacterial phyla are all considered Gram-negative. Species outside the kingdom of Bacteria will return a value `NA`. Functions [mo_is_gram_negative()] and [mo_is_gram_positive()] always return `TRUE` or `FALSE` (except when the input is `NA` or the MO code is `UNKNOWN`), thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
 #' 
 #' Determination of yeasts - [mo_is_yeast()] - will be based on the taxonomic kingdom and class. *Budding yeasts* are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). *True yeasts* are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return `TRUE`. It returns `FALSE` otherwise (except when the input is `NA` or the MO code is `UNKNOWN`).
 #' 
@@ -52,7 +52,7 @@
 #'
 #' The function [mo_url()] will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
 #' 
-#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See the [microorganisms] data set for more info.
+#' SNOMED codes - [mo_snomed()] - are from the `r SNOMED_VERSION$current_source`. See *Source* and the [microorganisms] data set for more info.
 #' @inheritSection mo_matching_score Matching Score for Microorganisms
 #' @inheritSection catalogue_of_life Catalogue of Life
 #' @inheritSection as.mo Source
@@ -65,7 +65,7 @@
 #' - A [numeric] in case of [mo_snomed()]
 #' - A [character] in all other cases
 #' @export
-#' @seealso [microorganisms]
+#' @seealso Data set [microorganisms]
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
@@ -225,6 +225,8 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   translate_AMR(shortnames, language = language, only_unknown = FALSE, only_affect_mo_names = TRUE)
 }
 
+
+
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, language = get_locale(), ...) {
@@ -362,25 +364,18 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
   x.mo <- as.mo(x, language = language, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
   
-  x.phylum <- mo_phylum(x.mo)
+  x <- rep(NA_character_, length(x))
-  # DETERMINE GRAM STAIN FOR BACTERIA
-  # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
-  # It says this:
-  # Kingdom Bacteria (Cavalier-Smith, 2002)
-  #    Subkingdom Posibacteria (Cavalier-Smith, 2002)
-  #   Direct Children:
-  #       Phylum  Actinobacteria (Cavalier-Smith, 2002)
-  #       Phylum  Chloroflexi (Garrity and Holt, 2002)
-  #       Phylum  Firmicutes (corrig. Gibbons and Murray, 1978)
-  #       Phylum  Tenericutes (Murray, 1984)
-  x <- NA_character_
   # make all bacteria Gram negative
   x[mo_kingdom(x.mo) == "Bacteria"] <- "Gram-negative"
-  # overwrite these phyla with Gram positive
+  # overwrite these 4 phyla with Gram-positives
-  x[x.phylum %in% c("Actinobacteria",
+  # Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097 (Cavalier-Smith, 2002)
-                    "Chloroflexi",
+  x[(mo_phylum(x.mo) %in% c("Actinobacteria",
-                    "Firmicutes",
+                            "Chloroflexi",
-                    "Tenericutes")
+                            "Firmicutes",
+                            "Tenericutes") &
+       # but class Negativicutes (of phylum Firmicutes) are Gram-negative!
+       mo_class(x.mo) != "Negativicutes")
+    # and of course our own ID for Gram-positives
     | x.mo == "B_GRAMP"] <- "Gram-positive"
   
   load_mo_failures_uncertainties_renamed(metadata)
@@ -475,11 +470,10 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
   }
   
   # show used version number once per session (pkg_env will reload every session)
-  if (message_not_thrown_before("intrinsic_resistant_version", entire_session = TRUE)) {
+  if (message_not_thrown_before("intrinsic_resistant_version.mo", entire_session = TRUE)) {
     message_("Determining intrinsic resistance based on ",
              format_eucast_version_nr(3.2, markdown = FALSE), ". ",
              font_red("This note will be shown once per session."))
-    remember_thrown_message("intrinsic_resistant_version", entire_session = TRUE)
   }
   
   # runs against internal vector: INTRINSIC_R (see zzz.R)
@@ -723,16 +717,17 @@ mo_validate <- function(x, property, language, ...) {
   
   if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
     # special case for mo_* functions where class is already <mo>
-    return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
+    x <- MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE]
-  }
 
-  # try to catch an error when inputting an invalid argument
+  } else {
-  # so the 'call.' can be set to FALSE
+    # try to catch an error when inputting an invalid argument
-  tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
+    # so the 'call.' can be set to FALSE
-           error = function(e) stop(e$message, call. = FALSE))
+    tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
+             error = function(e) stop(e$message, call. = FALSE))
     
-  if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
+    if (!all(x[!is.na(x)] %in% MO_lookup[, property, drop = TRUE]) | has_Becker_or_Lancefield) {
-    x <- exec_as.mo(x, property = property, language = language, ...)
+      x <- exec_as.mo(x, property = property, language = language, ...)
+    }
   }
   
   if (property == "mo") {
@@ -754,8 +749,7 @@ find_mo_col <- function(fn) {
   }, silent = TRUE)
   if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
     if (message_not_thrown_before(fn = fn)) {
-      message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
+      message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
-      remember_thrown_message(fn = fn)
     }
     return(df[, mo, drop = TRUE])
   } else {

R/plot.R

@@ -25,16 +25,15 @@
 
 #' Plotting for Classes `rsi`, `mic` and `disk`
 #' 
-#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base R and `ggplot2`.
+#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
-#' @inheritSection lifecycle Stable Lifecycle
+#' @inheritSection lifecycle Maturing Lifecycle
 #' @inheritSection AMR Read more on Our Website!
-#' @param x,data MIC values created with [as.mic()] or disk diffusion values created with [as.disk()]
+#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
-#' @param mapping aesthetic mappings to use for [`ggplot()`][ggplot2::ggplot()]
-#' @param main,title title of the plot
-#' @param xlab,ylab axis title
 #' @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()]
 #' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
+#' @param main,title title of the plot
+#' @param xlab,ylab axis title
 #' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
 #' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
@@ -46,7 +45,7 @@
 #' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
 #' @name plot
 #' @rdname plot
-#' @return The `ggplot` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
+#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
 #' @param ... arguments passed on to [as.rsi()]
 #' @examples 
 #' some_mic_values <- random_mic(size = 100)
@@ -63,9 +62,9 @@
 #' 
 #' \donttest{
 #' if (require("ggplot2")) {
-#'   ggplot(some_mic_values)
+#'   autoplot(some_mic_values)
-#'   ggplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
+#'   autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
-#'   ggplot(some_rsi_values)
+#'   autoplot(some_rsi_values)
 #' }
 #' }
 NULL
@@ -75,22 +74,22 @@ NULL
 #' @export
 #' @rdname plot
 plot.mic <- function(x,
-                     main = paste("MIC values of", deparse(substitute(x))),
-                     ylab = "Frequency",
-                     xlab = "Minimum Inhibitory Concentration (mg/L)",
                      mo = NULL,
                      ab = NULL,
                      guideline = "EUCAST",
+                     main = paste("MIC values of", deparse(substitute(x))),
+                     ylab = "Frequency",
+                     xlab = "Minimum Inhibitory Concentration (mg/L)",
                      colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
                      language = get_locale(),
                      expand = TRUE,
                      ...) {
-  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -161,12 +160,12 @@ plot.mic <- function(x,
 #' @export
 #' @noRd
 barplot.mic <- function(height,
-                        main = paste("MIC values of", deparse(substitute(height))),
-                        ylab = "Frequency",
-                        xlab = "Minimum Inhibitory Concentration (mg/L)",
                         mo = NULL,
                         ab = NULL,
                         guideline = "EUCAST",
+                        main = paste("MIC values of", deparse(substitute(height))),
+                        ylab = "Frequency",
+                        xlab = "Minimum Inhibitory Concentration (mg/L)",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
                         language = get_locale(),
                         expand = TRUE,
@@ -202,28 +201,27 @@ barplot.mic <- function(height,
        ...)
 }
 
-#' @method ggplot mic
+#' @method autoplot mic
 #' @rdname plot
 # will be exported using s3_register() in R/zzz.R
-ggplot.mic <- function(data,
+autoplot.mic <- function(object,
-                       mapping = NULL,
+                         mo = NULL,
-                       title = paste("MIC values of", deparse(substitute(data))),
+                         ab = NULL,
-                       ylab = "Frequency",
+                         guideline = "EUCAST",
-                       xlab = "Minimum Inhibitory Concentration (mg/L)",
+                         title = paste("MIC values of", deparse(substitute(object))),
-                       mo = NULL,
+                         ylab = "Frequency",
-                       ab = NULL,
+                         xlab = "Minimum Inhibitory Concentration (mg/L)",
-                       guideline = "EUCAST",
+                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                       colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+                         language = get_locale(),
-                       language = get_locale(),
+                         expand = TRUE,
-                       expand = TRUE,
+                         ...) {
-                       ...) {
   stop_ifnot_installed("ggplot2")
-  meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -243,7 +241,7 @@ ggplot.mic <- function(data,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
   
-  x <- plot_prepare_table(data, expand = expand)
+  x <- plot_prepare_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(x = x, 
                                               mo = mo, 
                                               ab = ab,
@@ -262,22 +260,20 @@ ggplot.mic <- function(data,
                     levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
                                            language = language),
                     ordered = TRUE)
-  if (!is.null(mapping)) {
+  p <- ggplot2::ggplot(df)
-    p <- ggplot2::ggplot(df, mapping = mapping)
-  } else {
-    p <- ggplot2::ggplot(df)
-  }
   
   if (any(colours_RSI %in% cols_sub$cols)) {
     vals <- c("Resistant" = colours_RSI[1],
               "Susceptible" = colours_RSI[2],
-              "Incr. exposure" = colours_RSI[3],
+              "Susceptible, incr. exp." = colours_RSI[3],
               "Intermediate" = colours_RSI[3])
     names(vals) <- translate_AMR(names(vals), language = language)
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) + 
+      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
       ggplot2::scale_fill_manual(values = vals,
-                                 name = NULL)
+                                 name = NULL,
+                                 limits = force)
   } else {
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
@@ -287,6 +283,7 @@ ggplot.mic <- function(data,
     ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
 }
 
+
 #' @method plot disk
 #' @export
 #' @importFrom graphics barplot axis mtext legend
@@ -420,21 +417,20 @@ barplot.disk <- function(height,
        ...)
 }
 
-#' @method ggplot disk
+#' @method autoplot disk
 #' @rdname plot
 # will be exported using s3_register() in R/zzz.R
-ggplot.disk <- function(data,
+autoplot.disk <- function(object,
-                        mapping = NULL,
+                          mo = NULL,
-                        title = paste("Disk zones of", deparse(substitute(data))),
+                          ab = NULL,
-                        ylab = "Frequency",
+                          title = paste("Disk zones of", deparse(substitute(object))),
-                        xlab = "Disk diffusion diameter (mm)",
+                          ylab = "Frequency",
-                        mo = NULL,
+                          xlab = "Disk diffusion diameter (mm)",
-                        ab = NULL,
+                          guideline = "EUCAST",
-                        guideline = "EUCAST",
+                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                        colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+                          language = get_locale(),
-                        language = get_locale(),
+                          expand = TRUE,
-                        expand = TRUE,
+                          ...) {
-                        ...) {
   stop_ifnot_installed("ggplot2")
   meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
@@ -461,7 +457,7 @@ ggplot.disk <- function(data,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
   
-  x <- plot_prepare_table(data, expand = expand)
+  x <- plot_prepare_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(x = x,
                                               mo = mo,
                                               ab = ab,
@@ -481,22 +477,20 @@ ggplot.disk <- function(data,
                     levels = translate_AMR(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
                                            language = language),
                     ordered = TRUE)
-  if (!is.null(mapping)) {
+  p <- ggplot2::ggplot(df)
-    p <- ggplot2::ggplot(df, mapping = mapping)
-  } else {
-    p <- ggplot2::ggplot(df)
-  }
   
   if (any(colours_RSI %in% cols_sub$cols)) {
     vals <- c("Resistant" = colours_RSI[1],
               "Susceptible" = colours_RSI[2],
-              "Incr. exposure" = colours_RSI[3],
+              "Susceptible, incr. exp." = colours_RSI[3],
               "Intermediate" = colours_RSI[3])
     names(vals) <- translate_AMR(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)
       ggplot2::scale_fill_manual(values = vals,
-                                 name = NULL)
+                                 name = NULL,
+                                 limits = force)
   } else {
     p <- p +
       ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
@@ -604,17 +598,16 @@ barplot.rsi <- function(height,
   axis(2, seq(0, max(x)))
 }
 
-#' @method ggplot rsi
+#' @method autoplot rsi
 #' @rdname plot
 # will be exported using s3_register() in R/zzz.R
-ggplot.rsi <- function(data,
+autoplot.rsi <- function(object,
-                       mapping = NULL,
+                         title = paste("Resistance Overview of", deparse(substitute(object))),
-                       title = paste("Resistance Overview of", deparse(substitute(data))),
+                         xlab = "Antimicrobial Interpretation",
-                       xlab = "Antimicrobial Interpretation",
+                         ylab = "Frequency",
-                       ylab = "Frequency",
+                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                       colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
+                         language = get_locale(),
-                       language = get_locale(),
+                         ...) {
-                       ...) {
   stop_ifnot_installed("ggplot2")
   meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
@@ -640,19 +633,15 @@ ggplot.rsi <- function(data,
     colours_RSI <- rep(colours_RSI, 3)
   }
   
-  df <- as.data.frame(table(data), stringsAsFactors = TRUE)
+  df <- as.data.frame(table(object), stringsAsFactors = TRUE)
   colnames(df) <- c("rsi", "count")
-  if (!is.null(mapping)) {
+  ggplot2::ggplot(df) +
-    p <- ggplot2::ggplot(df, mapping = mapping)
-  } else {
-    p <- ggplot2::ggplot(df)
-  }
-  
-  p +
     ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) + 
+    # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
     ggplot2::scale_fill_manual(values = c("R" = colours_RSI[1],
                                           "S" = colours_RSI[2],
-                                          "I" = colours_RSI[3])) +
+                                          "I" = colours_RSI[3]),
+                               limits = force) +
     ggplot2::labs(title = title, x = xlab, y = ylab) +
     ggplot2::theme(legend.position = "none")
 }
@@ -663,6 +652,7 @@ plot_prepare_table <- function(x, expand) {
   if (is.mic(x)) {
     if (expand == TRUE) {
       # expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
+      valid_lvls <- levels(x)
       extra_range <- max(x) / 2
       while (min(extra_range) / 2 > min(x)) {
         extra_range <- c(min(extra_range) / 2, extra_range)
@@ -671,7 +661,7 @@ plot_prepare_table <- function(x, expand) {
       extra_range <- rep(0, length(extra_range))
       names(extra_range) <- nms
       x <- table(droplevels(x, as.mic = FALSE))
-      extra_range <- extra_range[!names(extra_range) %in% names(x)]
+      extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
       x <- as.table(c(x, extra_range))
     } else {
       x <- table(droplevels(x, as.mic = FALSE))
@@ -696,7 +686,7 @@ plot_prepare_table <- function(x, expand) {
 plot_name_of_I <- function(guideline) {
   if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
     # interpretation since 2019
-    "Incr. exposure"
+    "Susceptible, incr. exp."
   } else {
     # interpretation until 2019
     "Intermediate"

R/proportion.R

@@ -167,12 +167,14 @@ resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,
                        only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "R",
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = "R",
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -181,12 +183,14 @@ susceptibility <- function(...,
                            minimum = 30,
                            as_percent = FALSE,
                            only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("S", "I"),
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = c("S", "I"),
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -195,12 +199,14 @@ proportion_R <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "R",
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = "R",
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -209,12 +215,14 @@ proportion_IR <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("I", "R"),
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = c("I", "R"),
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -223,12 +231,14 @@ proportion_I <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "I",
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = "I",
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -237,12 +247,14 @@ proportion_SI <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = c("S", "I"),
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = c("S", "I"),
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -251,12 +263,14 @@ proportion_S <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
-  rsi_calc(...,
+  tryCatch(
-           ab_result = "S",
+    rsi_calc(...,
-           minimum = minimum,
+             ab_result = "S",
-           as_percent = as_percent,
+             minimum = minimum,
-           only_all_tested = only_all_tested,
+             as_percent = as_percent,
-           only_count = FALSE)
+             only_all_tested = only_all_tested,
+             only_count = FALSE),
+    error = function(e) stop_(e$message, call = -5))
 }
 
 #' @rdname proportion
@@ -268,13 +282,15 @@ proportion_df <- function(data,
                           as_percent = FALSE,
                           combine_SI = TRUE,
                           combine_IR = FALSE) {
-  rsi_calc_df(type = "proportion",
+  tryCatch(
-              data = data,
+    rsi_calc_df(type = "proportion",
-              translate_ab = translate_ab,
+                data = data,
-              language = language,
+                translate_ab = translate_ab,
-              minimum = minimum,
+                language = language,
-              as_percent = as_percent,
+                minimum = minimum,
-              combine_SI = combine_SI,
+                as_percent = as_percent,
-              combine_IR = combine_IR,
+                combine_SI = combine_SI,
-              combine_SI_missing = missing(combine_SI))
+                combine_IR = combine_IR,
+                combine_SI_missing = missing(combine_SI)),
+    error = function(e) stop_(e$message, call = -5))
 }

R/random.R

@@ -27,12 +27,12 @@
 #'
 #' 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
+#' @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()]
-#' @param prob_RSI a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)
+#' @param prob_RSI a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
 #' @param ... ignored, only in place to allow future extensions
-#' @details The base R function [sample()] is used for generating values.
+#' @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.
 #' @return class `<mic>` for [random_mic()] (see [as.mic()]) and class `<disk>` for [random_disk()] (see [as.disk()])
@@ -55,19 +55,36 @@
 #' random_disk(100, "Klebsiella pneumoniae", "ampicillin")    # range 11-17
 #' random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 12-27
 #' }
-random_mic <- function(size, mo = NULL, ab = NULL, ...) {
+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)
+  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  if (is.null(size)) {
+    size <- NROW(get_current_data(arg_name = "size", call = -3))
+  }
   random_exec("MIC", size = size, mo = mo, ab = ab)
 }
 
 #' @rdname random
 #' @export
-random_disk <- function(size, mo = NULL, ab = NULL, ...) {
+random_disk <- 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)
+  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  if (is.null(size)) {
+    size <- NROW(get_current_data(arg_name = "size", call = -3))
+  }
   random_exec("DISK", size = size, mo = mo, ab = ab)
 }
 
 #' @rdname random
 #' @export
-random_rsi <- function(size, prob_RSI = c(0.33, 0.33, 0.33), ...) {
+random_rsi <- function(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) {
+  meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
+  meet_criteria(prob_RSI, allow_class = c("numeric", "integer"), has_length = 3)
+  if (is.null(size)) {
+    size <- NROW(get_current_data(arg_name = "size", call = -3))
+  }
   sample(as.rsi(c("R", "S", "I")), size = size, replace = TRUE, prob = prob_RSI)
 }
 
@@ -105,21 +122,20 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
   }
  
   if (type == "MIC") {
-    # all valid MIC levels
+    # set range
-    valid_range <- as.mic(levels(as.mic(1)))
+    mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
-    set_range_max <- max(df$breakpoint_R)
+
-    if (log(set_range_max, 2) %% 1 == 0) {
+    # get highest/lowest +/- random 1 to 3 higher factors of two
-      # return powers of 2
+    max_range <- mic_range[min(length(mic_range),
-      valid_range <- unique(as.double(valid_range))
+                               which(mic_range == max(df$breakpoint_R)) + sample(c(1:3), 1))]
-      # add 1-3 higher MIC levels to set_range_max
+    min_range <- mic_range[max(1,
-      set_range_max <- 2 ^ (log(set_range_max, 2) + sample(c(1:3), 1))
+                               which(mic_range == min(df$breakpoint_S)) - sample(c(1:3), 1))]
-      set_range <- as.mic(valid_range[log(valid_range, 2) %% 1 == 0 & valid_range <= set_range_max])
+
-    } else {
+    mic_range_new <- mic_range[mic_range <= max_range & mic_range >= min_range]
-      # no power of 2, return factors of 2 to left and right side
+    if (length(mic_range_new) == 0) {
-      valid_mics <- suppressWarnings(as.mic(set_range_max / (2 ^ c(-3:3))))
+      mic_range_new <- mic_range
-      set_range <- valid_mics[!is.na(valid_mics)]
     }
-    out <- as.mic(sample(set_range, size = size, replace = TRUE))
+    out <- as.mic(sample(mic_range_new, size = size, replace = TRUE))
     # 50% chance that lowest will get <= and highest will get >=
     if (stats::runif(1) > 0.5) {
       out[out == min(out)] <- paste0("<=", out[out == min(out)])

R/resistance_predict.R

@@ -23,10 +23,11 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Predict antimicrobial resistance
+#' 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
 #' @param year_min lowest year to use in the prediction model, dafaults to the lowest year in `col_date`
@@ -99,9 +100,9 @@
 #'                        info = FALSE,
 #'                        minimum = 15)
 #'                        
-#'   ggplot(data)
+#'   autoplot(data)
 #'
-#'   ggplot(as.data.frame(data),
+#'   ggplot(data,
 #'          aes(x = year)) +
 #'     geom_col(aes(y = value),
 #'              fill = "grey75") +
@@ -351,20 +352,6 @@ plot.resistance_predict <- function(x, main = paste("Resistance Prediction of",
          col = "grey40")
 }
 
-
-#' @method ggplot resistance_predict
-#' @rdname resistance_predict
-# will be exported using s3_register() in R/zzz.R
-ggplot.resistance_predict <- function(x,
-                               main = paste("Resistance Prediction of", x_name),
-                               ribbon = TRUE,
-                               ...) {
-  x_name <- paste0(ab_name(attributes(x)$ab), " (", attributes(x)$ab, ")")
-  meet_criteria(main, allow_class = "character", has_length = 1)
-  meet_criteria(ribbon, allow_class = "logical", has_length = 1)
-  ggplot_rsi_predict(x = x, main = main, ribbon = ribbon, ...)
-}
-
 #' @rdname resistance_predict
 #' @export
 ggplot_rsi_predict <- function(x,
@@ -407,3 +394,23 @@ ggplot_rsi_predict <- function(x,
                         colour = "grey40")
   p
 }
+
+#' @method autoplot resistance_predict
+#' @rdname resistance_predict
+# will be exported using s3_register() in R/zzz.R
+autoplot.resistance_predict <- function(object,
+                                        main = paste("Resistance Prediction of", x_name),
+                                        ribbon = TRUE,
+                                        ...) {
+  x_name <- paste0(ab_name(attributes(object)$ab), " (", attributes(object)$ab, ")")
+  meet_criteria(main, allow_class = "character", has_length = 1)
+  meet_criteria(ribbon, allow_class = "logical", has_length = 1)
+  ggplot_rsi_predict(x = object, main = main, ribbon = ribbon, ...)
+}
+
+#' @method fortify resistance_predict
+#' @noRd
+# will be exported using s3_register() in R/zzz.R
+fortify.resistance_predict <- function(model, data, ...) {
+  as.data.frame(model)
+}

R/rsi.R

@@ -89,7 +89,7 @@
 #'   A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
 #' - **S = Susceptible**\cr
 #'   A microorganism is categorised as *Susceptible, standard dosing regimen*, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
-#' - **I = Increased exposure, but still susceptible**\cr
+#' - **I = Susceptible, Increased exposure**\cr
 #'   A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
 #'
 #' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
@@ -284,10 +284,25 @@ as.rsi.default <- function(x, ...) {
       }
     }
     
-    x <- as.character(unlist(x))
+    # trim leading and trailing spaces, new lines, etc.
+    x <- trimws2(as.character(unlist(x)))
     x.bak <- x
-    
     na_before <- length(x[is.na(x) | x == ""])
+    
+    # correct for translations
+    trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    trans_S <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    trans_I <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern %in% c("Incr. exposure", "Susceptible, incr. exp.", "Intermediate")),
+                                   LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED %in% colnames(TRANSLATIONS)]])
+    x <- gsub(paste0(unique(trans_R[!is.na(trans_R)]), collapse = "|"), "R", x, ignore.case = TRUE)
+    x <- gsub(paste0(unique(trans_S[!is.na(trans_S)]), collapse = "|"), "S", x, ignore.case = TRUE)
+    x <- gsub(paste0(unique(trans_I[!is.na(trans_I)]), collapse = "|"), "I", x, ignore.case = TRUE)
+    # replace all English textual input
+    x[x %like% "([^a-z]|^)res(is(tant)?)?"] <- "R"
+    x[x %like% "([^a-z]|^)sus(cep(tible)?)?"] <- "S"
+    x[x %like% "([^a-z]|^)int(er(mediate)?)?|incr.*exp"] <- "I"
     # remove all spaces
     x <- gsub(" +", "", x)
     # remove all MIC-like values: numbers, operators and periods
@@ -295,6 +310,8 @@ as.rsi.default <- function(x, ...) {
     # remove everything between brackets, and 'high' and 'low'
     x <- gsub("([(].*[)])", "", x)
     x <- gsub("(high|low)", "", x, ignore.case = TRUE)
+    # some labs now report "H" instead of "I" to not interfere with EUCAST prior to 2019
+    x <- gsub("H", "I", x, ignore.case = TRUE)
     # disallow more than 3 characters
     x[nchar(x) > 3] <- NA
     # set to capitals
@@ -349,7 +366,7 @@ as.rsi.mic <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
     # try to get current column, which will only be available when in across()
     ab <- tryCatch(cur_column_dplyr(),
                    error = function(e) ab)
@@ -395,13 +412,18 @@ as.rsi.mic <- function(x,
     uti <- rep(uti, length(x))
   }
   
-  message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
+  agent_formatted <- paste0("'", font_bold(ab), "'")
-           ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
+  agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
-           ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found, 
+  if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
+    agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
+  }
+  message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+           agent_formatted,
+           mo_var_found, 
            " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
                                     font_bold(guideline_coerced),
                                     "manually defined 'reference_data'"),
-           " ... ",
+           "... ",
            appendLF = FALSE,
            as_note = FALSE)
   
@@ -438,7 +460,7 @@ as.rsi.disk <- function(x,
   
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", 0)), error = function(e) FALSE)) {
+  if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
     # try to get current column, which will only be available when in across()
     ab <- tryCatch(cur_column_dplyr(),
                    error = function(e) ab)
@@ -484,13 +506,18 @@ as.rsi.disk <- function(x,
     uti <- rep(uti, length(x))
   }
   
-  message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (",
+  agent_formatted <- paste0("'", font_bold(ab), "'")
-           ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
+  agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
-           ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found, 
+  if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
+    agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
+  }
+  message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
+           agent_formatted,
+           mo_var_found, 
            " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
                                     font_bold(guideline_coerced),
                                     "manually defined 'reference_data'"),
-           " ... ",
+           "... ",
            appendLF = FALSE,
            as_note = FALSE)
   
@@ -624,10 +651,9 @@ as.rsi.data.frame <- function(x,
     if (is.null(col_mo.bak)) {
       col_mo <- search_type_in_df(x = x, type = "mo")
     }
+    x_mo <- as.mo(x[, col_mo, drop = TRUE])
   }
 
-  x_mo <- as.mo(x %pm>% pm_pull(col_mo))
-
   for (i in seq_len(length(ab_cols))) {
     if (types[i] == "mic") {
       x[, ab_cols[i]] <- as.rsi(x = x %pm>% 
@@ -658,11 +684,11 @@ as.rsi.data.frame <- function(x,
       show_message <- FALSE
       ab <- ab_cols[i]
       ab_coerced <- suppressWarnings(as.ab(ab))
-      if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I"), na.rm = TRUE)) {
+      if (!all(x[, ab_cols[i], drop = TRUE] %in% c("R", "S", "I", NA), na.rm = TRUE)) {
         show_message <- TRUE
         # only print message if values are not already clean
         message_("=> Cleaning values in column '", font_bold(ab), "' (",
-                 ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
+                 ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
                  ab_name(ab_coerced, tolower = TRUE), ")... ",
                  appendLF = FALSE,
                  as_note = FALSE)
@@ -670,7 +696,7 @@ as.rsi.data.frame <- function(x,
         show_message <- TRUE
         # only print message if class not already set
         message_("=> Assigning class <rsi> to already clean column '", font_bold(ab), "' (",
-                 ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""),
+                 ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
                  ab_name(ab_coerced, tolower = TRUE), ")... ",
                  appendLF = FALSE,
                  as_note = FALSE)
@@ -750,7 +776,6 @@ exec_as.rsi <- function(method,
   if (guideline_coerced != guideline) {
     if (message_not_thrown_before("as.rsi")) {
       message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
-      remember_thrown_message("as.rsi")
     }
   }
   
@@ -789,7 +814,6 @@ exec_as.rsi <- function(method,
       if (guideline_coerced %unlike% "EUCAST") {
         if (message_not_thrown_before("as.rsi2")) {
           warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
-          remember_thrown_message("as.rsi2")
         }
       } else {
         new_rsi[i] <- "R"
@@ -854,7 +878,6 @@ exec_as.rsi <- function(method,
     message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
     if (message_not_thrown_before("as.rsi3")) {
       warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
-      remember_thrown_message("as.rsi3")
     }
     warned <- TRUE
   }
@@ -915,7 +938,7 @@ freq.rsi <- function(x, ...) {
   if (!is.na(ab)) {
     cleaner::freq.default(x = x, ...,
                           .add_header = list(
-                            Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", ab_atc(ab), ")"),
+                            Drug = paste0(ab_name(ab, language = NULL), " (", ab, ", ", paste(ab_atc(ab), collapse = "/"), ")"),
                             `Drug group` = ab_group(ab, language = NULL),
                             `%SI` = percentage(susceptibility(x, minimum = 0, as_percent = FALSE),
                                                digits = digits)))
@@ -1038,6 +1061,15 @@ unique.rsi <- function(x, incomparables = FALSE, ...) {
   y
 }
 
+#' @method rep rsi
+#' @export
+#' @noRd
+rep.rsi <- function(x, ...) {
+  y <- NextMethod()
+  attributes(y) <- attributes(x)
+  y
+}
+
 check_reference_data <- function(reference_data) {
   if (!identical(reference_data, AMR::rsi_translation)) {
     class_rsi <- vapply(FUN.VALUE = character(1), rsi_translation, function(x) paste0("<", class(x), ">", collapse = " and "))

R/rsi_calc.R

@@ -27,7 +27,7 @@ dots2vars <- function(...) {
   # this function is to give more informative output about 
   # variable names in count_* and proportion_* functions
   dots <- substitute(list(...))
-  vector_and(as.character(dots)[2:length(dots)], quotes = FALSE)
+  as.character(dots)[2:length(dots)]
 }
 
 rsi_calc <- function(...,
@@ -152,7 +152,6 @@ rsi_calc <- function(...,
                "  your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n",
                "  your_data %>% mutate(across(where(is.rsi.eligible), as.rsi))",
                call = FALSE)
-      remember_thrown_message("rsi_calc")
     }
   }
   
@@ -163,8 +162,30 @@ rsi_calc <- function(...,
   if (denominator < minimum) {
     if (data_vars != "") {
       data_vars <- paste(" for", data_vars)
+      # also add group name if used in dplyr::group_by()
+      cur_group <- import_fn("cur_group", "dplyr", error_on_fail = FALSE)
+      if (!is.null(cur_group)) {
+        group_df <- tryCatch(cur_group(), error = function(e) data.frame())
+        if (NCOL(group_df) > 0) {
+          # transform factors to characters
+          group <- vapply(FUN.VALUE = character(1), group_df, function(x) {
+            if (is.numeric(x)) {
+              format(x)
+            } else if (is.logical(x)) {
+              as.character(x)
+            } else {
+              paste0('"', x, '"')
+            }
+          })
+          data_vars <- paste0(data_vars, " in group: ", paste0(names(group), " = ", group, collapse = ", "))
+        }
+      }
     }
-    warning_("Introducing NA: only ", denominator, " results available", data_vars, " (`minimum` = ", minimum, ").", call = FALSE)
+    warning_("Introducing NA: ",
+             ifelse(denominator == 0, "no", paste("only", denominator)),
+             " results available",
+             data_vars,
+             " (`minimum` = ", minimum, ").", call = FALSE)
     fraction <- NA_real_
   } else {
     fraction <- numerator / denominator
@@ -206,7 +227,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
   translate_ab <- get_translate_ab(translate_ab)
   
   # select only groups and antibiotics
-  if (inherits(data, "grouped_df")) {
+  if (is_null_or_grouped_tbl(data)) {
     data_has_groups <- TRUE
     groups <- setdiff(names(attributes(data)$groups), ".rows")
     data <- data[, c(groups, colnames(data)[vapply(FUN.VALUE = logical(1), data, is.rsi)]), drop = FALSE]

R/translate.R

@@ -29,7 +29,7 @@
 #' @inheritSection lifecycle Stable Lifecycle
 #' @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/master/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.). 
 #'
-#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. Please note that currently not all these languages have translations available for all antimicrobial agents and colloquial microorganism names. 
+#' Currently supported languages are: `r vector_and(gsub(";.*", "", ISOcodes::ISO_639_2[which(ISOcodes::ISO_639_2$Alpha_2 %in% LANGUAGES_SUPPORTED), "Name"]), quotes = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.
 #'
 #' Please suggest your own translations [by creating a new issue on our repository](https://github.com/msberends/AMR/issues/new?title=Translations).
 #'
@@ -53,17 +53,17 @@
 #' mo_name("CoNS", language = "en")
 #' #> "Coagulase-negative Staphylococcus (CoNS)"
 #'
-#' # German
+#' # Danish
-#' mo_name("CoNS", language = "de")
+#' mo_name("CoNS", language = "nl")
-#' #> "Koagulase-negative Staphylococcus (KNS)"
+#' #> "Koagulase-negative stafylokokker (CoNS)"
 #' 
 #' # Dutch
 #' mo_name("CoNS", language = "nl")
 #' #> "Coagulase-negatieve Staphylococcus (CNS)"
 #'
-#' # Spanish
+#' # German
-#' mo_name("CoNS", language = "es")
+#' mo_name("CoNS", language = "de")
-#' #> "Staphylococcus coagulasa negativo (SCN)"
+#' #> "Koagulase-negative Staphylococcus (KNS)"
 #'
 #' # Italian
 #' mo_name("CoNS", language = "it")
@@ -72,6 +72,10 @@
 #' # Portuguese
 #' mo_name("CoNS", language = "pt")
 #' #> "Staphylococcus coagulase negativo (CoNS)"
+#'
+#' # Spanish
+#' mo_name("CoNS", language = "es")
+#' #> "Staphylococcus coagulasa negativo (SCN)"
 get_locale <- function() {
   # AMR versions 1.3.0 and prior used the environmental variable:
   if (!identical("", Sys.getenv("AMR_locale"))) {
@@ -108,6 +112,8 @@ coerce_language_setting <- function(lang) {
     "de"
   } else if (grepl("^(Dutch|Nederlands|nl_|NL_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "nl"
+  } else if (grepl("^(Danish|Dansk|da_|DA_)", lang, ignore.case = FALSE, perl = TRUE)) {
+    "da"
   } else if (grepl("^(Spanish|Espa.+ol|es_|ES_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "es"
   } else if (grepl("^(Italian|Italiano|it_|IT_)", lang, ignore.case = FALSE, perl = TRUE)) {
@@ -136,7 +142,7 @@ translate_AMR <- function(from,
     return(from)
   }
   
-  df_trans <- translations_file # internal data file
+  df_trans <- TRANSLATIONS # internal data file
   from.bak <- from
   from_unique <- unique(from)
   from_unique_translated <- from_unique

R/vctrs.R

@@ -0,0 +1,74 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2021 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/   #
+# ==================================================================== #
+
+# These are all S3 implementations for the vctrs package, 
+# that is used internally by tidyverse packages such as dplyr.
+# 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
+vec_ptype2.character.ab <- function(x, y, ...) {
+  x
+}
+vec_ptype2.ab.character <- function(x, y, ...) {
+  y
+}
+vec_cast.character.ab <- function(x, to, ...) {
+  unclass(x)
+}
+
+# S3: mo
+vec_ptype2.character.mo <- function(x, y, ...) {
+  x
+}
+vec_ptype2.mo.character <- function(x, y, ...) {
+  y
+}
+vec_cast.character.mo <- function(x, to, ...) {
+  unclass(x)
+}
+
+# S3: disk
+vec_ptype2.integer.disk <- function(x, y, ...) {
+  x
+}
+vec_ptype2.disk.integer <- function(x, y, ...) {
+  y
+}
+vec_cast.integer.disk <- function(x, to, ...) {
+  unclass(x)
+}
+
+# S3: ab_selector
+# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
+vec_ptype2.character.ab_selector <- function(x, y, ...) {
+  x
+}
+vec_ptype2.ab_selector.character <- function(x, y, ...) {
+  y
+}
+vec_cast.character.ab_selector <- function(x, to, ...) {
+  unclass(x)
+}

R/zzz.R

@@ -38,7 +38,7 @@ if (utf8_supported && !is_latex) {
   pkg_env$info_icon <- "i"
 }
 
-.onLoad <- function(libname, pkgname) {
+.onLoad <- function(...) {
   # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
   # without the need to depend on other packages. This was suggested by the 
   # developers of the vctrs package: 
@@ -56,15 +56,29 @@ if (utf8_supported && !is_latex) {
   # Support for frequency tables from the cleaner package
   s3_register("cleaner::freq", "mo")
   s3_register("cleaner::freq", "rsi")
-  # Support from skim() from the skimr package
+  # Support for skim() from the skimr package
   s3_register("skimr::get_skimmers", "mo")
   s3_register("skimr::get_skimmers", "rsi")
   s3_register("skimr::get_skimmers", "mic")
   s3_register("skimr::get_skimmers", "disk")
-  s3_register("ggplot2::ggplot", "rsi")
+  # Support for autoplot() from the ggplot2 package
-  s3_register("ggplot2::ggplot", "mic")
+  s3_register("ggplot2::autoplot", "rsi")
-  s3_register("ggplot2::ggplot", "disk")
+  s3_register("ggplot2::autoplot", "mic")
-  s3_register("ggplot2::ggplot", "resistance_predict")
+  s3_register("ggplot2::autoplot", "disk")
+  s3_register("ggplot2::autoplot", "resistance_predict")
+  # Support vctrs package for use in e.g. dplyr verbs
+  s3_register("vctrs::vec_ptype2", "ab.character")
+  s3_register("vctrs::vec_ptype2", "character.ab")
+  s3_register("vctrs::vec_cast", "character.ab")
+  s3_register("vctrs::vec_ptype2", "mo.character")
+  s3_register("vctrs::vec_ptype2", "character.mo")
+  s3_register("vctrs::vec_cast", "character.mo")
+  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", "disk.integer")
+  s3_register("vctrs::vec_ptype2", "integer.disk")
+  s3_register("vctrs::vec_cast", "integer.disk")
   
   # if mo source exists, fire it up (see mo_source())
   try({
@@ -75,13 +89,18 @@ if (utf8_supported && !is_latex) {
   
   
   # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
+  # they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
   assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
   assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
   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 --------------------------------------------------------
 

_pkgdown.yml

@@ -32,6 +32,7 @@ development:
 
 news:
   one_page: true
+  cran_dates: true
 
 navbar:
   title: "AMR (for R)"
@@ -88,32 +89,11 @@ navbar:
     - text: "Source Code"
       icon: "fab fa-github"
       href: "https://github.com/msberends/AMR"
-    - text: "Survey"
+    # - text: "Survey"
-      icon: "fa-clipboard-list"
+    #   icon: "fa-clipboard-list"
-      href: "survey.html"
+    #   href: "survey.html"
 
 reference:
-  - title: "Background information on included data"
-    desc: >
-      Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
-      for more information about how to work with functions in this package.
-    contents:
-    - "`AMR`"
-    - "`example_isolates`"
-    - "`microorganisms`"
-    - "`microorganisms.codes`"
-    - "`microorganisms.old`"
-    - "`antibiotics`"
-    - "`intrinsic_resistant`"
-    - "`dosage`"
-    - "`catalogue_of_life`"
-    - "`catalogue_of_life_version`"
-    - "`WHOCC`"
-    - "`lifecycle`"
-    - "`example_isolates_unclean`"
-    - "`rsi_translation`"
-    - "`WHONET`"
-    
   - title: "Preparing data: microorganisms"
     desc: >
       These functions are meant to get taxonomically valid properties of microorganisms from any input.
@@ -165,6 +145,27 @@ reference:
     - "`resistance_predict`"
     - "`guess_ab_col`"
 
+  - title: "Background information on included data"
+    desc: >
+      Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
+      for more information about how to work with functions in this package.
+    contents:
+    - "`AMR`"
+    - "`example_isolates`"
+    - "`microorganisms`"
+    - "`microorganisms.codes`"
+    - "`microorganisms.old`"
+    - "`antibiotics`"
+    - "`intrinsic_resistant`"
+    - "`dosage`"
+    - "`catalogue_of_life`"
+    - "`catalogue_of_life_version`"
+    - "`WHOCC`"
+    - "`lifecycle`"
+    - "`example_isolates_unclean`"
+    - "`rsi_translation`"
+    - "`WHONET`"
+    
   - title: "Other: miscellaneous functions"
     desc: >
       These functions are mostly for internal use, but some of
@@ -202,20 +203,14 @@ reference:
 authors:
   Matthijs S. Berends:
     href: https://www.rug.nl/staff/m.s.berends/
-  Christian F. Luz:
-    href: https://www.rug.nl/staff/c.f.luz/
-  Alexander W. Friedrich:
-    href: https://www.rug.nl/staff/a.w.friedrich/
-  Bhanu N. M. Sinha:
-    href: https://www.rug.nl/staff/b.sinha/
-  Casper J. Albers:
-    href: https://www.rug.nl/staff/c.j.albers/
-  Corinna Glasner:
-    href: https://www.rug.nl/staff/c.glasner/
 
 template:
-  # this requires the 'preferably' package, https://github.com/amirmasoudabdol/preferably/
+  bootstrap: 3
-  # package: preferably
+  opengraph:
+    twitter:
+      creator: "@msberends"
+      site: "@univgroningen"
+      card: summary_large_image
   assets: "pkgdown/logos" # use logos in this folder
   params:
     noindex: false

data-raw/_install_deps.R

@@ -24,12 +24,22 @@
 # ==================================================================== #
 
 # some old R instances have trouble installing tinytest, so we ship it too
-install.packages("data-raw/tinytest_1.2.4.10.tar.gz")
+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("covr", repos = "https://cran.rstudio.com/")
 
-pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
+pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
-cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
+                     unlist(strsplit(unlist(packageDescription("AMR",
+                                                               fields = c("Suggests", "Enhances", "LinkingTo"))),
+                                     split = ", ?")))
+pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
+cat("################################################\n")
+cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
+cat("################################################\n")
+
+if (.Platform$OS.type != "unix") {
+  # no compiling on Windows here
+  options(install.packages.compile.from.source = FALSE)
+}
 
 to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
 if (length(to_install) == 0) {
@@ -37,10 +47,24 @@ if (length(to_install) == 0) {
 }
 for (i in seq_len(length(to_install))) {
   cat("Installing package", to_install[i], "\n")
-  tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
+  tryCatch(install.packages(to_install[i],
+                            type = "source",
+                            repos = "https://cran.rstudio.com/",
+                            dependencies = c("Depends", "Imports", "LinkingTo"),
+                            quiet = FALSE),
            # message = function(m) invisible(),
            warning = function(w) message(w$message),
            error = function(e) message(e$message))
+  if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
+    tryCatch(install.packages(to_install[i],
+                              type = "binary",
+                              repos = "https://cran.rstudio.com/",
+                              dependencies = c("Depends", "Imports", "LinkingTo"),
+                              quiet = FALSE),
+             # message = function(m) invisible(),
+             warning = function(w) message(w$message),
+             error = function(e) message(e$message))
+  }
 }
 
 to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
@@ -49,9 +73,10 @@ if (length(to_update) == 0) {
   message("\nNothing to update\n")
 }
 for (i in seq_len(length(to_update))) {
-  cat("Updating package", to_update[i], "\n")
+  cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
   tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
            # message = function(m) invisible(),
            warning = function(w) message(w$message),
            error = function(e) message(e$message))
+  cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
 }

data-raw/_internals.R

@@ -34,7 +34,7 @@ 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_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
+EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
                                        skip = 10,
                                        sep = "\t",
                                        stringsAsFactors = FALSE,
@@ -54,7 +54,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
   select(-sorting_rule)
 
 # Translations
-translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
+TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
                                        sep = "\t",
                                        stringsAsFactors = FALSE,
                                        header = TRUE,
@@ -68,7 +68,9 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
                                        quote = "")
 
 # for checking input in `language` argument in e.g. mo_*() and ab_*() functions
-LANGUAGES_SUPPORTED <- sort(c("en", colnames(translations_file)[nchar(colnames(translations_file)) == 2]))
+LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
+
+# 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")) {
@@ -114,60 +116,73 @@ MO_COPS <- create_species_cons_cops("CoPS")
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
 globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
-AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
+AB_AMINOGLYCOSIDES <- antibiotics %>% filter(group %like% "aminoglycoside") %>% pull(ab)
-AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
+AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
-CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
+AB_ANTIFUNGALS <- AB_lookup %>% filter(group %like% "antifungal") %>% pull(ab)
-CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
+AB_ANTIMYCOBACTERIALS <- AB_lookup %>% filter(group %like% "antimycobacterial") %>% pull(ab)
-CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
+AB_CARBAPENEMS <- antibiotics %>% filter(group %like% "carbapenem") %>% pull(ab)
-CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
+AB_CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(ab)
-CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
+AB_CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
-CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
+AB_CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
-FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
+AB_CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
-LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
+AB_CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab)
-GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
+AB_CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab)
-GLYCOPEPTIDES_EXCEPT_LIPO <- GLYCOPEPTIDES[!GLYCOPEPTIDES %in% LIPOGLYCOPEPTIDES]
+AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
-LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide") %>% pull(ab) %>% c("PRL")
+AB_FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>% pull(ab)
-MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
+AB_GLYCOPEPTIDES <- antibiotics %>% filter(group %like% "glycopeptide") %>% pull(ab)
-OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
+AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
-PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
+AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES]
-POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
+AB_LINCOSAMIDES <- antibiotics %>% filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>% pull(ab)
-STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
+AB_MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>% pull(ab)
-TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
+AB_OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
-TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
+AB_PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
-UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
+AB_POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
-BETALACTAMS <- c(PENICILLINS, CEPHALOSPORINS, CARBAPENEMS)
+AB_QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab)
-
+AB_STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
+AB_TETRACYCLINES <- antibiotics %>% filter(group %like% "tetracycline") %>% pull(ab)
+AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
+AB_TRIMETHOPRIMS <- antibiotics %>% filter(group %like% "trimethoprim") %>% pull(ab)
+AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
+AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
+# this will be used for documentation:
 DEFINED_AB_GROUPS <- ls(envir = globalenv())
 DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
 
 # Export to package as internal data ----
-usethis::use_data(eucast_rules_file, 
+usethis::use_data(EUCAST_RULES_DF, 
-                  translations_file,
+                  TRANSLATIONS,
                   LANGUAGES_SUPPORTED,
+                  # EXAMPLE_ISOLATES,
                   MO_CONS,
                   MO_COPS,
-                  AMINOGLYCOSIDES,
+                  AB_AMINOGLYCOSIDES,
-                  AMINOPENICILLINS,
+                  AB_AMINOPENICILLINS,
-                  CARBAPENEMS,
+                  AB_ANTIFUNGALS,
-                  CEPHALOSPORINS,
+                  AB_ANTIMYCOBACTERIALS,
-                  CEPHALOSPORINS_1ST,
+                  AB_CARBAPENEMS,
-                  CEPHALOSPORINS_2ND,
+                  AB_CEPHALOSPORINS,
-                  CEPHALOSPORINS_3RD,
+                  AB_CEPHALOSPORINS_1ST,
-                  CEPHALOSPORINS_EXCEPT_CAZ,
+                  AB_CEPHALOSPORINS_2ND,
-                  FLUOROQUINOLONES,
+                  AB_CEPHALOSPORINS_3RD,
-                  LIPOGLYCOPEPTIDES,
+                  AB_CEPHALOSPORINS_4TH,
-                  GLYCOPEPTIDES,
+                  AB_CEPHALOSPORINS_5TH,
-                  GLYCOPEPTIDES_EXCEPT_LIPO,
+                  AB_CEPHALOSPORINS_EXCEPT_CAZ,
-                  LINCOSAMIDES,
+                  AB_FLUOROQUINOLONES,
-                  MACROLIDES,
+                  AB_LIPOGLYCOPEPTIDES,
-                  OXAZOLIDINONES,
+                  AB_GLYCOPEPTIDES,
-                  PENICILLINS,
+                  AB_GLYCOPEPTIDES_EXCEPT_LIPO,
-                  POLYMYXINS,
+                  AB_LINCOSAMIDES,
-                  STREPTOGRAMINS,
+                  AB_MACROLIDES,
-                  TETRACYCLINES,
+                  AB_OXAZOLIDINONES,
-                  TETRACYCLINES_EXCEPT_TGC,
+                  AB_PENICILLINS,
-                  UREIDOPENICILLINS,
+                  AB_POLYMYXINS,
-                  BETALACTAMS,
+                  AB_QUINOLONES,
+                  AB_STREPTOGRAMINS,
+                  AB_TETRACYCLINES,
+                  AB_TETRACYCLINES_EXCEPT_TGC,
+                  AB_TRIMETHOPRIMS,
+                  AB_UREIDOPENICILLINS,
+                  AB_BETALACTAMS,
                   DEFINED_AB_GROUPS,
                   internal = TRUE,
                   overwrite = TRUE,

data-raw/ab.md5

@@ -1 +1 @@
-f6b4a2325c4bf3a8d4da337c8cfa07be
+9f708801889d2eaf974c6eb85c83a8e7

data-raw/antibiotics.txt

@@ -1,511 +1,511 @@
-"ab"	"atc"	"cid"	"name"	"group"	"atc_group1"	"atc_group2"	"abbreviations"	"synonyms"	"oral_ddd"	"oral_units"	"iv_ddd"	"iv_units"	"loinc"
+"ab"	"cid"	"name"	"group"	"atc"	"atc_group1"	"atc_group2"	"abbreviations"	"synonyms"	"oral_ddd"	"oral_units"	"iv_ddd"	"iv_units"	"loinc"
-"AMA"	"J04AA01"	4649	"4-aminosalicylic acid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	"c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")"	12	"g"			"character(0)"
+"AMA"	4649	"4-aminosalicylic acid"	"Antimycobacterials"	"J04AA01"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	"c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")"	12	"g"			"character(0)"
-"FCT"	"D01AE21"	3366	"5-fluorocytosine"	"Antifungals/antimycotics"	"Antifungals for topical use"	"Other antifungals for topical use"	"c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")"	"c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")"					"c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")"
+"FCT"	3366	"5-fluorocytosine"	"Antifungals/antimycotics"	"D01AE21"	"Antifungals for topical use"	"Other antifungals for topical use"	"c(\"5flc\", \"fcu\", \"fluo\", \"fluy\")"	"c(\"alcobon\", \"ancobon\", \"ancotil\", \"ancotyl\", \"flucitosina\", \"flucystine\", \"flucytosin\", \"flucytosine\", \"flucytosinum\", \"flucytosone\", \"fluocytosine\", \"fluorcytosine\")"					"c(\"10974-4\", \"23805-5\", \"25142-1\", \"25143-9\", \"3639-2\", \"46218-4\")"
-"ACM"		6450012	"Acetylmidecamycin"	"Macrolides/lincosamides"			""	""					""
+"ACM"	6450012	"Acetylmidecamycin"	"Macrolides/lincosamides"				""	""					""
-"ASP"		49787020	"Acetylspiramycin"	"Macrolides/lincosamides"			""	"c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")"					"character(0)"
+"ASP"	49787020	"Acetylspiramycin"	"Macrolides/lincosamides"				""	"c(\"acetylspiramycin\", \"foromacidin b\", \"spiramycin ii\")"					"character(0)"
-"ALS"	"J04BA03"	8954	"Aldesulfone sodium"	"Other antibacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")"	0.33	"g"			"character(0)"
+"ALS"	8954	"Aldesulfone sodium"	"Other antibacterials"	"J04BA03"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"c(\"adesulfone sodium\", \"aldapsone\", \"aldesulfona sodica\", \"aldesulfone\", \"aldesulfone sodique\", \"aldesulfone sodium\", \"diamidin\", \"diasone\", \"diasone sodium\", \"diazon\", \"novotrone\", \"sodium aldesulphone\", \"sodium sulfoxone\", \"sulfoxone sodium\")"	0.33	"g"			"character(0)"
-"AMK"	"J01GB06"	37768	"Amikacin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")"	"c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")"			1	"g"	"c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
+"AMK"	37768	"Amikacin"	"Aminoglycosides"	"c(\"D06AX12\", \"J01GB06\", \"S01AA21\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"ak\", \"ami\", \"amik\", \"amk\", \"an\")"	"c(\"amicacin\", \"amikacillin\", \"amikacin\", \"amikacin base\", \"amikacin dihydrate\", \"amikacin sulfate\", \"amikacina\", \"amikacine\", \"amikacinum\", \"amikavet\", \"amikin\", \"amiklin\", \"amikozit\", \"amukin\", \"arikace\", \"briclin\", \"lukadin\", \"mikavir\", \"pierami\", \"potentox\")"			1	"g"	"c(\"13546-7\", \"15098-7\", \"17798-0\", \"31097-9\", \"31098-7\", \"31099-5\", \"3319-1\", \"3320-9\", \"3321-7\", \"35669-1\", \"50802-8\", \"50803-6\", \"56628-1\", \"59378-0\", \"80972-3\")"
-"AKF"			"Amikacin/fosfomycin"	"Aminoglycosides"			""	""					""
+"AKF"		"Amikacin/fosfomycin"	"Aminoglycosides"				""	""					""
-"AMX"	"J01CA04"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"ac\", \"amox\", \"amx\")"	"c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\", 
+"AMX"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"J01CA04"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"ac\", \"amox\", \"amx\")"	"c(\"actimoxi\", \"amoclen\", \"amolin\", \"amopen\", \"amopenixin\", \"amoxibiotic\", \"amoxicaps\", \"amoxicilina\", \"amoxicillin\", \"amoxicilline\", \"amoxicillinum\", \"amoxiden\", \"amoxil\", \"amoxivet\", \"amoxy\", \"amoxycillin\", \"anemolin\", \"aspenil\", \"biomox\", \"bristamox\", \"cemoxin\", \"clamoxyl\", \"delacillin\", \"dispermox\", \"efpenix\", \"flemoxin\", \"hiconcil\", \"histocillin\", \"hydroxyampicillin\", \"ibiamox\", \"imacillin\", \"lamoxy\", \"metafarma capsules\", \"metifarma capsules\", \"moxacin\", \"moxatag\", \"ospamox\", \"pamoxicillin\", 
 \"piramox\", \"robamox\", \"sawamox pm\", \"tolodina\", \"unicillin\", \"utimox\", \"vetramox\")"	1.5	"g"	3	"g"	"c(\"16365-9\", \"25274-2\", \"3344-9\", \"80133-2\")"
-"AMC"	"J01CR02"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")"	"c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")"	1.5	"g"	3	"g"	"character(0)"
+"AMC"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR02"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"a/c\", \"amcl\", \"aml\", \"aug\", \"xl\")"	"c(\"amocla\", \"amoclan\", \"amoclav\", \"amoxsiklav\", \"augmentan\", \"augmentin\", \"augmentin xr\", \"augmentine\", \"auspilic\", \"clamentin\", \"clamobit\", \"clavamox\", \"clavinex\", \"clavoxilin plus\", \"clavulin\", \"clavumox\", \"coamoxiclav\", \"eumetinex\", \"kmoxilin\", \"spectramox\", \"spektramox\", \"viaclav\", \"xiclav\")"	1.5	"g"	3	"g"	"character(0)"
-"AXS"		465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"			""	""					""
+"AXS"	465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"				""	""					""
-"AMB"	"J02AA01"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Antibiotics"	"c(\"amf\", \"amfb\", \"amph\")"	"c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")"			35	"mg"	"c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
+"AMB"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"c(\"A01AB04\", \"A07AA07\", \"G01AA03\", \"J02AA01\")"	"Antimycotics for systemic use"	"Antibiotics"	"c(\"amf\", \"amfb\", \"amph\")"	"c(\"abelcet\", \"abelecet\", \"ambisome\", \"amfotericina b\", \"amphocin\", \"amphomoronal\", \"amphortericin b\", \"amphotec\", \"amphotericin\", \"amphotericin b\", \"amphotericine b\", \"amphotericinum b\", \"amphozone\", \"anfotericine b\", \"fungilin\", \"fungisome\", \"fungisone\", \"fungizone\", \"halizon\")"	40	"mg"	35	"mg"	"c(\"16370-9\", \"3353-0\", \"3354-8\", \"40707-2\", \"40757-7\", \"49859-2\")"
-"AMH"			"Amphotericin B-high"	"Aminoglycosides"			"c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")"	""					""
+"AMH"		"Amphotericin B-high"	"Aminoglycosides"				"c(\"amfo b high\", \"amhl\", \"ampho b high\", \"amphotericin high\")"	""					""
-"AMP"	"J01CA01"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"am\", \"amp\", \"ampi\")"	"c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\", 
+"AMP"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"c(\"J01CA01\", \"S01AA19\")"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"am\", \"amp\", \"ampi\")"	"c(\"acillin\", \"adobacillin\", \"amblosin\", \"amcill\", \"amfipen\", \"amfipen v\", \"amipenix s\", \"ampichel\", \"ampicil\", \"ampicilina\", \"ampicillin\", \"ampicillin a\", \"ampicillin acid\", \"ampicillin anhydrate\", \"ampicillin anhydrous\", \"ampicillin base\", \"ampicillin sodium\", \"ampicillina\", \"ampicilline\", \"ampicillinum\", \"ampicin\", \"ampifarm\", \"ampikel\", \"ampimed\", \"ampipenin\", \"ampiscel\", \"ampisyn\", \"ampivax\", \"ampivet\", \"amplacilina\", \"amplin\", \"amplipenyl\", \"amplisom\", \"amplital\", \"anhydrous ampicillin\", \"austrapen\", 
 \"binotal\", \"bonapicillin\", \"britacil\", \"campicillin\", \"copharcilin\", \"delcillin\", \"deripen\", \"divercillin\", \"doktacillin\", \"duphacillin\", \"grampenil\", \"guicitrina\", \"guicitrine\", \"lifeampil\", \"marcillin\", \"morepen\", \"norobrittin\", \"nuvapen\", \"olin kid\", \"omnipen\", \"orbicilina\", \"pen a oral\", \"pen ampil\", \"penbristol\", \"penbritin\", \"penbritin paediatric\", \"penbritin syrup\", \"penbrock\", \"penicline\", \"penimic\", \"pensyn\", \"pentrex\", \"pentrexl\", \"pentrexyl\", \"pentritin\", \"pfizerpen a\", \"polycillin\", \"polyflex\", 
 \"ponecil\", \"princillin\", \"principen\", \"qidamp\", \"racenacillin\", \"rosampline\", \"roscillin\", \"semicillin\", \"semicillin r\", \"servicillin\", \"sumipanto\", \"synpenin\", \"texcillin\", \"tokiocillin\", \"tolomol\", \"totacillin\", \"totalciclina\", \"totapen\", \"trifacilina\", \"ukapen\", \"ultrabion\", \"ultrabron\", \"vampen\", \"viccillin\", \"viccillin s\", \"vidocillin\", \"wypicil\")"	2	"g"	6	"g"	"c(\"21066-6\", \"3355-5\", \"33562-0\", \"33919-2\", \"43883-8\", \"43884-6\", \"87604-5\")"
-"SAM"	"J01CR01"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")"	""			6	"g"	""
+"SAM"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"a/s\", \"ab\", \"ams\", \"amsu\", \"apsu\", \"sam\")"	""			6	"g"	""
-"AMR"		73341	"Amprolium"	"Other antibacterials"			""	"c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")"					"character(0)"
+"AMR"	73341	"Amprolium"	"Other antibacterials"				""	"c(\"amprocidum\", \"amprolio\", \"amprolium\", \"amprovine\")"					"character(0)"
-"ANI"	"J02AX06"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid"	"c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")"			0.1	"g"	"58420-1"
+"ANI"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"J02AX06"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid"	"c(\"anidulafungin\", \"anidulafungina\", \"anidulafungine\", \"anidulafunginum\", \"ecalta\", \"eraxis\")"			0.1	"g"	"58420-1"
-"APL"		6602341	"Apalcillin"	"Beta-lactams/penicillins"			""	"c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")"					"character(0)"
+"APL"	6602341	"Apalcillin"	"Beta-lactams/penicillins"				""	"c(\"apalcilina\", \"apalcillin\", \"apalcilline\", \"apalcillinum\")"					"character(0)"
-"APR"		3081545	"Apramycin"	"Aminoglycosides"			""	"c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")"					"character(0)"
+"APR"	3081545	"Apramycin"	"Aminoglycosides"				""	"c(\"ambylan\", \"apralan\", \"apramicina\", \"apramycin\", \"apramycine\", \"apramycinum\", \"nebramycin ii\")"					"character(0)"
-"ARB"		68682	"Arbekacin"	"Aminoglycosides"			""	"c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")"					"character(0)"
+"ARB"	68682	"Arbekacin"	"Aminoglycosides"	"J01GB12"			""	"c(\"arbekacin\", \"arbekacina\", \"arbekacine\", \"arbekacini sulfas\", \"arbekacinum\", \"habekacin\", \"haberacin\")"			0.2	"g"	"character(0)"
-"APX"		71961	"Aspoxicillin"	"Beta-lactams/penicillins"			""	"c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")"					"character(0)"
+"APX"	71961	"Aspoxicillin"	"Beta-lactams/penicillins"	"J01CA19"			""	"c(\"aspoxicilina\", \"aspoxicillan\", \"aspoxicillin\", \"aspoxicilline\", \"aspoxicillinum\")"			4	"g"	"character(0)"
-"AST"		5284517	"Astromicin"	"Aminoglycosides"			""	"c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")"					"character(0)"
+"AST"	5284517	"Astromicin"	"Aminoglycosides"				""	"c(\"astromicin\", \"astromicin a\", \"astromicina\", \"astromicine\", \"astromicinum\", \"fortimicin a\")"					"character(0)"
-"AVB"		9835049	"Avibactam"	"Beta-lactams/penicillins"			""	"c(\"avibactam\", \"avibactam free acid\")"					"character(0)"
+"AVB"	9835049	"Avibactam"	"Beta-lactams/penicillins"				""	"c(\"avibactam\", \"avibactam free acid\")"					"character(0)"
-"AVI"		71674	"Avilamycin"	"Other antibacterials"			""	"c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")"					"character(0)"
+"AVI"	71674	"Avilamycin"	"Other antibacterials"				""	"c(\"avilamycin\", \"avilamycina\", \"avilamycine\", \"avilamycinum\", \"surmax\")"					"character(0)"
-"AVO"		16131159	"Avoparcin"	"Glycopeptides"			""	""					""
+"AVO"	16131159	"Avoparcin"	"Glycopeptides"				""	""					""
-"AZD"	"J01CE04"	15574941	"Azidocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")"	1.5	"g"			"character(0)"
+"AZD"	15574941	"Azidocillin"	"Beta-lactams/penicillins"	"J01CE04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"azidocilina\", \"azidocillin\", \"azidocillina\", \"azidocilline\", \"azidocillinum\")"	1.5	"g"			"character(0)"
-"AZM"	"J01FA10"	447043	"Azithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"az\", \"azi\", \"azit\", \"azm\")"	"c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")"	0.3	"g"	0.5	"g"	"c(\"16420-2\", \"25233-8\")"
+"AZM"	447043	"Azithromycin"	"Macrolides/lincosamides"	"c(\"J01FA10\", \"S01AA26\")"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"az\", \"azi\", \"azit\", \"azm\")"	"c(\"aritromicina\", \"azasite\", \"azenil\", \"azifast\", \"azigram\", \"azimakrol\", \"azithramycine\", \"azithromycin\", \"azithromycine\", \"azithromycinum\", \"azitrocin\", \"azitromax\", \"azitromicina\", \"azitromicine\", \"azitromin\", \"aziwok\", \"aztrin\", \"azyter\", \"azythromycin\", \"hemomycin\", \"misultina\", \"mixoterin\", \"setron\", \"sumamed\", \"tromix\", \"trulimax\", \"zentavion\", \"zithrax\", \"zithromac\", \"zithromax\", \"zithromax iv\", \"zithromycin\", \"zitrim\", \"zitromax\", \"zitrotek\", \"zmax sr\")"	0.3	"g"	0.5	"g"	"c(\"16420-2\", \"25233-8\")"
-"AZL"	"J01CA09"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"az\", \"azl\", \"azlo\")"	""			12	"g"	""
+"AZL"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"J01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"az\", \"azl\", \"azlo\")"	""			12	"g"	""
-"ATM"	"J01DF01"	5742832	"Aztreonam"	"Beta-lactams/penicillins"	"Other beta-lactam antibacterials"	"Monobactams"	"c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")"	"c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")"			4	"g"	"c(\"16423-6\", \"25234-6\", \"3369-6\")"
+"ATM"	5742832	"Aztreonam"	"Beta-lactams/penicillins"	"J01DF01"	"Other beta-lactam antibacterials"	"Monobactams"	"c(\"at\", \"atm\", \"azm\", \"azt\", \"aztr\")"	"c(\"azactam\", \"azetreonam\", \"azthreonam\", \"aztreonam\", \"primbactam\")"			4	"g"	"c(\"16423-6\", \"25234-6\", \"3369-6\")"
-"AZA"			"Aztreonam/avibactam"	"Beta-lactams/penicillins"			""	""					""
+"AZA"		"Aztreonam/avibactam"	"Beta-lactams/penicillins"				""	""					""
-"BAM"	"J01CA06"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")"	1.2	"g"			"character(0)"
+"BAM"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"J01CA06"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"bacampicilina\", \"bacampicillin\", \"bacampicilline\", \"bacampicillinum\", \"penglobe\")"	1.2	"g"			"character(0)"
-"BAC"	"R02AB04"	78358334	"Bacitracin zinc"	"Other antibacterials"			"baci"	""					""
+"BAC"	78358334	"Bacitracin zinc"	"Other antibacterials"	"R02AB04"			"baci"	""					""
-"BDQ"		5388906	"Bedaquiline"	"Other antibacterials"			""	"c(\"bedaquiline\", \"sirturo\")"					"80637-2"
+"BDQ"	5388906	"Bedaquiline"	"Other antibacterials"	"J04AK05"			""	"c(\"bedaquiline\", \"sirturo\")"	86	"mg"			"80637-2"
-"BEK"		439318	"Bekanamycin"	"Aminoglycosides"			""	"c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")"					"character(0)"
+"BEK"	439318	"Bekanamycin"	"Aminoglycosides"	"J01GB13"			""	"c(\"aminodeoxykanamycin\", \"becanamicina\", \"bekanamycin\", \"bekanamycine\", \"bekanamycinum\", \"nebramycin v\")"			0.6	"g"	"character(0)"
-"BNB"	"J01CE08"		"Benzathine benzylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	""			3.6	"g"	""
+"BNB"		"Benzathine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE08"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	""			3.6	"g"	""
-"BNP"	"J01CE10"	64725	"Benzathine phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"bicillin v\", \"biphecillin\")"	2	"g"			"character(0)"
+"BNP"	64725	"Benzathine phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE10"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"bicillin v\", \"biphecillin\")"	2	"g"			"character(0)"
-"PEN"	"J01CE01"	5904	"Benzylpenicillin"	"Beta-lactams/penicillins"	"Combinations of antibacterials"	"Combinations of antibacterials"	"c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")"	"c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
+"PEN"	5904	"Benzylpenicillin"	"Beta-lactams/penicillins"	"c(\"J01CE01\", \"S01AA14\")"	"Combinations of antibacterials"	"Combinations of antibacterials"	"c(\"bepe\", \"pen\", \"peni\", \"peni g\", \"penicillin\", \"penicillin g\", \"pg\")"	"c(\"abbocillin\", \"ayercillin\", \"bencilpenicilina\", \"benzopenicillin\", \"benzyl penicillin\", \"benzylpenicillin\", \"benzylpenicillin g\", \"benzylpenicilline\", \"benzylpenicillinum\", \"bicillin\", \"cillora\", \"cilloral\", \"cilopen\", \"compocillin g\", \"cosmopen\", \"dropcillin\", \"free penicillin g\", \"free penicillin ii\", \"galofak\", \"gelacillin\", \"liquacillin\", \"megacillin\", \"pencillin g\", \"penicillin\", \"penicilling\", \"pentids\", \"permapen\", \"pfizerpen\", \"pfizerpen g\", \"pharmacillin\", \"pradupen\", \"specilline g\", \"ursopen\"
 )"			3.6	"g"	"3913-1"
-"BES"		10178705	"Besifloxacin"	"Quinolones"			""	"besifloxacin"					"character(0)"
+"BES"	10178705	"Besifloxacin"	"Quinolones"	"S01AE08"			""	"besifloxacin"					"character(0)"
-"BIA"		71339	"Biapenem"	"Carbapenems"			""	"c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")"					"character(0)"
+"BIA"	71339	"Biapenem"	"Carbapenems"	"J01DH05"			""	"c(\"biapenem\", \"biapenern\", \"bipenem\", \"omegacin\")"			1.2	"g"	"character(0)"
-"BCZ"		65807	"Bicyclomycin (Bicozamycin)"	"Other antibacterials"			""	"c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")"					"character(0)"
+"BCZ"	65807	"Bicyclomycin (Bicozamycin)"	"Other antibacterials"				""	"c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")"					"character(0)"
-"BDP"	"J01EA02"	68760	"Brodimoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	""	"c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")"	0.2	"g"			"character(0)"
+"BDP"	68760	"Brodimoprim"	"Trimethoprims"	"J01EA02"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	""	"c(\"brodimoprim\", \"brodimoprima\", \"brodimoprime\", \"brodimoprimum\", \"bromdimoprim\", \"hyprim\", \"unitrim\")"	0.2	"g"			"character(0)"
-"BUT"		47472	"Butoconazole"	"Antifungals/antimycotics"			""	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
+"BUT"	47472	"Butoconazole"	"Antifungals/antimycotics"	"G01AF15"			""	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
-"CDZ"	"J01DD09"	44242317	"Cadazolid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cadazolid"			2	"g"	"character(0)"
+"CDZ"	44242317	"Cadazolid"	"Oxazolidinones"				""	"cadazolid"					"character(0)"
-"CLA"	"J04AA03"		"Calcium aminosalicylate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	""	15				""
+"CLA"		"Calcium aminosalicylate"	"Antimycobacterials"	"J04AA03"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	""	15	"g"			""
-"CAP"	"J04AB30"	135565060	"Capreomycin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"c(\"\", \"capr\")"	""			1	"g"	""
+"CAP"	135565060	"Capreomycin"	"Antimycobacterials"	"J04AB30"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"c(\"\", \"capr\")"	""			1	"g"	""
-"CRB"	"J01CA03"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"bar\", \"carb\", \"cb\")"	"c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")"			12	"g"	"3434-8"
+"CRB"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"J01CA03"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"bar\", \"carb\", \"cb\")"	"c(\"anabactyl\", \"carbenicilina\", \"carbenicillin\", \"carbenicillina\", \"carbenicilline\", \"carbenicillinum\", \"geopen\", \"pyopen\")"			12	"g"	"3434-8"
-"CRN"	"J01CA05"	93184	"Carindacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")"	4	"g"			"character(0)"
+"CRN"	93184	"Carindacillin"	"Beta-lactams/penicillins"	"J01CA05"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"carindacilina\", \"carindacillin\", \"carindacilline\", \"carindacillinum\")"	4	"g"			"character(0)"
-"CAR"		6540466	"Carumonam"	"Other antibacterials"			""	"c(\"carumonam\", \"carumonamum\")"					"character(0)"
+"CAR"	6540466	"Carumonam"	"Other antibacterials"	"J01DF02"			""	"c(\"carumonam\", \"carumonamum\")"			2	"g"	"character(0)"
-"CAS"	"J02AX04"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp"	"c(\"cancidas\", \"capsofungin\", \"caspofungin\")"			50	"mg"	"58419-3"
+"CAS"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"J02AX04"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp"	"c(\"cancidas\", \"capsofungin\", \"caspofungin\")"			50	"mg"	"58419-3"
-"CAC"	"J01DB10"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")"					"character(0)"
+"CAC"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"J01DB10"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefacetril\", \"cefacetrile\", \"cefacetrilo\", \"cefacetrilum\", \"celospor\", \"celtol\", \"cephacetrile\", \"cristacef\", \"vetrimast\")"					"character(0)"
-"CEC"	"J01DC04"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")"	"c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")"	1	"g"			"c(\"16564-7\", \"21149-0\")"
+"CEC"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"J01DC04"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"ccl\", \"cec\", \"cf\", \"cfac\", \"cfc\", \"cfcl\", \"cfr\", \"fac\")"	"c(\"alenfral\", \"alfacet\", \"ceclor\", \"ceclor cd\", \"cefaclor\", \"cefaclor anhydrous\", \"cefaclor monohydrate\", \"cefacloro\", \"cefaclorum\", \"cefeaclor\", \"cephaclor\", \"dystaclor mr\", \"keflor\", \"kefral\", \"raniclor\")"	1	"g"			"c(\"16564-7\", \"21149-0\")"
-"CFR"	"J01DB05"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfdx\", \"cfr\", \"fad\")"	"c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")"	2	"g"			"16565-4"
+"CFR"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"J01DB05"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfdx\", \"cfr\", \"fad\")"	"c(\"cefadrops\", \"cefadroxil\", \"cefadroxil anhydrous\", \"cefadroxilo\", \"cefadroxilum\", \"cefradroxil\", \"cephadroxil\", \"duricef\", \"sumacef\", \"ultracef\")"	2	"g"			"16565-4"
-"RID"	"J01DB02"	5773	"Cefaloridine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa"	"c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")"			3	"g"	"character(0)"
+"RID"	5773	"Cefaloridine"	"Cephalosporins (1st gen.)"	"J01DB02"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa"	"c(\"aliporina\", \"ampligram\", \"cefaloridin\", \"cefaloridina\", \"cefaloridine\", \"cefaloridinum\", \"cefalorizin\", \"ceflorin\", \"cepaloridin\", \"cepalorin\", \"cephalomycine\", \"cephaloridin\", \"cephaloridine\", \"cephaloridinum\", \"ceporan\", \"ceporin\", \"ceporine\", \"cilifor\", \"deflorin\", \"faredina\", \"floridin\", \"glaxoridin\", \"intrasporin\", \"keflodin\", \"keflordin\", \"kefloridin\", \"kefspor\", \"lloncefal\", \"loridine\", \"sasperin\", \"sefacin\", \"verolgin\", \"vioviantine\")"			3	"g"	"character(0)"
-"MAN"	"J01DC03"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfam\", \"cfmn\")"	"c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")"			6	"g"	"3441-3"
+"MAN"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"J01DC03"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfam\", \"cfmn\")"	"c(\"cefadole\", \"cefamandol\", \"cefamandole\", \"cefamandolum\", \"cephadole\", \"cephamandole\", \"kefamandol\", \"kefdole\", \"mancef\")"			6	"g"	"3441-3"
-"CTZ"	"J01DB07"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")"	1	"g"			"character(0)"
+"CTZ"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"J01DB07"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"bricef\", \"cefatrix\", \"cefatrizine\", \"cefatrizino\", \"cefatrizinum\", \"cepticol\", \"cetrazil\", \"latocef\", \"orosporina\", \"trizina\")"	1	"g"			"character(0)"
-"CZD"	"J01DB06"	71736	"Cefazedone"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")"			3	"g"	"character(0)"
+"CZD"	71736	"Cefazedone"	"Cephalosporins (1st gen.)"	"J01DB06"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefazedon\", \"cefazedona\", \"cefazedone\", \"cefazedone acid\", \"cefazedonum\", \"refosporen\", \"refosporene\", \"refosporin\")"			3	"g"	"character(0)"
-"CZO"	"J01DB04"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")"	"c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")"			3	"g"	"c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")"
+"CZO"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"J01DB04"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfz\", \"cfzl\", \"cz\", \"czol\", \"faz\", \"kz\")"	"c(\"atirin\", \"cefamezin\", \"cefamezine\", \"cefazina\", \"cefazolin\", \"cefazolin acid\", \"cefazolina\", \"cefazoline\", \"cefazolinum\", \"cephamezine\", \"cephazolidin\", \"cephazolin\", \"cephazoline\", \"elzogram\", \"firmacef\", \"kefzol\", \"liviclina\", \"totacef\")"			3	"g"	"c(\"16566-2\", \"25235-3\", \"3442-1\", \"3443-9\", \"80962-4\")"
-"CFB"		127527	"Cefbuperazone"	"Other antibacterials"			""	"c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")"					"character(0)"
+"CFB"	127527	"Cefbuperazone"	"Other antibacterials"	"J01DC13"			""	"c(\"cefbuperazona\", \"cefbuperazone\", \"cefbuperazonum\", \"cefbuperzaone\", \"cerbuperazone\", \"tomiporan\")"			2	"g"	"character(0)"
-"CCP"		6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"			""	"c(\"cefcamate\", \"cefcapene\")"					"character(0)"
+"CCP"	6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"	"J01DD17"			""	"c(\"cefcamate\", \"cefcapene\")"	0.45	"g"			"character(0)"
-"CCX"		5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefcamate pivoxil\", \"cefcapene piroxil\")"					"character(0)"
+"CCX"	5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefcamate pivoxil\", \"cefcapene piroxil\")"					"character(0)"
-"CDR"	"J01DD15"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")"	"c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")"	0.6	"g"			"character(0)"
+"CDR"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"J01DD15"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cd\", \"cdn\", \"cdr\", \"cfd\", \"din\")"	"c(\"cefdinir\", \"cefdinirum\", \"cefdinyl\", \"cefdirnir\", \"ceftinex\", \"cefzon\", \"omnicef\")"	0.6	"g"			"character(0)"
-"DIT"	"J01DD16"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn"	"cefditoren"	0.4	"g"			"character(0)"
+"DIT"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"J01DD16"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn"	"cefditoren"	0.4	"g"			"character(0)"
-"DIX"		6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")"					"character(0)"
+"DIX"	6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")"					"character(0)"
-"FEP"	"J01DE01"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")"	"c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")"			4	"g"	"38363-8"
+"FEP"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"J01DE01"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"c(\"cfep\", \"cfpi\", \"cpe\", \"cpm\", \"fep\", \"pm\", \"xpm\")"	"c(\"axepim\", \"cefepima\", \"cefepime\", \"cefepimum\", \"cepimax\", \"cepimex\", \"maxcef\", \"maxipime\")"			4	"g"	"38363-8"
-"CPC"		9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.)"			"c(\"cicl\", \"xpml\")"	""					""
+"CPC"	9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.)"				"c(\"cicl\", \"xpml\")"	""					""
-"FPT"		9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"			""	""					""
+"FPT"	9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"				""	""					""
-"FPZ"			"Cefepime/zidebactam"	"Other antibacterials"			""	""					""
+"FPZ"		"Cefepime/zidebactam"	"Other antibacterials"				""	""					""
-"CAT"	"J01DD10"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")"	1	"g"			"character(0)"
+"CAT"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"J01DD10"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefetamet\", \"cefetametum\", \"cepime o\", \"deacetoxycefotaxime\")"	1	"g"			"character(0)"
-"CPI"		5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefetamet pivoxyl\", \"globocef\")"					"character(0)"
+"CPI"	5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefetamet pivoxyl\", \"globocef\")"					"character(0)"
-"CCL"		71719688	"Cefetecol (Cefcatacol)"	"Cephalosporins (4th gen.)"			""	""					""
+"CCL"	71719688	"Cefetecol (Cefcatacol)"	"Cephalosporins (4th gen.)"				""	""					""
-"CZL"		193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"			""	"c(\"cefetrizole\", \"cefetrizolum\")"					"character(0)"
+"CZL"	193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"				""	"c(\"cefetrizole\", \"cefetrizolum\")"					"character(0)"
-"FDC"		77843966	"Cefiderocol"	"Other antibacterials"			""	"cefiderocol"					"character(0)"
+"FDC"	77843966	"Cefiderocol"	"Other antibacterials"	"J01DI04"			""	"cefiderocol"					"character(0)"
-"CFM"	"J01DD08"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")"	"c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")"	0.4	"g"			"c(\"16567-0\", \"25236-1\")"
+"CFM"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"J01DD08"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfe\", \"cfix\", \"cfxm\", \"dcfm\", \"fix\", \"ix\")"	"c(\"cefixim\", \"cefixima\", \"cefixime\", \"cefixime anhydrous\", \"cefiximum\", \"cefixoral\", \"cefspan\", \"cephoral\", \"denvar\", \"necopen\", \"suprax\", \"tricef\", \"unixime\")"	0.4	"g"			"c(\"16567-0\", \"25236-1\")"
-"CMX"	"J01DD05"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")"			2	"g"	"character(0)"
+"CMX"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"J01DD05"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"bestron\", \"cefmax\", \"cefmenoxima\", \"cefmenoxime\", \"cefmenoximum\")"			2	"g"	"character(0)"
-"CMZ"	"J01DC09"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")"			4	"g"	"character(0)"
+"CMZ"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"J01DC09"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefmetazole\", \"cefmetazolo\", \"cefmetazolum\")"			4	"g"	"character(0)"
-"CNX"		71141	"Cefminox"	"Other antibacterials"			""	"c(\"cefminox\", \"cefminoxum\")"					"character(0)"
+"CNX"	71141	"Cefminox"	"Other antibacterials"	"J01DC12"			""	"c(\"cefminox\", \"cefminoxum\")"			4	"g"	"character(0)"
-"DIZ"	"J01DD09"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")"			2	"g"	"character(0)"
+"DIZ"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"J01DD09"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefodizima\", \"cefodizime\", \"cefodizime acid\", \"cefodizimum\", \"cefodizme\", \"diezime\", \"modivid\", \"neucef\", \"timecef\")"			2	"g"	"character(0)"
-"CID"	"J01DC06"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")"			1	"g"	"c(\"25237-9\", \"3444-7\")"
+"CID"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"J01DC06"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefonicid\", \"cefonicido\", \"cefonicidum\", \"monocef\")"			1	"g"	"c(\"25237-9\", \"3444-7\")"
-"CFP"	"J01DD12"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")"	"c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")"			4	"g"	"3445-4"
+"CFP"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"J01DD12"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfp\", \"cfpz\", \"cp\", \"cpz\", \"fop\", \"per\")"	"c(\"bioperazone\", \"cefobid\", \"cefoperazine\", \"cefoperazon\", \"cefoperazone\", \"cefoperazone acid\", \"cefoperazono\", \"cefoperazonum\", \"cefozon\", \"medocef\", \"myticef\", \"pathozone\", \"peracef\")"			4	"g"	"3445-4"
-"CSL"	"J01DD62"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	""			4	"g"	""
+"CSL"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"J01DD62"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	""			4	"g"	""
-"CND"	"J01DC11"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")"			4	"g"	"character(0)"
+"CND"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"J01DC11"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"ceforanide\", \"ceforanido\", \"ceforanidum\", \"precef\", \"radacef\")"			4	"g"	"character(0)"
-"CSE"		9830519	"Cefoselis"	"Cephalosporins (4th gen.)"			""	"c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")"					"character(0)"
+"CSE"	9830519	"Cefoselis"	"Cephalosporins (4th gen.)"				""	"c(\"cefoselis\", \"cefoselis sulfate\", \"winsef\")"					"character(0)"
-"CTX"	"J01DD01"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")"	"c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")"			4	"g"	"c(\"25238-7\", \"3446-2\", \"80961-6\")"
+"CTX"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"J01DD01"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfot\", \"cft\", \"cftx\", \"ct\", \"ctx\", \"fot\", \"tax\", \"xct\")"	"c(\"cefotaxim\", \"cefotaxim hikma\", \"cefotaxima\", \"cefotaxime\", \"cefotaxime acid\", \"cefotaximum\", \"cephotaxime\", \"claforan\", \"omnatax\")"			4	"g"	"c(\"25238-7\", \"3446-2\", \"80961-6\")"
-"CTC"		9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.)"			"c(\"cxcl\", \"xctl\")"	""					""
+"CTC"	9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.)"				"c(\"cxcl\", \"xctl\")"	""					""
-"CTS"		9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"			""	""					""
+"CTS"	9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"				""	""					""
-"CTT"	"J01DC05"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")"	"c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")"			4	"g"	"c(\"25239-5\", \"3447-0\")"
+"CTT"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"J01DC05"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cftt\", \"cn\", \"cte\", \"ctn\", \"ctt\", \"tans\")"	"c(\"apacef\", \"cefotetan\", \"cefotetan free acid\", \"cefotetanum\")"			4	"g"	"c(\"25239-5\", \"3447-0\")"
-"CTF"	"J01DC07"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")"	1.2	"g"	4	"g"	"character(0)"
+"CTF"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"J01DC07"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"c(\"cefotiam\", \"cefotiam?\", \"cefotiamum\", \"ceradolan\", \"ceradon\", \"haloapor\")"	1.2	"g"	4	"g"	"character(0)"
-"CHE"		125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefotiam cilexetil\", \"pansporin t\")"					"character(0)"
+"CHE"	125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefotiam cilexetil\", \"pansporin t\")"					"character(0)"
-"FOV"		9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"			""	""					""
+"FOV"	9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"				""	""					""
-"FOX"	"J01DC01"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")"	"c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")"			6	"g"	"c(\"25240-3\", \"3448-8\")"
+"FOX"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"J01DC01"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfox\", \"cfx\", \"cfxt\", \"cx\", \"fox\", \"fx\")"	"c(\"cefoxitin\", \"cefoxitina\", \"cefoxitine\", \"cefoxitinum\", \"cefoxotin\", \"cephoxitin\", \"mefoxin\", \"mefoxitin\", \"rephoxitin\")"			6	"g"	"c(\"25240-3\", \"3448-8\")"
-"FOX1"			"Cefoxitin screening"	"Cephalosporins (2nd gen.)"			"cfsc"	""					""
+"FOX1"		"Cefoxitin screening"	"Cephalosporins (2nd gen.)"				"cfsc"	""					""
-"ZOP"		9571080	"Cefozopran"	"Cephalosporins (4th gen.)"			""	"cefozopran"					"character(0)"
+"ZOP"	9571080	"Cefozopran"	"Cephalosporins (4th gen.)"	"J01DE03"			""	"cefozopran"			4	"g"	"character(0)"
-"CFZ"		68597	"Cefpimizole"	"Cephalosporins (3rd gen.)"			""	"c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")"					"character(0)"
+"CFZ"	68597	"Cefpimizole"	"Cephalosporins (3rd gen.)"				""	"c(\"cefpimizol\", \"cefpimizole\", \"cefpimizole sodium\", \"cefpimizolum\")"					"character(0)"
-"CPM"	"J01DD11"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")"			2	"g"	"character(0)"
+"CPM"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.)"	"J01DD11"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"c(\"cefpiramide\", \"cefpiramide acid\", \"cefpiramido\", \"cefpiramidum\")"			2	"g"	"character(0)"
-"CPO"	"J01DE02"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"c(\"\", \"cfpr\")"	"c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")"			4	"g"	"character(0)"
+"CPO"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"J01DE02"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"c(\"\", \"cfpr\")"	"c(\"broact\", \"cefpiroma\", \"cefpirome\", \"cefpiromum\", \"cefrom\", \"cerfpirome\", \"keiten\")"			4	"g"	"character(0)"
-"CPD"	"J01DD13"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")"	"c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")"	0.4	"g"			"25241-1"
+"CPD"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"J01DD13"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfpd\", \"cfpo\", \"cpd\", \"pod\", \"px\")"	"c(\"cefpodoxim acid\", \"cefpodoxima\", \"cefpodoxime\", \"cefpodoxime acid\", \"cefpodoximum\", \"epoxim\")"	0.4	"g"			"25241-1"
-"CPX"		6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")"					"character(0)"
+"CPX"	6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefodox\", \"cefoprox\", \"cefpodoxime proxetil\", \"cepodem\", \"orelox\", \"otreon\", \"podomexef\", \"simplicef\", \"vantin\")"					"character(0)"
-"CDC"			"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.)"			"c(\"\", \"cecl\")"	""					""
+"CDC"		"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.)"				"c(\"\", \"cecl\")"	""					""
-"CPR"	"J01DC10"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cpr\", \"cpz\", \"fp\")"	"c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")"	1	"g"			"character(0)"
+"CPR"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"J01DC10"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cpr\", \"cpz\", \"fp\")"	"c(\"arzimol\", \"brisoral\", \"cefprozil\", \"cefprozil anhydrous\", \"cefprozil hydrate\", \"cefprozilo\", \"cefprozilum\", \"cefzil\", \"cronocef\", \"procef\", \"serozil\")"	1	"g"			"character(0)"
-"CEQ"		5464355	"Cefquinome"	"Cephalosporins (4th gen.)"			""	"c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")"					"character(0)"
+"CEQ"	5464355	"Cefquinome"	"Cephalosporins (4th gen.)"				""	"c(\"cefquinoma\", \"cefquinome\", \"cefquinomum\", \"cobactan\")"					"character(0)"
-"CRD"	"J01DB11"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")"	2.1				"character(0)"
+"CRD"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"J01DB11"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"cefroxadine\", \"cefroxadino\", \"cefroxadinum\")"	2.1	"g"			"character(0)"
-"CFS"	"J01DD03"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfsl\", \"cfsu\")"	"c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")"			4	"g"	"c(\"131-3\", \"25242-9\")"
+"CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"J01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfsl\", \"cfsu\")"	"c(\"cefsulodin\", \"cefsulodine\", \"cefsulodino\", \"cefsulodinum\")"			4	"g"	"c(\"131-3\", \"25242-9\")"
-"CSU"		68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"			""	"c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")"					"character(0)"
+"CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"				""	"c(\"cefsumide\", \"cefsumido\", \"cefsumidum\")"					"character(0)"
-"CPT"	"J01DI02"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"			"c(\"\", \"cfro\")"	"c(\"teflaro\", \"zinforo\")"			1.2		"character(0)"
+"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02"			"c(\"\", \"cfro\")"	"c(\"teflaro\", \"zinforo\")"			1.2	"g"	"character(0)"
-"CPA"			"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"			""	""					""
+"CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"				""	""					""
-"CAZ"	"J01DD02"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")"	"c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")"			4	"g"	"c(\"21151-6\", \"3449-6\", \"80960-8\")"
+"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"caz\", \"cefta\", \"cfta\", \"cftz\", \"taz\", \"tz\", \"xtz\")"	"c(\"ceftazidim\", \"ceftazidima\", \"ceftazidime\", \"ceftazidimum\", \"ceptaz\", \"fortaz\", \"fortum\", \"pentacef\", \"tazicef\", \"tazidime\")"			4	"g"	"c(\"21151-6\", \"3449-6\", \"80960-8\")"
-"CZA"	"J01DD52"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"\", \"cfav\")"	"c(\"avycaz\", \"zavicefta\")"			6	"g"	""
+"CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"				"c(\"\", \"cfav\")"	"c(\"avycaz\", \"zavicefta\")"					""
-"CCV"	"J01DD52"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"czcl\", \"xtzl\")"	""			6		""
+"CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"czcl\", \"xtzl\")"	""			6	"g"	""
-"CEM"		6537431	"Cefteram"	"Cephalosporins (3rd gen.)"			""	"c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")"					"character(0)"
+"CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18"			""	"c(\"cefteram\", \"cefterame\", \"cefteramum\", \"ceftetrame\")"	0.4	"g"			"character(0)"
-"CPL"		5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"			""	"c(\"cefteram pivoxil\", \"tomiron\")"					"character(0)"
+"CPL"	5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefteram pivoxil\", \"tomiron\")"					"character(0)"
-"CTL"	"J01DB12"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")"			3	"g"	"character(0)"
+"CTL"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"J01DB12"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"ceftezol\", \"ceftezole\", \"ceftezolo\", \"ceftezolum\", \"demethylcefazolin\")"			3	"g"	"character(0)"
-"CTB"	"J01DD14"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cb\", \"cfbu\", \"ctb\", \"tib\")"	"c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")"	0.4	"g"			"character(0)"
+"CTB"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"J01DD14"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cb\", \"cfbu\", \"ctb\", \"tib\")"	"c(\"ceftem\", \"ceftibuten\", \"ceftibuten hydrate\", \"ceftibutene\", \"ceftibuteno\", \"ceftibutenum\", \"cephem\", \"ceprifran\", \"isocef\", \"keimax\")"	0.4	"g"			"character(0)"
-"TIO"		6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"			""	"c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")"					"character(0)"
+"TIO"	6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"				""	"c(\"ceftiofur\", \"ceftiofurum\", \"excede\", \"excenel\", \"naxcel\")"					"character(0)"
-"CZX"	"J01DD07"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")"	"c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")"			4	"g"	"c(\"25243-7\", \"3450-4\")"
+"CZX"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"J01DD07"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"cfzx\", \"ctz\", \"cz\", \"czx\", \"tiz\", \"zox\")"	"c(\"cefizox\", \"ceftisomin\", \"ceftix\", \"ceftizoxima\", \"ceftizoxime\", \"ceftizoximum\", \"epocelin\", \"eposerin\")"			4	"g"	"c(\"25243-7\", \"3450-4\")"
-"CZP"		9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"			""	""					""
+"CZP"	9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"				""	""					""
-"BPR"	"J01DI01"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"			""	"ceftobiprole"			1.5		"character(0)"
+"BPR"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"				""	"ceftobiprole"					"character(0)"
-"CFM1"	"J01DI01"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"	""	""			1.5		""
+"CFM1"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"J01DI01"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	""			1.5	"g"	""
-"CEI"	"J01DI54"		"Ceftolozane/enzyme inhibitor"	"Cephalosporins (5th gen.)"	"Other beta-lactam antibacterials"	"Other cephalosporins"	""	""			3		""
+"CEI"		"Ceftolozane/enzyme inhibitor"	"Cephalosporins (5th gen.)"	"J01DI54"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	""			3	"g"	""
-"CZT"			"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"			""	""					""
+"CZT"		"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"				""	""					""
-"CRO"	"J01DD04"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")"	"c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")"			2	"g"	"c(\"25244-5\", \"3451-2\", \"80957-4\")"
+"CRO"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"J01DD04"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"axo\", \"cax\", \"cftr\", \"cro\", \"ctr\", \"frx\", \"tx\")"	"c(\"biotrakson\", \"cefatriaxone\", \"cefatriaxone hydrate\", \"ceftriaxon\", \"ceftriaxona\", \"ceftriaxone\", \"ceftriaxone sodium\", \"ceftriaxonum\", \"ceftriazone\", \"cephtriaxone\", \"longacef\", \"rocefin\", \"rocephalin\", \"rocephin\", \"rocephine\", \"rophex\")"			2	"g"	"c(\"25244-5\", \"3451-2\", \"80957-4\")"
-"CXM"	"J01DC02"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")"	"c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")"	0.5	"g"	3	"g"	"c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
+"CXM"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"c(\"J01DC02\", \"S01AA27\")"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"cfrx\", \"cfur\", \"cfx\", \"crm\", \"cxm\", \"fur\", \"rox\", \"xm\")"	"c(\"biofuroksym\", \"cefuril\", \"cefuroxim\", \"cefuroxime\", \"cefuroximine\", \"cefuroximo\", \"cefuroximum\", \"cephuroxime\", \"kefurox\", \"sharox\", \"zinacef\", \"zinacef danmark\")"	0.5	"g"	3	"g"	"c(\"25245-2\", \"3452-0\", \"80608-3\", \"80617-4\")"
-"CXA"		6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.)"			"c(\"\", \"cfax\")"	"c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")"					"character(0)"
+"CXA"	6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.)"				"c(\"\", \"cfax\")"	"c(\"altacef\", \"bioracef\", \"cefaks\", \"cefazine\", \"ceftin\", \"cefuroximaxetil\", \"cefuroxime axetil\", \"celocid\", \"cepazine\", \"cethixim\", \"cetoxil\", \"coliofossim\", \"elobact\", \"forcef\", \"furoxime\", \"kalcef\", \"maxitil\", \"medoxm\", \"nivador\", \"zinnat\")"					"character(0)"
-"CFM2"	"J01RA03"		"Cefuroxime/metronidazole"	"Other antibacterials"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
+"CFM2"		"Cefuroxime/metronidazole"	"Other antibacterials"	"J01RA03"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"ZON"		6336505	"Cefuzonam"	"Other antibacterials"			""	"c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")"					"character(0)"
+"ZON"	6336505	"Cefuzonam"	"Other antibacterials"				""	"c(\"cefuzonam\", \"cefuzonam sodium\", \"cefuzoname\", \"cefuzonamum\")"					"character(0)"
-"LEX"	"J01DB01"	27447	"Cephalexin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"\", \"cflx\")"	"c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\", 
+"LEX"	27447	"Cephalexin"	"Cephalosporins (1st gen.)"	"J01DB01"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"\", \"cflx\")"	"c(\"alcephin\", \"alexin\", \"alsporin\", \"anhydrous cefalexin\", \"anhydrous cephalexin\", \"biocef\", \"carnosporin\", \"cefablan\", \"cefadal\", \"cefadin\", \"cefadina\", \"cefaleksin\", \"cefalessina\", \"cefalexin\", \"cefalexin anhydrous\", \"cefalexina\", \"cefalexine\", \"cefalexinum\", \"cefalin\", \"cefaloto\", \"cefaseptin\", \"ceflax\", \"ceforal\", \"cefovit\", \"celexin\", \"cepastar\", \"cepexin\", \"cephacillin\", \"cephalexin\", \"cephalexin anhydrous\", \"cephalexine\", \"cephalexinum\", \"cephanasten\", \"cephaxin\", \"cephin\", \"ceporex\", \"ceporex forte\", 
 \"ceporexin\", \"ceporexine\", \"cerexin\", \"cerexins\", \"cophalexin\", \"durantel\", \"durantel ds\", \"erocetin\", \"factagard\", \"felexin\", \"ibilex\", \"ibrexin\", \"inphalex\", \"kefalospes\", \"keflet\", \"keflex\", \"kefolan\", \"keforal\", \"keftab\", \"kekrinal\", \"kidolex\", \"lafarine\", \"larixin\", \"lenocef\", \"lexibiotico\", \"lonflex\", \"lopilexin\", \"madlexin\", \"mamalexin\", \"mamlexin\", \"medoxine\", \"neokef\", \"neolexina\", \"novolexin\", \"optocef\", \"oracef\", \"oriphex\", \"oroxin\", \"ortisporina\", \"ospexin\", \"palitrex\", \"panixine disperdose\", 
 \"pectril\", \"pyassan\", \"roceph\", \"roceph distab\", \"sanaxin\", \"sartosona\", \"sencephalin\", \"sepexin\", \"servispor\", \"sialexin\", \"sinthecillin\", \"sporicef\", \"sporidex\", \"syncle\", \"synecl\", \"tepaxin\", \"tokiolexin\", \"uphalexin\", \"voxxim\", \"winlex\", \"zozarine\")"	2	"g"			"c(\"21175-5\", \"3453-8\")"
-"CEP"	"J01DB03"	6024	"Cephalothin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfal\", \"cflt\")"	"c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")"			4	"g"	"c(\"25246-0\", \"3454-6\")"
+"CEP"	6024	"Cephalothin"	"Cephalosporins (1st gen.)"	"J01DB03"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfal\", \"cflt\")"	"c(\"cefalothin\", \"cefalotin\", \"cefalotina\", \"cefalotina fabra\", \"cefalotine\", \"cefalotinum\", \"cemastin\", \"cephalothinum\", \"cephalotin\", \"coaxin\", \"keflin\", \"seffin\")"			4	"g"	"c(\"25246-0\", \"3454-6\")"
-"HAP"	"J01DB08"	30699	"Cephapirin"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")"			4	"g"	"10980-1"
+"HAP"	30699	"Cephapirin"	"Cephalosporins (1st gen.)"	"J01DB08"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"c(\"ambrocef\", \"cefadyl\", \"cefapilin\", \"cefapirin\", \"cefapirina\", \"cefapirine\", \"cefapirinum\", \"cefaprin\", \"cefaprin sodium\", \"cefatrex\", \"cefatrexyl\", \"cephapirine\", \"metricure\")"			4	"g"	"10980-1"
-"CED"	"J01DB09"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfra\", \"cfrd\")"	"c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")"	2	"g"	2	"g"	"character(0)"
+"CED"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"J01DB09"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"c(\"cfra\", \"cfrd\")"	"c(\"anspor\", \"cefradin\", \"cefradina\", \"cefradine\", \"cefradinum\", \"cekodin\", \"cephradin\", \"cephradine\", \"eskacef\", \"infexin\", \"megace f\", \"megacef\", \"sefril\", \"velocef\", \"velosef\")"	2	"g"	2	"g"	"character(0)"
-"CTO"		71402	"Cetocycline"	"Tetracyclines"			""	"c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")"					"character(0)"
+"CTO"	71402	"Cetocycline"	"Tetracyclines"				""	"c(\"cetocycline\", \"cetocyline\", \"cetotetrine\")"					"character(0)"
-"CHL"	"J01BA01"	5959	"Chloramphenicol"	"Amphenicols"	"Amphenicols"	"Amphenicols"	"c(\"c\", \"chl\", \"chlo\", \"cl\")"	"c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\", 
+"CHL"	5959	"Chloramphenicol"	"Amphenicols"	"c(\"D06AX02\", \"D10AF03\", \"G01AA05\", \"J01BA01\", \"S01AA01\", \"S02AA01\", \"S03AA08\")"	"Amphenicols"	"Amphenicols"	"c(\"c\", \"chl\", \"chlo\", \"cl\")"	"c(\"alficetyn\", \"ambofen\", \"amphenicol\", \"amphicol\", \"amseclor\", \"anacetin\", \"aquamycetin\", \"austracil\", \"austracol\", \"biocetin\", \"biophenicol\", \"catilan\", \"ch loramex\", \"chemiceticol\", \"chemicetin\", \"chemicetina\", \"chlomin\", \"chlomycol\", \"chloramex\", \"chloramfenikol\", \"chloramficin\", \"chloramfilin\", \"chloramphenicol\", \"chloramphenicole\", \"chloramphenicolum\", \"chloramsaar\", \"chlorasol\", \"chlorbiotic\", \"chloricol\", \"chlormycetin r\", \"chlornitromycin\", \"chloroamphenicol\", \"chlorocaps\", \"chlorocid\", 
 \"chlorocid s\", \"chlorocide\", \"chlorocidin c\", \"chlorocidin c tetran\", \"chlorocin\", \"chlorocol\", \"chlorofair\", \"chloroject l\", \"chloromax\", \"chloromycetin\", \"chloromycetny\", \"chloromyxin\", \"chloronitrin\", \"chloroptic\", \"chloroptic s.o.p\", \"chloroptic s.o.p.\", \"chlorovules\", \"chlorsig\", \"cidocetine\", \"ciplamycetin\", \"cloramfen\", \"cloramfenicol\", \"cloramfenicolo\", \"cloramficin\", \"cloramical\", \"cloramicol\", \"cloramidina\", \"cloranfenicol\", \"cloroamfenicolo\", \"clorocyn\", \"cloromisan\", \"cloromissan\", \"clorosintex\", 
 \"comycetin\", \"cylphenicol\", \"desphen\", \"detreomycin\", \"detreomycine\", \"dextromycetin\", \"doctamicina\", \"duphenicol\", \"econochlor\", \"embacetin\", \"emetren\", \"enicol\", \"enteromycetin\", \"erbaplast\", \"ertilen\", \"f armicetina\", \"farmicetina\", \"fenicol\", \"globenicol\", \"glorous\", \"halomycetin\", \"hortfenicol\", \"interomycetine\", \"intramycetin\", \"intramyctin\", \"isicetin\", \"ismicetina\", \"isophenicol\", \"isopto fenicol\", \"juvamycetin\", \"kamaver\", \"kemicetina\", \"kemicetine\", \"kloramfenikol\", \"klorita\", \"klorocid s\", 
 \"laevomycetinum\", \"leukamycin\", \"leukomyan\", \"leukomycin\", \"levocin\", \"levomicetina\", \"levomitsetin\", \"levomycetin\", \"levoplast\", \"levosin\", \"levovetin\", \"loromicetina\", \"loromisan\", \"loromisin\", \"mastiphen\", \"mediamycetine\", \"medichol\", \"micloretin\", \"micochlorine\", \"micoclorina\", \"microcetina\", \"mychel\", \"mycinol\", \"myclocin\", \"mycochlorin\", \"myscel\", \"normimycin v\", \"novochlorocap\", \"novomycetin\", \"novophenicol\", \"ocuphenicol\", \"oftalent\", \"oleomycetin\", \"opclor\", \"opelor\", \"ophthochlor\", \"ophthocort\", 
 \"ophtochlor\", \"optomycin\", \"otachron\", \"otophen\", \"pantovernil\", \"paraxin\", \"pentamycetin\", \"quemicetina\", \"rivomycin\", \"romphenil\", \"ronfenil\", \"ronphenil\", \"septicol\", \"sificetina\", \"sintomicetina\", \"sintomicetine r\", \"sno phenicol\", \"soluthor\", \"stanomycetin\", \"synthomycetin\", \"synthomycetine\", \"synthomycine\", \"syntomycin\", \"tevcocin\", \"tevcosin\", \"tifomycin\", \"tifomycine\", \"tiromycetin\", \"treomicetina\", \"unimycetin\", \"veticol\", \"vice ton\", \"viceton\")"	3	"g"	3	"g"	"c(\"15101-9\", \"16603-3\", \"16604-1\", \"25247-8\", \"29214-4\", \"29346-4\", \"29347-2\", \"3455-3\")"
-"CTE"	"J01AA03"	54675777	"Chlortetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")"	1	"g"			"87600-3"
+"CTE"	54675777	"Chlortetracycline"	"Tetracyclines"	"c(\"A01AB21\", \"D06AA02\", \"J01AA03\", \"S01AA02\")"	"Tetracyclines"	"Tetracyclines"	""	"c(\"acronize\", \"aueromycin\", \"aureocina\", \"aureomycin\", \"aureomykoin\", \"biomitsin\", \"biomycin\", \"biomycin a\", \"chlormax\", \"chlorotetracycline\", \"chlortetracycline\", \"chlortetracyclinum\", \"chrysomykine\", \"clortetraciclina\", \"duomycin\", \"flamycin\", \"uromycin\")"	1	"g"			"87600-3"
-"CIC"		19003	"Ciclacillin"	"Beta-lactams/penicillins"			""	"c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")"					"character(0)"
+"CIC"	19003	"Ciclacillin"	"Beta-lactams/penicillins"				""	"c(\"bastcillin\", \"calthor\", \"ciclacilina\", \"ciclacillin\", \"ciclacilline\", \"ciclacillinum\", \"ciclacillum\", \"citosarin\", \"cyclacillin\", \"cyclapen\", \"noblicil\", \"orfilina\", \"peamezin\", \"syngacillin\", \"ultracillin\", \"vastcillin\", \"vipicil\", \"wyvital\")"					"character(0)"
-"CIX"	"D01AE14"	47472	"Ciclopirox"	"Antifungals/antimycotics"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
+"CIX"	47472	"Ciclopirox"	"Antifungals/antimycotics"	"c(\"D01AE14\", \"G01AX12\")"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
-"CIN"	"J01MB06"	2762	"Cinoxacin"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"c(\"cino\", \"cnox\")"	"c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")"	1	"g"			"character(0)"
+"CIN"	2762	"Cinoxacin"	"Quinolones"	"J01MB06"	"Quinolone antibacterials"	"Other quinolones"	"c(\"cino\", \"cnox\")"	"c(\"azolinic acid\", \"cinobac\", \"cinobactin\", \"cinoxacin\", \"cinoxacine\", \"cinoxacino\", \"cinoxacinum\", \"clinoxacin\", \"noxigram\", \"uronorm\")"	1	"g"			"character(0)"
-"CIP"	"J01MA02"	2764	"Ciprofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"ci\", \"cip\", \"cipr\", \"cp\")"	"c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\", 
+"CIP"	2764	"Ciprofloxacin"	"Quinolones"	"c(\"J01MA02\", \"S01AE03\", \"S02AA15\", \"S03AA07\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"ci\", \"cip\", \"cipr\", \"cp\")"	"c(\"alcon cilox\", \"auripro\", \"bacquinor\", \"baflox\", \"baycip\", \"bernoflox\", \"cetraxal\", \"ciflox\", \"cifloxin\", \"ciloxan\", \"ciplus\", \"ciprecu\", \"ciprine\", \"ciprinol\", \"cipro i.v.\", \"cipro iv\", \"cipro xl\", \"cipro xr\", \"ciprobay\", \"ciprobay uro\", \"ciprocinol\", \"ciprodar\", \"ciproflox\", \"ciprofloxacin\", \"ciprofloxacina\", \"ciprofloxacine\", \"ciprofloxacino\", \"ciprofloxacinum\", \"ciprogis\", \"ciprolin\", \"ciprolon\", \"cipromycin\", \"ciproquinol\", \"ciprowin\", \"ciproxan\", \"ciproxin\", \"ciproxina\", \"ciproxine\", \"ciriax\", 
 \"citopcin\", \"corsacin\", \"cyprobay\", \"fimoflox\", \"flociprin\", \"ipiflox\", \"italnik\", \"linhaliq\", \"otiprio\", \"probiox\", \"proflaxin\", \"quinolid\", \"quintor\", \"rancif\", \"roxytal\", \"septicide\", \"sophixin ofteno\", \"spitacin\", \"superocin\", \"velmonit\", \"velomonit\", \"zumaflox\")"	1	"g"	0.8	"g"	"c(\"14031-9\", \"14032-7\", \"14058-2\", \"14059-0\", \"25248-6\", \"34636-1\", \"3484-3\")"
-"CLR"	"J01FA09"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")"	"c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\", 
+"CLR"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"J01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"ch\", \"cla\", \"clar\", \"clm\", \"clr\")"	"c(\"abbotic\", \"astromen\", \"biaxin\", \"biaxin filmtab\", \"biaxin hp\", \"biaxin xl\", \"biaxin xl filmtab\", \"bicrolid\", \"clacee\", \"clacid\", \"clacine\", \"clambiotic\", \"clarem\", \"claribid\", \"claricide\", \"claridar\", \"claripen\", \"clarith\", \"clarithromycin\", \"clarithromycine\", \"clarithromycinum\", \"claritromicina\", \"clathromycin\", \"crixan\", \"cyllid\", \"cyllind\", \"fromilid\", \"heliclar\", \"klabax\", \"klacid\", \"klaciped\", \"klaricid\", \"klaricid h.p\", \"klaricid h.p.\", \"klaricid pediatric\", \"klaricid xl\", \"klarid\", \"klarin\", 
 \"kofron\", \"mabicrol\", \"macladin\", \"maclar\", \"veclam\", \"vikrol\", \"zeclar\")"	0.5	"g"	1	"g"	"c(\"16619-9\", \"25253-6\", \"34638-7\", \"80559-8\")"
-"CLA1"		5280980	"Clavulanic acid"	"Other antibacterials"			""	"c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")"					"character(0)"
+"CLA1"	5280980	"Clavulanic acid"	"Other antibacterials"				""	"c(\"acide clavulanique\", \"acido clavulanico\", \"acidum clavulanicum\", \"clavulanate\", \"clavulanate acid\", \"clavulanate lithium\", \"clavulanic acid\", \"clavulansaeure\", \"clavulansaure\", \"clavulinic acid\", \"clavulox\", \"sodium clavulanate\")"					"character(0)"
-"CLX"		60063	"Clinafloxacin"	"Quinolones"			""	"clinafloxacin"					"character(0)"
+"CLX"	60063	"Clinafloxacin"	"Quinolones"				""	"clinafloxacin"					"character(0)"
-"CLI"	"J01FF01"	446598	"Clindamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")"	"c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")"	1.2	"g"	1.8	"g"	"c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")"
+"CLI"	446598	"Clindamycin"	"Macrolides/lincosamides"	"c(\"D10AF01\", \"G01AA10\", \"J01FF01\")"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"c(\"cc\", \"cd\", \"cli\", \"clin\", \"cm\", \"da\")"	"c(\"antirobe\", \"chlolincocin\", \"clindaderm\", \"clindamicina\", \"clindamycin\", \"clindamycine\", \"clindamycinum\", \"clinimycin\", \"dalacin c\", \"dalacine\", \"klimicin\", \"sobelin\")"	1.2	"g"	1.8	"g"	"c(\"16621-5\", \"16622-3\", \"25249-4\", \"3486-8\")"
-"CLF"	"J04BA01"	2794	"Clofazimine"	"Antimycobacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")"	0.1	"g"			"character(0)"
+"CLF"	2794	"Clofazimine"	"Antimycobacterials"	"J04BA01"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"c(\"chlofazimine\", \"clofazimin\", \"clofazimina\", \"clofazimine\", \"clofaziminum\", \"lampren\", \"lamprene\", \"riminophenazine\")"	0.1	"g"			"character(0)"
-"CLF1"	"J01XX03"	2799	"Clofoctol"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	""	"c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")"					"character(0)"
+"CLF1"	2799	"Clofoctol"	"Other antibacterials"	"J01XX03"	"Other antibacterials"	"Other antibacterials"	""	"c(\"clofoctol\", \"clofoctolo\", \"clofoctolum\", \"gramplus\", \"octofene\")"					"character(0)"
-"CLM"	"J01CE07"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")"	1	"g"			"character(0)"
+"CLM"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"J01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"chlomethocillin\", \"clometacillin\", \"clometocilina\", \"clometocillin\", \"clometocilline\", \"clometocillinum\", \"rixapen\")"	1	"g"			"character(0)"
-"CLM1"	"J01AA11"	54680675	"Clomocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")"	1	"g"			"character(0)"
+"CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11"	"Tetracyclines"	"Tetracyclines"	""	"c(\"chlormethylencycline\", \"clomociclina\", \"clomocyclin\", \"clomocycline\", \"clomocyclinum\", \"megaclor\")"	1	"g"			"character(0)"
-"CTR"	"G01AF02"	2812	"Clotrimazole"	"Antifungals/antimycotics"			"clot"	"c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\", 
+"CTR"	2812	"Clotrimazole"	"Antifungals/antimycotics"	"c(\"A01AB18\", \"D01AC01\", \"G01AF02\")"			"clot"	"c(\"canesten\", \"canesten cream\", \"canesten solution\", \"canestene\", \"canestine\", \"canifug\", \"chlotrimazole\", \"cimitidine\", \"clomatin\", \"clotrimaderm\", \"clotrimaderm cream\", \"clotrimazol\", \"clotrimazole\", \"clotrimazolum\", \"cutistad\", \"desamix f\", \"diphenylmethane\", \"empecid\", \"esparol\", \"fem care\", \"femcare\", \"gyne lotrimin\", \"jidesheng\", \"kanesten\", \"klotrimazole\", \"lotrimax\", \"lotrimin\", \"lotrimin af\", \"lotrimin af cream\", \"lotrimin af lotion\", \"lotrimin af solution\", \"lotrimin cream\", \"lotrimin lotion\", 
 \"lotrimin solution\", \"monobaycuten\", \"mycelax\", \"mycelex\", \"mycelex cream\", \"mycelex g\", \"mycelex otc\", \"mycelex solution\", \"mycelex troches\", \"mycelex twin pack\", \"myclo cream\", \"myclo solution\", \"myclo spray solution\", \"mycofug\", \"mycosporin\", \"mykosporin\", \"nalbix\", \"otomax\", \"pedisafe\", \"rimazole\", \"stiemazol\", \"tibatin\", \"trimysten\", \"veltrim\")"					"character(0)"
-"CLO"	"J01CF02"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"\", \"clox\")"	"c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")"	2	"g"	2	"g"	"c(\"16628-0\", \"25250-2\")"
+"CLO"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"J01CF02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"\", \"clox\")"	"c(\"chloroxacillin\", \"clossacillina\", \"cloxacilina\", \"cloxacillin\", \"cloxacillin sodium\", \"cloxacilline\", \"cloxacillinna\", \"cloxacillinum\", \"cloxapen\", \"methocillin s\", \"orbenin\", \"syntarpen\", \"tegopen\")"	2	"g"	2	"g"	"c(\"16628-0\", \"25250-2\")"
-"COL"	"J01XB01"	5311054	"Colistin"	"Polymyxins"	"Other antibacterials"	"Polymyxins"	"c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")"	"c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")"			9	"MU"	"c(\"16645-4\", \"29493-4\")"
+"COL"	5311054	"Colistin"	"Polymyxins"	"c(\"A07AA10\", \"J01XB01\")"	"Other antibacterials"	"Polymyxins"	"c(\"cl\", \"coli\", \"cs\", \"cst\", \"ct\")"	"c(\"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"totazina\")"	9	"MU"	9	"MU"	"c(\"16645-4\", \"29493-4\")"
-"COP"			"Colistin/polysorbate"	"Other antibacterials"			""	""					""
+"COP"		"Colistin/polysorbate"	"Other antibacterials"				""	""					""
-"CYC"	"J04AB01"	6234	"Cycloserine"	"Oxazolidinones"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl"	"c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")"	0.75	"g"			"c(\"16702-3\", \"25251-0\", \"3519-6\")"
+"CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl"	"c(\"cicloserina\", \"closerin\", \"closina\", \"cyclorin\", \"cycloserin\", \"cycloserine\", \"cycloserinum\", \"farmiserina\", \"micoserina\", \"miroserina\", \"miroseryn\", \"novoserin\", \"oxamicina\", \"oxamycin\", \"seromycin\", \"tebemicina\", \"tisomycin\", \"wasserina\")"	0.75	"g"			"c(\"16702-3\", \"25251-0\", \"3519-6\")"
-"DAL"	"J01XA04"	23724878	"Dalbavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb"	"c(\"dalbavancin\", \"dalvance\")"			1.5		"character(0)"
+"DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb"	"c(\"dalbavancin\", \"dalvance\")"			1.5	"g"	"character(0)"
-"DAN"		71335	"Danofloxacin"	"Quinolones"			""	"c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")"					"character(0)"
+"DAN"	71335	"Danofloxacin"	"Quinolones"				""	"c(\"advocin\", \"danofloxacin\", \"danofloxacine\", \"danofloxacino\", \"danofloxacinum\")"					"character(0)"
-"DPS"	"J04BA02"	2955	"Dapsone"	"Other antibacterials"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\", 
+"DPS"	2955	"Dapsone"	"Other antibacterials"	"c(\"D10AX05\", \"J04BA02\")"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"c(\"aczone\", \"araldite ht\", \"atrisone\", \"avlosulfon\", \"avlosulfone\", \"avlosulphone\", \"avsulfor\", \"bis sulfone\", \"bissulfone\", \"bissulphone\", \"croysulfone\", \"croysulphone\", \"dapson\", \"dapsona\", \"dapsone\", \"dapsonum\", \"di sulfone\", \"diaphenyl sulfone\", \"diaphenylsulfon\", \"diaphenylsulfone\", \"diaphenylsulphon\", \"diaphenylsulphone\", \"dimitone\", \"diphenasone\", \"diphone\", \"disulfone\", \"disulone\", \"disulphone\", \"dubronax\", \"dubronaz\", \"dumitone\", \"eporal\", \"metabolite c\", \"novophone\", \"protogen\", \"servidapson\", 
 \"slphadione\", \"sulfadione\", \"sulfona\", \"sulfone ucb\", \"sulfonyldianiline\", \"sulphadione\", \"sulphonyldianiline\", \"sumicure s\", \"tarimyl\", \"udolac\", \"wln: zr dswr dz\")"	50	"mg"			"9747-7"
-"DAP"	"J01XX09"	16134395	"Daptomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"dap\", \"dapt\")"	"c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")"			0.28	"g"	"character(0)"
+"DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09"	"Other antibacterials"	"Other antibacterials"	"c(\"dap\", \"dapt\")"	"c(\"cidecin\", \"cubicin\", \"dapcin\", \"daptomicina\", \"daptomycine\", \"daptomycinum\")"			0.28	"g"	"character(0)"
-"DFX"		487101	"Delafloxacin"	"Quinolones"			""	"c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")"					"character(0)"
+"DFX"	487101	"Delafloxacin"	"Quinolones"	"J01MA23"			""	"c(\"baxdela\", \"delafloxacin\", \"delafloxacinum\")"	0.9	"g"	0.6	"g"	"character(0)"
-"DLM"	"J04AK06"	6480466	"Delamanid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"c(\"delamanid\", \"deltyba\")"	0.2				"character(0)"
+"DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"c(\"delamanid\", \"deltyba\")"	0.2	"g"			"character(0)"
-"DEM"	"J01AA01"	54680690	"Demeclocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")"	0.6	"g"			"c(\"10982-7\", \"29494-2\")"
+"DEM"	54680690	"Demeclocycline"	"Tetracyclines"	"c(\"D06AA01\", \"J01AA01\")"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bioterciclin\", \"clortetrin\", \"deganol\", \"demeclociclina\", \"demeclocycline\", \"demeclocyclinum\", \"demeclor\", \"demetraclin\", \"diuciclin\", \"elkamicina\", \"ledermycin\", \"mexocine\", \"novotriclina\", \"perciclina\", \"sumaclina\")"	0.6	"g"			"c(\"10982-7\", \"29494-2\")"
-"DKB"	"J01GB09"	470999	"Dibekacin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")"			0.14	"g"	"character(0)"
+"DKB"	470999	"Dibekacin"	"Aminoglycosides"	"J01GB09"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"debecacin\", \"dibekacin\", \"dibekacin sulfate\", \"dibekacina\", \"dibekacine\", \"dibekacinum\", \"dideoxykanamycin b\", \"kappati\", \"orbicin\", \"panamicin\")"			0.14	"g"	"character(0)"
-"DIC"	"J01CF01"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"\", \"dicl\")"	"c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")"	2	"g"	2	"g"	"c(\"10984-3\", \"16769-2\", \"25252-8\")"
+"DIC"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"J01CF01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"\", \"dicl\")"	"c(\"dichloroxacillin\", \"diclossacillina\", \"dicloxaciclin\", \"dicloxacilin\", \"dicloxacilina\", \"dicloxacillin\", \"dicloxacillin sodium\", \"dicloxacillina\", \"dicloxacilline\", \"dicloxacillinum\", \"dicloxacycline\", \"dycill\", \"dynapen\", \"maclicine\", \"nm|| dicloxacillin\", \"pathocil\")"	2	"g"	2	"g"	"c(\"10984-3\", \"16769-2\", \"25252-8\")"
-"DIF"		56206	"Difloxacin"	"Quinolones"			""	"difloxacin"					"character(0)"
+"DIF"	56206	"Difloxacin"	"Quinolones"				""	"difloxacin"					"character(0)"
-"DIR"	"J01FA13"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")"	0.5	"g"			"character(0)"
+"DIR"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"J01FA13"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"dirithromycin\", \"dirithromycine\", \"dirithromycinum\", \"diritromicina\", \"divitross\", \"dynabac\", \"noriclan\", \"valodin\")"	0.5	"g"			"character(0)"
-"DOR"	"J01DH04"	73303	"Doripenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")"			1.5		"character(0)"
+"DOR"	73303	"Doripenem"	"Carbapenems"	"J01DH04"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"c(\"doribax\", \"doripenem\", \"doripenem hydrate\", \"finibax\")"			1.5	"g"	"character(0)"
-"DOX"	"J01AA02"	54671203	"Doxycycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"dox\", \"doxy\")"	"c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")"	0.1	"g"	0.1	"g"	"c(\"10986-8\", \"21250-6\", \"26902-7\")"
+"DOX"	54671203	"Doxycycline"	"Tetracyclines"	"c(\"A01AB22\", \"J01AA02\")"	"Tetracyclines"	"Tetracyclines"	"c(\"dox\", \"doxy\")"	"c(\"atridox\", \"azudoxat\", \"deoxymykoin\", \"dossiciclina\", \"doxcycline anhydrous\", \"doxiciclina\", \"doxitard\", \"doxivetin\", \"doxycen\", \"doxychel\", \"doxycin\", \"doxycyclin\", \"doxycycline\", \"doxycycline calcium\", \"doxycycline hyclate\", \"doxycyclinum\", \"doxylin\", \"doxysol\", \"doxytec\", \"doxytetracycline\", \"hydramycin\", \"investin\", \"jenacyclin\", \"liviatin\", \"monodox\", \"oracea\", \"periostat\", \"ronaxan\", \"spanor\", \"supracyclin\", \"vibramycin\", \"vibramycin novum\", \"vibramycine\", \"vibravenos\", \"zenavod\")"	0.1	"g"	0.1	"g"	"c(\"10986-8\", \"21250-6\", \"26902-7\")"
-"ECO"	"J01XDXX"	3198	"Econazole"	"Antifungals/antimycotics"			"econ"	"c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")"					"character(0)"
+"ECO"	3198	"Econazole"	"Antifungals/antimycotics"	"c(\"D01AC03\", \"G01AF05\")"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"c(\"econazol\", \"econazole\", \"econazolum\", \"ecostatin\", \"ecostatin cream\", \"palavale\", \"pevaryl\", \"spectazole\", \"spectazole cream\")"					"character(0)"
-"ENX"	"J01MA04"	3229	"Enoxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"enox\")"	"c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")"	0.8	"g"			"c(\"16816-1\", \"3590-7\")"
+"ENX"	3229	"Enoxacin"	"Quinolones"	"J01MA04"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"enox\")"	"c(\"almitil\", \"bactidan\", \"bactidron\", \"comprecin\", \"enofloxacine\", \"enoksetin\", \"enoram\", \"enoxacin\", \"enoxacina\", \"enoxacine\", \"enoxacino\", \"enoxacinum\", \"enoxen\", \"enoxin\", \"enoxor\", \"flumark\", \"penetrex\")"	0.8	"g"			"c(\"16816-1\", \"3590-7\")"
-"ENR"		71188	"Enrofloxacin"	"Quinolones"			""	"c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")"					"character(0)"
+"ENR"	71188	"Enrofloxacin"	"Quinolones"				""	"c(\"baytril\", \"enrofloxacin\", \"enrofloxacine\", \"enrofloxacino\", \"enrofloxacinum\")"					"character(0)"
-"ENV"		135565326	"Enviomycin (Tuberactinomycin)"	"Antimycobacterials"			""	"c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")"					"character(0)"
+"ENV"	135565326	"Enviomycin (Tuberactinomycin)"	"Antimycobacterials"				""	"c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")"					"character(0)"
-"EPE"			"Eperozolid"	"Other antibacterials"			""	""					""
+"EPE"		"Eperozolid"	"Other antibacterials"				""	""					""
-"EPC"	"J01CA07"	71392	"Epicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")"	2	"g"	2	"g"	"character(0)"
+"EPC"	71392	"Epicillin"	"Beta-lactams/penicillins"	"J01CA07"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"dexacillin\", \"dihydroampicillin\", \"epicilina\", \"epicillin\", \"epicilline\", \"epicillinum\")"	2	"g"	2	"g"	"character(0)"
-"EPP"		68916	"Epiroprim"	"Other antibacterials"			""	"c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")"					"character(0)"
+"EPP"	68916	"Epiroprim"	"Other antibacterials"				""	"c(\"epiroprim\", \"epiroprima\", \"epiroprime\", \"epiroprimum\")"					"character(0)"
-"ERV"	"J01AA13"	54726192	"Eravacycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"erav"	"eravacycline"					"character(0)"
+"ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"eravacycline"					"character(0)"
-"ETP"	"J01DH03"	150610	"Ertapenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"erta\", \"etp\")"	"c(\"ertapenem\", \"invanz\")"			1	"g"	"character(0)"
+"ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"erta\", \"etp\")"	"c(\"ertapenem\", \"invanz\")"			1	"g"	"character(0)"
-"ERY"	"J01FA01"	12560	"Erythromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"e\", \"em\", \"ery\", \"eryt\")"	"c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\", 
+"ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"c(\"D10AF02\", \"J01FA01\", \"S01AA17\")"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"e\", \"em\", \"ery\", \"eryt\")"	"c(\"abboticin\", \"abomacetin\", \"acneryne\", \"acnesol\", \"akne cordes losung\", \"aknederm ery gel\", \"aknemycin\", \"austrias\", \"benzamycin\", \"derimer\", \"deripil\", \"dotycin\", \"dumotrycin\", \"emuvin\", \"emycin\", \"endoeritrin\", \"erecin\", \"erisone\", \"eritomicina\", \"eritrocina\", \"eritromicina\", \"ermycin\", \"eryacne\", \"eryacnen\", \"eryc sprinkles\", \"erycen\", \"erycette\", \"erycin\", \"erycinum\", \"eryderm\", \"erydermer\", \"erygel\", \"eryhexal\", \"erymax\", \"erymed\", \"erysafe\", \"erytab\", \"erythrocin\", \"erythrocin stearate\", 
 \"erythroderm\", \"erythrogran\", \"erythroguent\", \"erythromid\", \"erythromycin\", \"erythromycin a\", \"erythromycin base\", \"erythromycin lactate\", \"erythromycine\", \"erythromycines\", \"erythromycinum\", \"erytop\", \"erytrociclin\", \"ilocaps\", \"ilosone\", \"iloticina\", \"ilotycin\", \"ilotycin gluceptate\", \"ilotycin t.s.\", \"inderm\", \"inderm gel\", \"indermretcin\", \"latotryd\", \"lederpax\", \"mephamycin\", \"mercina\", \"oftamolets\", \"paediathrocin\", \"pantoderm\", \"pantodrin\", \"pantomicina\", \"pce dispertab\", \"pharyngocin\", \"primacine\", 
 \"propiocine\", \"proterytrin\", \"retcin\", \"robimycin\", \"romycin\", \"sansac\", \"skid gel e\", \"staticin\", \"stiemicyn\", \"stiemycin\", \"theramycin z\", \"tiloryth\", \"tiprocin\", \"torlamicina\", \"udima ery gel\", \"wyamycin s\")"	2	"g"	1	"g"	"c(\"12298-6\", \"16829-4\", \"25275-9\", \"3597-2\")"
-"ETH"	"J04AK02"	14052	"Ethambutol"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha"	"c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")"	1.2	"g"	1.2	"g"	"c(\"25404-5\", \"3607-9\")"
+"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha"	"c(\"aethambutolum\", \"ebutol\", \"etambutol\", \"etambutolo\", \"etapiam\", \"ethambutol\", \"ethambutolum\", \"myambutol\", \"mycobutol\", \"purderal\", \"servambutol\")"	1.2	"g"	1.2	"g"	"c(\"25404-5\", \"3607-9\")"
-"ETI"	"J04AM03"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
+"ETI"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"J04AM03"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"ETI1"	"J04AD03"	2761171	"Ethionamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\", 
+"ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"c(\"aethionamidum\", \"aetina\", \"aetiva\", \"amidazin\", \"amidazine\", \"ethatyl\", \"ethimide\", \"ethina\", \"ethinamide\", \"ethionamide\", \"ethionamidum\", \"ethioniamide\", \"ethylisothiamide\", \"ethyonomide\", \"etimid\", \"etiocidan\", \"etionamid\", \"etionamida\", \"etionamide\", \"etioniamid\", \"etionid\", \"etionizin\", \"etionizina\", \"etionizine\", \"fatoliamid\", \"iridocin\", \"iridocin bayer\", \"iridozin\", \"isothin\", \"isotiamida\", \"itiocide\", \"nicotion\", \"nisotin\", \"nizotin\", \"rigenicid\", \"sertinon\", \"teberus\", \"thianid\", \"thianide\", 
 \"thioamide\", \"thiodine\", \"thiomid\", \"thioniden\", \"tianid\", \"tiomid\", \"trecator\", \"trecator sc\", \"trekator\", \"trescatyl\", \"trescazide\", \"tubenamide\", \"tubermin\", \"tuberoid\", \"tuberoson\")"	0.75	"g"			"16845-0"
-"ETO"		6034	"Ethopabate"	"Other antibacterials"			""	"c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")"					"character(0)"
+"ETO"	6034	"Ethopabate"	"Other antibacterials"				""	"c(\"amprol plus\", \"ethopabat\", \"ethopabate\", \"ethyl pabate\")"					"character(0)"
-"FAR"	"J01DI03"	65894	"Faropenem"	"Other antibacterials"			""	"c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")"	0.75				"character(0)"
+"FAR"	65894	"Faropenem"	"Other antibacterials"	"J01DI03"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	"c(\"faropenem\", \"faropenem sodium\", \"fropenem\", \"fropenum sodium\")"	0.75	"g"			"character(0)"
-"FDX"		10034073	"Fidaxomicin"	"Other antibacterials"			""	"c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")"					"character(0)"
+"FDX"	10034073	"Fidaxomicin"	"Other antibacterials"	"A07AA12"			""	"c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")"	0.4	"g"			"character(0)"
-"FIN"		11567473	"Finafloxacin"	"Quinolones"			""	"finafloxacin"					"character(0)"
+"FIN"	11567473	"Finafloxacin"	"Quinolones"				""	"finafloxacin"					"character(0)"
-"FLA"		46783781	"Flavomycin"	"Other antibacterials"			""	"moenomycin complex"					"character(0)"
+"FLA"	46783781	"Flavomycin"	"Other antibacterials"				""	"moenomycin complex"					"character(0)"
-"FLE"	"J01MA08"	3357	"Fleroxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"fler\")"	"c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")"	0.4	"g"	0.4	"g"	"character(0)"
+"FLE"	3357	"Fleroxacin"	"Quinolones"	"J01MA08"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"fler\")"	"c(\"fleroxacin\", \"fleroxacine\", \"fleroxacino\", \"fleroxacinum\", \"fleroxicin\", \"megalocin\", \"megalone\", \"megalosin\", \"quinodis\")"	0.4	"g"	0.4	"g"	"character(0)"
-"FLO"		65864	"Flomoxef"	"Other antibacterials"			""	"c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")"					"character(0)"
+"FLO"	65864	"Flomoxef"	"Other antibacterials"	"J01DC14"			""	"c(\"flomoxef\", \"flomoxefo\", \"flomoxefum\")"			2	"g"	"character(0)"
-"FLR"		114811	"Florfenicol"	"Other antibacterials"			""	"c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")"					"87599-7"
+"FLR"	114811	"Florfenicol"	"Other antibacterials"				""	"c(\"aquafen\", \"florfenicol\", \"nuflor\", \"nuflor gold\")"					"87599-7"
-"FLC"	"J01CF05"	21319	"Flucloxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"clox\", \"flux\")"	"c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")"	2	"g"	2	"g"	"character(0)"
+"FLC"	21319	"Flucloxacillin"	"Beta-lactams/penicillins"	"J01CF05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"clox\", \"flux\")"	"c(\"floxacillin\", \"floxapen\", \"floxapen sodium salt\", \"fluclox\", \"flucloxacilina\", \"flucloxacillin\", \"flucloxacilline\", \"flucloxacillinum\", \"fluorochloroxacillin\")"	2	"g"	2	"g"	"character(0)"
-"FLU"	"J02AC01"	3365	"Fluconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"c(\"fluc\", \"fluz\", \"flz\")"	"c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")"	0.2	"g"	0.2	"g"	"c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")"
+"FLU"	3365	"Fluconazole"	"Antifungals/antimycotics"	"c(\"D01AC15\", \"J02AC01\")"	"Antimycotics for systemic use"	"Triazole derivatives"	"c(\"fluc\", \"fluz\", \"flz\")"	"c(\"alflucoz\", \"alfumet\", \"biocanol\", \"biozole\", \"biozolene\", \"canzol\", \"cryptal\", \"diflazon\", \"diflucan\", \"dimycon\", \"elazor\", \"flucazol\", \"fluconazol\", \"fluconazole\", \"fluconazole capsules\", \"fluconazolum\", \"flucostat\", \"flukezol\", \"flunazol\", \"flunizol\", \"flusol\", \"fluzon\", \"fluzone\", \"forcan\", \"fuconal\", \"fungata\", \"loitin\", \"oxifugol\", \"pritenzol\", \"syscan\", \"trican\", \"triconal\", \"triflucan\", \"zoltec\")"	0.2	"g"	0.2	"g"	"c(\"10987-6\", \"16870-8\", \"25255-1\", \"80530-9\")"
-"FLM"	"J01MB07"	3374	"Flumequine"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")"	1.2	"g"			"character(0)"
+"FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"apurone\", \"fantacin\", \"flumequine\", \"flumequino\", \"flumequinum\", \"flumigal\", \"flumiquil\", \"flumisol\", \"flumix\", \"imequyl\")"	1.2	"g"			"character(0)"
-"FLR1"	"J01FA14"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")"	0.75	"g"			"character(0)"
+"FLR1"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"J01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"flurithromicina\", \"flurithromycime\", \"flurithromycin\", \"flurithromycine\", \"flurithromycinum\", \"fluritromicina\", \"fluritromycinum\", \"flurizic\")"	0.75	"g"			"character(0)"
-"FFL"		214356	"Fosfluconazole"	"Antifungals/antimycotics"			""	"c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")"					"character(0)"
+"FFL"	214356	"Fosfluconazole"	"Antifungals/antimycotics"				""	"c(\"fosfluconazole\", \"phosfluconazole\", \"procif\", \"prodif\")"					"character(0)"
-"FOS"	"J01XX01"	446987	"Fosfomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")"	"c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")"	3	"g"	8	"g"	"character(0)"
+"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01"	"Other antibacterials"	"Other antibacterials"	"c(\"ff\", \"fm\", \"fo\", \"fof\", \"fos\", \"fosf\")"	"c(\"fosfocina\", \"fosfomicina\", \"fosfomycin\", \"fosfomycin sodium\", \"fosfomycine\", \"fosfomycinum\", \"fosfonomycin\", \"monuril\", \"monurol\", \"phosphonemycin\", \"phosphonomycin\", \"veramina\")"	3	"g"	8	"g"	"character(0)"
-"FMD"		572	"Fosmidomycin"	"Other antibacterials"			""	"c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")"					"character(0)"
+"FMD"	572	"Fosmidomycin"	"Other antibacterials"				""	"c(\"fosmidomycin\", \"fosmidomycina\", \"fosmidomycine\", \"fosmidomycinum\")"					"character(0)"
-"FRM"		8378	"Framycetin"	"Aminoglycosides"			"c(\"\", \"fram\")"	"c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", 
+"FRM"	8378	"Framycetin"	"Aminoglycosides"	"c(\"D09AA01\", \"R01AX08\", \"S01AA07\")"			"c(\"\", \"fram\")"	"c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", 
 \"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")"					"character(0)"
-"FRZ"		5323714	"Furazolidone"	"Other antibacterials"			""	"c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\", 
+"FRZ"	5323714	"Furazolidone"	"Other antibacterials"	"G01AX06"			""	"c(\"bifuron\", \"corizium\", \"coryzium\", \"diafuron\", \"enterotoxon\", \"furall\", \"furaxon\", \"furaxone\", \"furazol\", \"furazolidine\", \"furazolidon\", \"furazolidona\", \"furazolidone\", \"furazolidonum\", \"furazolum\", \"furazon\", \"furidon\", \"furovag\", \"furox aerosol powder\", \"furoxal\", \"furoxane\", \"furoxon\", \"furoxone\", \"furoxone liquid\", \"furoxone swine mix\", \"furozolidine\", \"giardil\", \"giarlam\", \"medaron\", \"neftin\", \"nicolen\", \"nifulidone\", \"nifuran\", \"nifurazolidone\", \"nifurazolidonum\", \"nitrofurazolidone\", \"nitrofurazolidonum\", 
 \"nitrofuroxon\", \"optazol\", \"ortazol\", \"puradin\", \"roptazol\", \"sclaventerol\", \"tikofuran\", \"topazone\", \"trichofuron\", \"tricofuron\", \"tricoron\", \"trifurox\", \"viofuragyn\")"					"character(0)"
-"FUS"	"J01XC01"	3000226	"Fusidic acid"	"Other antibacterials"	"Other antibacterials"	"Steroid antibacterials"	"c(\"fa\", \"fusi\")"	"c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")"	1.5	"g"	1.5	"g"	"character(0)"
+"FUS"	3000226	"Fusidic acid"	"Other antibacterials"	"c(\"D06AX01\", \"D09AA02\", \"J01XC01\", \"S01AA13\")"	"Other antibacterials"	"Steroid antibacterials"	"c(\"fa\", \"fusi\")"	"c(\"acide fusidique\", \"acido fusidico\", \"acidum fusidicum\", \"flucidin\", \"fucidate\", \"fucidate sodium\", \"fucidic acid\", \"fucidin\", \"fucidin acid\", \"fucithalmic\", \"fusidate\", \"fusidate acid\", \"fusidic acid\", \"fusidine\", \"fusidinic acid\", \"ramycin\")"	1.5	"g"	1.5	"g"	"character(0)"
-"GAM"		59364992	"Gamithromycin"	"Macrolides/lincosamides"			""	"gamithromycin"					"character(0)"
+"GAM"	59364992	"Gamithromycin"	"Macrolides/lincosamides"				""	"gamithromycin"					"character(0)"
-"GRN"		124093	"Garenoxacin"	"Quinolones"			""	"c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")"					"character(0)"
+"GRN"	124093	"Garenoxacin"	"Quinolones"	"J01MA19"			""	"c(\"ganefloxacin\", \"garenfloxacin\", \"garenoxacin\")"	0.4	"g"			"character(0)"
-"GAT"	"J01MA16"	5379	"Gatifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"gati\")"	"c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")"	0.4	"g"	0.4	"g"	"character(0)"
+"GAT"	5379	"Gatifloxacin"	"Quinolones"	"c(\"J01MA16\", \"S01AE06\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"gati\")"	"c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")"	0.4	"g"	0.4	"g"	"character(0)"
-"GEM"	"J01MA15"	9571107	"Gemifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")"	0.32				"character(0)"
+"GEM"	9571107	"Gemifloxacin"	"Quinolones"	"J01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")"	0.32	"g"			"character(0)"
-"GEN"	"J01GB03"	3467	"Gentamicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"cn\", \"gen\", \"gent\", \"gm\")"	"c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")"			0.24	"g"	"c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
+"GEN"	3467	"Gentamicin"	"Aminoglycosides"	"c(\"D06AX07\", \"J01GB03\", \"S01AA11\", \"S02AA14\", \"S03AA06\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"cn\", \"gen\", \"gent\", \"gm\")"	"c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")"			0.24	"g"	"c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
-"GEH"			"Gentamicin-high"	"Aminoglycosides"			"c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")"	""					""
+"GEH"		"Gentamicin-high"	"Aminoglycosides"				"c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")"	""					""
-"GEP"		25101874	"Gepotidacin"	"Other antibacterials"			""	"gepotidacin"					"character(0)"
+"GEP"	25101874	"Gepotidacin"	"Other antibacterials"				""	"gepotidacin"					"character(0)"
-"GRX"	"J01MA11"	72474	"Grepafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"grep\")"	"grepafloxacin"	0.4	"g"			"character(0)"
+"GRX"	72474	"Grepafloxacin"	"Quinolones"	"J01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"grep\")"	"grepafloxacin"	0.4	"g"			"character(0)"
-"GRI"		441140	"Griseofulvin"	"Antifungals/antimycotics"			""	"c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", 
+"GRI"	441140	"Griseofulvin"	"Antifungals/antimycotics"	"c(\"D01AA08\", \"D01BA01\")"			""	"c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", 
-\"grisovin\", \"grisovin fp\", \"grizeofulvin\", \"grysio\", \"guservin\", \"lamoryl\", \"likuden\", \"likunden\", \"murfulvin\", \"poncyl\", \"spirofulvin\", \"sporostatin xan\", \"xuanjing\")"					"12402-4"
+\"grisovin\", \"grisovin fp\", \"grizeofulvin\", \"grysio\", \"guservin\", \"lamoryl\", \"likuden\", \"likunden\", \"murfulvin\", \"poncyl\", \"spirofulvin\", \"sporostatin xan\", \"xuanjing\")"	0.5	"g"			"12402-4"
-"HAB"		175989	"Habekacin"	"Aminoglycosides"			""	"c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")"					"character(0)"
+"HAB"	175989	"Habekacin"	"Aminoglycosides"				""	"c(\"arbekacin sulfate\", \"habekacin\", \"habekacin sulfate\", \"habekacin xsulfate\")"					"character(0)"
-"HCH"	"J02AA02"	11979956	"Hachimycin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Antibiotics"	""	"c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")"					"character(0)"
+"HCH"	11979956	"Hachimycin"	"Antifungals/antimycotics"	"c(\"D01AA03\", \"G01AA06\", \"J02AA02\")"	"Antimycotics for systemic use"	"Antibiotics"	""	"c(\"cabimicina\", \"hachimicina\", \"hachimycin\", \"hachimycine\", \"hachimycinum\", \"trichomycinum\", \"trichonat\")"					"character(0)"
-"HET"	"J01CA18"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")"	2	"g"			"character(0)"
+"HET"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"J01CA18"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"etacillina\", \"hetacilina\", \"hetacillin\", \"hetacilline\", \"hetacillinum\", \"phenazacillin\", \"versapen\")"	2	"g"			"character(0)"
-"HYG"		56928061	"Hygromycin"	"Aminoglycosides"			""	"c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")"					"character(0)"
+"HYG"	56928061	"Hygromycin"	"Aminoglycosides"				""	"c(\"antihelmycin\", \"hydromycin b\", \"hygrovetine\")"					"character(0)"
-"ICL"		213043	"Iclaprim"	"Other antibacterials"			""	"c(\"iclaprim\", \"mersarex\")"					"character(0)"
+"ICL"	213043	"Iclaprim"	"Other antibacterials"	"J01EA03"			""	"c(\"iclaprim\", \"mersarex\")"					"character(0)"
-"IPM"	"J01DH51"	104838	"Imipenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"imci\", \"imi\", \"imip\", \"imp\")"	"c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")"			2	"g"	"c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")"
+"IPM"	104838	"Imipenem"	"Carbapenems"	"J01DH51"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"imci\", \"imi\", \"imip\", \"imp\")"	"c(\"imipemide\", \"imipenem\", \"imipenem anhydrous\", \"imipenem/cilastatin\", \"imipenemum\", \"imipenen\", \"primaxin\", \"tienamycin\")"			2	"g"	"c(\"17010-0\", \"25257-7\", \"27331-8\", \"3688-9\")"
-"IPE"			"Imipenem/EDTA"	"Carbapenems"			""	""					""
+"IPE"		"Imipenem/EDTA"	"Carbapenems"				""	""					""
-"IMR"			"Imipenem/relebactam"	"Carbapenems"			""	""					""
+"IMR"		"Imipenem/relebactam"	"Carbapenems"				""	""					""
-"ISV"		6918485	"Isavuconazole"	"Antifungals/antimycotics"			"c(\"\", \"isav\")"	"isavuconazole"					"character(0)"
+"ISV"	6918485	"Isavuconazole"	"Antifungals/antimycotics"	"J02AC05"			"c(\"\", \"isav\")"	"isavuconazole"	0.2	"g"	0.2	"g"	"character(0)"
-"ISE"	"J01GB11"	3037209	"Isepamicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")"			0.4	"g"	"character(0)"
+"ISE"	3037209	"Isepamicin"	"Aminoglycosides"	"J01GB11"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"isepacin\", \"isepalline\", \"isepamicin\", \"isepamicina\", \"isepamicine\", \"isepamicinum\")"			0.4	"g"	"character(0)"
-"ISO"	"D01AC05"	3760	"Isoconazole"	"Antifungals/antimycotics"	"Antimycotics for topic use"	"Triazole derivatives"	""	"c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")"					"character(0)"
+"ISO"	3760	"Isoconazole"	"Antifungals/antimycotics"	"c(\"D01AC05\", \"G01AF07\")"	"Antimycotics for topic use"	"Triazole derivatives"	""	"c(\"isoconazol\", \"isoconazole\", \"isoconazolum\", \"travogen\")"					"character(0)"
-"INH"	"J04AC01"	3767	"Isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh"	"c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\", 
+"INH"	3767	"Isoniazid"	"Antimycobacterials"	"J04AC01"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh"	"c(\"abdizide\", \"andrazide\", \"anidrasona\", \"antimicina\", \"antituberkulosum\", \"armacide\", \"armazid\", \"armazide\", \"atcotibine\", \"azt + isoniazid\", \"azuren\", \"bacillin\", \"cemidon\", \"chemiazid\", \"chemidon\", \"continazine\", \"cortinazine\", \"cotinazin\", \"cotinizin\", \"defonin\", \"dibutin\", \"diforin\", \"dinacrin\", \"ditubin\", \"ebidene\", \"eralon\", \"ertuban\", \"eutizon\", \"evalon\", \"fetefu\", \"fimalene\", \"hid rasonil\", \"hidranizil\", \"hidrasonil\", \"hidrulta\", \"hidrun\", \"hycozid\", \"hydrazid\", \"hydrazide\", \"hyozid\", \"i.a.i.\", 
 \"idrazil\", \"inizid\", \"iscotin\", \"isidrina\", \"ismazide\", \"isobicina\", \"isocid\", \"isocidene\", \"isocotin\", \"isohydrazide\", \"isokin\", \"isolyn\", \"isonerit\", \"isonex\", \"isoniacid\", \"isoniazid\", \"isoniazid sa\", \"isoniazida\", \"isoniazide\", \"isoniazidum\", \"isonicazide\", \"isonicid\", \"isonico\", \"isonicotan\", \"isonicotil\", \"isonicotinhydrazid\", \"isonicotinohydrazide\", \"isonide\", \"isonidrin\", \"isonikazid\", \"isonilex\", \"isonin\", \"isonindon\", \"isonirit\", \"isoniton\", \"isonizida\", \"isonizide\", \"isotamine\", \"isotebe\", 
 \"isotebezid\", \"isotinyl\", \"isozid\", \"isozide\", \"isozyd\", \"laniazid\", \"laniozid\", \"lanizid\", \"mayambutol\", \"mybasan\", \"neoteben\", \"neoxin\", \"neumandin\", \"niadrin\", \"nicazide\", \"nicetal\", \"nicizina\", \"niconyl\", \"nicotibina\", \"nicotibine\", \"nicotisan\", \"nicozide\", \"nidaton\", \"nidrazid\", \"nikozid\", \"niplen\", \"nitadon\", \"niteban\", \"nydrazid\", \"nyscozid\", \"pelazid\", \"percin\", \"phthisen\", \"pycazide\", \"pyreazid\", \"pyricidin\", \"pyridicin\", \"pyrizidin\", \"raumanon\", \"razide\", \"retozide\", \"rifater\", \"rimicid\", 
 \"rimifon\", \"rimiphone\", \"rimitsid\", \"robiselin\", \"robisellin\", \"roxifen\", \"sanohidrazina\", \"sauterazid\", \"sauterzid\", \"stanozide\", \"tebecid\", \"tebenic\", \"tebexin\", \"tebilon\", \"teebaconin\", \"tekazin\", \"tibazide\", \"tibemid\", \"tibiazide\", \"tibinide\", \"tibison\", \"tibivis\", \"tibizide\", \"tibusan\", \"tisiodrazida\", \"tizide\", \"tubazid\", \"tubazide\", \"tubeco\", \"tubecotubercid\", \"tuberian\", \"tubicon\", \"tubilysin\", \"tubizid\", \"tubomel\", \"unicocyde\", \"unicozyde\", \"vazadrine\", \"vederon\", \"zidafimia\", \"zinadon\", 
 \"zonazide\")"	0.3	"g"	0.3	"g"	"c(\"25451-6\", \"26756-7\", \"3697-0\", \"40371-7\")"
-"ITR"	"J02AC02"	3793	"Itraconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra"	"c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")"	0.2	"g"	0.2	"g"	"c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")"
+"ITR"	3793	"Itraconazole"	"Antifungals/antimycotics"	"J02AC02"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra"	"c(\"itraconazol\", \"itraconazole\", \"itraconazolum\", \"itraconzaole\", \"itrazole\", \"oriconazole\", \"sporanox\")"	0.2	"g"	0.2	"g"	"c(\"10989-2\", \"12392-7\", \"25258-5\", \"27081-9\", \"32184-4\", \"32185-1\", \"80531-7\")"
-"JOS"	"J01FA07"	5282165	"Josamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")"	2	"g"			"character(0)"
+"JOS"	5282165	"Josamycin"	"Macrolides/lincosamides"	"J01FA07"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"josacine\", \"josamicina\", \"josamycin\", \"josamycine\", \"josamycinum\")"	2	"g"			"character(0)"
-"KAN"	"J01GB04"	6032	"Kanamycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")"	"c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")"			1	"g"	"c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")"
+"KAN"	6032	"Kanamycin"	"Aminoglycosides"	"c(\"A07AA08\", \"J01GB04\", \"S01AA24\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"hlk\", \"k\", \"kan\", \"kana\", \"km\")"	"c(\"kanamicina\", \"kanamycin\", \"kanamycin a\", \"kanamycin base\", \"kanamycine\", \"kanamycinum\", \"kantrex\", \"kenamycin a\", \"klebcil\", \"liposomal kanamycin\")"	3	"g"	1	"g"	"c(\"23889-9\", \"3698-8\", \"3699-6\", \"3700-2\", \"47395-9\")"
-"KAH"			"Kanamycin-high"	"Aminoglycosides"			"c(\"\", \"k_h\", \"kahl\")"	""					""
+"KAH"		"Kanamycin-high"	"Aminoglycosides"				"c(\"\", \"k_h\", \"kahl\")"	""					""
-"KAC"			"Kanamycin/cephalexin"	"Aminoglycosides"			""	""					""
+"KAC"		"Kanamycin/cephalexin"	"Aminoglycosides"				""	""					""
-"KET"	"J02AB02"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Imidazole derivatives"	"c(\"keto\", \"ktc\")"	"c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")"	0.2	"g"			"c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")"
+"KET"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"c(\"D01AC08\", \"G01AF11\", \"H02CA03\", \"J02AB02\")"	"Antimycotics for systemic use"	"Imidazole derivatives"	"c(\"keto\", \"ktc\")"	"c(\"extina\", \"fungarest\", \"fungoral\", \"ketocanazole\", \"ketoconazol\", \"ketoconazole\", \"ketoconazolum\", \"ketoderm\", \"nizoral\", \"xolegel\")"	0.2	"g"			"c(\"10990-0\", \"12393-5\", \"25259-3\", \"60091-6\", \"60092-4\")"
-"KIT"			"Kitasamycin (Leucomycin)"	"Macrolides/lincosamides"			""	""					""
+"KIT"		"Kitasamycin (Leucomycin)"	"Macrolides/lincosamides"				""	""					""
-"LAS"		5360807	"Lasalocid"	"Other antibacterials"			""	"c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")"					"87598-9"
+"LAS"	5360807	"Lasalocid"	"Other antibacterials"				""	"c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")"					"87598-9"
-"LTM"	"J01DD06"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"mox\", \"moxa\")"	"c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")"			4	"g"	"character(0)"
+"LTM"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"J01DD06"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"mox\", \"moxa\")"	"c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")"			4	"g"	"character(0)"
-"LMU"		25185057	"Lefamulin"	"Other antibacterials"			""	"lefamulin"					"character(0)"
+"LMU"	25185057	"Lefamulin"	"Other antibacterials"	"J01XX12"			""	"lefamulin"					"character(0)"
-"LEN"		65646	"Lenampicillin"	"Beta-lactams/penicillins"			""	"c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")"					"character(0)"
+"LEN"	65646	"Lenampicillin"	"Beta-lactams/penicillins"				""	"c(\"lenampicilina\", \"lenampicillin\", \"lenampicillin hcl\", \"lenampicilline\", \"lenampicillinum\")"					"character(0)"
-"LVX"	"J01MA12"	149096	"Levofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"le\", \"lev\", \"levo\", \"lvx\")"	"c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")"	0.5	"g"	0.5	"g"	"c(\"21368-6\", \"30532-6\", \"30533-4\")"
+"LVX"	149096	"Levofloxacin"	"Quinolones"	"c(\"J01MA12\", \"S01AE05\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"le\", \"lev\", \"levo\", \"lvx\")"	"c(\"aeroquin\", \"cravit\", \"cravit hydrate\", \"cravit iv\", \"cravit ophthalmic\", \"elequine\", \"floxacin\", \"floxel\", \"iquix hydrate\", \"leroxacin\", \"lesacin\", \"levaquin\", \"levaquin hydrate\", \"levo floxacin\", \"levofiexacin\", \"levofloxacin\", \"levofloxacin hydrate\", \"levofloxacine\", \"levofloxacino\", \"levofloxacinum\", \"levokacin\", \"levoxacin\", \"mosardal\", \"nofaxin\", \"oftaquix\", \"quixin\", \"reskuin\", \"tavanic\", \"unibiotic\", \"venaxan\", \"volequin\")"	0.5	"g"	0.5	"g"	"c(\"21368-6\", \"30532-6\", \"30533-4\")"
-"LND"		9850038	"Levonadifloxacin"	"Quinolones"			""	"levonadifloxacin"					"character(0)"
+"LND"	9850038	"Levonadifloxacin"	"Quinolones"	"J01MA24"			""	"levonadifloxacin"					"character(0)"
-"LSP"			"Linco-spectin (lincomycin/spectinomycin)"	"Other antibacterials"			""	""					""
+"LSP"		"Linco-spectin (lincomycin/spectinomycin)"	"Other antibacterials"				""	""					""
-"LIN"	"J01FF02"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc"	"c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")"	1.8	"g"	1.8	"g"	"87597-1"
+"LIN"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"J01FF02"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc"	"c(\"cillimycin\", \"jiemycin\", \"lincolcina\", \"lincolnensin\", \"lincomicina\", \"lincomycin\", \"lincomycin a\", \"lincomycine\", \"lincomycinum\")"	1.8	"g"	1.8	"g"	"87597-1"
-"LNZ"	"J01XX08"	441401	"Linezolid"	"Oxazolidinones"	"Other antibacterials"	"Other antibacterials"	"c(\"line\", \"lnz\", \"lz\", \"lzd\")"	"c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")"	1.2	"g"	1.2	"g"	"c(\"34202-2\", \"80609-1\")"
+"LNZ"	441401	"Linezolid"	"Oxazolidinones"	"J01XX08"	"Other antibacterials"	"Other antibacterials"	"c(\"line\", \"lnz\", \"lz\", \"lzd\")"	"c(\"linezlid\", \"linezoid\", \"linezolid\", \"linezolide\", \"linezolidum\", \"zivoxid\", \"zyvoxa\", \"zyvoxam\", \"zyvoxid\")"	1.2	"g"	1.2	"g"	"c(\"34202-2\", \"80609-1\")"
-"LFE"			"Linoprist-flopristin"	"Other antibacterials"			""	""					""
+"LFE"		"Linoprist-flopristin"	"Other antibacterials"				""	""					""
-"LOM"	"J01MA07"	3948	"Lomefloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"lmf\", \"lom\", \"lome\")"	"c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")"	0.4				"character(0)"
+"LOM"	3948	"Lomefloxacin"	"Quinolones"	"c(\"J01MA07\", \"S01AE04\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"lmf\", \"lom\", \"lome\")"	"c(\"lomefloxacin\", \"lomefloxacine\", \"lomefloxacino\", \"lomefloxacinum\", \"maxaquin\")"	0.4	"g"			"character(0)"
-"LOR"	"J01DC08"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"\", \"lora\")"	"c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")"	0.6	"g"			"character(0)"
+"LOR"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"J01DC08"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"c(\"\", \"lora\")"	"c(\"anhydrous loracarbef\", \"lorabid\", \"loracarbef\", \"loracarbefum\", \"lorbef\", \"loribid\")"	0.6	"g"			"character(0)"
-"LYM"	"J01AA04"	54707177	"Lymecycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")"	0.6	"g"	0.6	"g"	"character(0)"
+"LYM"	54707177	"Lymecycline"	"Tetracyclines"	"J01AA04"	"Tetracyclines"	"Tetracyclines"	""	"c(\"biovetin\", \"chlortetracyclin\", \"ciclisin\", \"ciclolysal\", \"infaciclina\", \"limeciclina\", \"lisinbiotic\", \"lymecyclin\", \"lymecycline\", \"lymecyclinum\", \"mucomycin\", \"ntetracycline\", \"tetralisal\", \"tetralysal\", \"vebicyclysal\")"	0.6	"g"	0.6	"g"	"character(0)"
-"MNA"	"J01XX06"	1292	"Mandelic acid"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	""	"c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")"	12	"g"			"character(0)"
+"MNA"	1292	"Mandelic acid"	"Other antibacterials"	"c(\"B05CA06\", \"J01XX06\")"	"Other antibacterials"	"Other antibacterials"	""	"c(\"acido mandelico\", \"almond acid\", \"amygdalic acid\", \"benzoglycolic acid\", \"hydroxyacetic acid\", \"kyselina mandlova\", \"mandelic acid\", \"paramandelic acid\", \"phenylglycolic acid\", \"uromaline\")"	12	"g"			"character(0)"
-"MAR"		60651	"Marbofloxacin"	"Quinolones"			""	"c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")"					"character(0)"
+"MAR"	60651	"Marbofloxacin"	"Quinolones"				""	"c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")"					"character(0)"
-"MEC"	"J01CA11"	36273	"Mecillinam (Amdinocillin)"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")"			1.2	"g"	"character(0)"
+"MEC"	36273	"Mecillinam (Amdinocillin)"	"Beta-lactams/penicillins"	"J01CA11"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")"			1.2	"g"	"character(0)"
-"MEL"		71306732	"Meleumycin"	"Macrolides/lincosamides"			""	""					""
+"MEL"	71306732	"Meleumycin"	"Macrolides/lincosamides"				""	""					""
-"MEM"	"J01DH02"	441130	"Meropenem"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")"	"c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")"			3	"g"	"41406-0"
+"MEM"	441130	"Meropenem"	"Carbapenems"	"J01DH02"	"Other beta-lactam antibacterials"	"Carbapenems"	"c(\"mem\", \"mer\", \"mero\", \"mp\", \"mrp\")"	"c(\"meronem\", \"meropen\", \"meropenem\", \"meropenem anhydrous\", \"meropenem hydrate\", \"meropenem trihydrate\", \"meropenemum\", \"merrem\", \"merrem i.v.\", \"merrem iv\")"			3	"g"	"41406-0"
-"MNC"			"Meropenem/nacubactam"	"Carbapenems"			""	""					""
+"MNC"		"Meropenem/nacubactam"	"Carbapenems"				""	""					""
-"MEV"	"J01DH52"		"Meropenem/vaborbactam"	"Carbapenems"	"Other beta-lactam antibacterials"	"Carbapenems"	""	""					""
+"MEV"		"Meropenem/vaborbactam"	"Carbapenems"	"J01DH52"	"Other beta-lactam antibacterials"	"Carbapenems"	""	""			3	"g"	""
-"MES"		176886	"Mesulfamide"	"Other antibacterials"			""	"c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")"					"character(0)"
+"MES"	176886	"Mesulfamide"	"Other antibacterials"				""	"c(\"mesulfamide\", \"mesulfamido\", \"mesulfamidum\")"					"character(0)"
-"MTC"	"J01AA05"	54675785	"Metacycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")"	0.6	"g"			"character(0)"
+"MTC"	54675785	"Metacycline"	"Tetracyclines"	"J01AA05"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bialatan\", \"metaciclina\", \"metacycline\", \"metacyclinum\", \"methacycline\", \"methacycline base\", \"methacyclinum\", \"methylenecycline\", \"physiomycine\", \"rondomycin\")"	0.6	"g"			"character(0)"
-"MTM"	"J01CA14"	6713928	"Metampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\", 
+"MTM"	6713928	"Metampicillin"	"Beta-lactams/penicillins"	"J01CA14"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"blomopen\", \"bonopen\", \"celinmicina\", \"elatocilline\", \"fedacilina kapseln\", \"filorex\", \"italcina kapseln\", \"magnipen\", \"metabacter ampullen\", \"metambac\", \"metampicilina\", \"metampicillin\", \"metampicillin sodium\", \"metampicillina\", \"metampicilline\", \"metampicillinum\", \"methampicillin\", \"metiskia ampullen\", \"micinovo\", \"micinovo ampullen\", \"pangocilin\", \"probiotic\", \"rastomycin k\", \"relyothenate\", \"ruticina\", \"rutizina\", \"rutizina ampullen\", \"sedomycin\", \"suvipen\", \"suvipen ampullen\", \"tampilen ampullen\", 
 \"teonicon trofen\", \"viderpen\", \"viderpin\", \"vioplex\")"	1.5	"g"	1.5	"g"	"character(0)"
-"MTH"	"J01XX05"	4101	"Methenamine"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	""	"c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\", 
+"MTH"	4101	"Methenamine"	"Other antibacterials"	"J01XX05"	"Other antibacterials"	"Other antibacterials"	""	"c(\"aceto hmt\", \"aminoform\", \"aminoformaldehyde\", \"ammoform\", \"ammonioformaldehyde\", \"antihydral\", \"cystamin\", \"cystex\", \"cystogen\", \"duirexol\", \"ekagom h\", \"esametilentetramina\", \"formamine\", \"formin\", \"h.m.t.\", \"heksa k\", \"herax uts\", \"heterin\", \"hexa b\", \"hexaform\", \"hexaloids\", \"hexamethylamine\", \"hexamethylenamine\", \"hexamethyleneamine\", \"hexamethylentetramin\", \"hexamine\", \"hexamine silver\", \"hexamine superfine\", \"hexaminum\", \"hexasan\", \"hexilmethylenamine\", \"metenamina\", \"metenamine\", \"methamin\", 
 \"methenamin\", \"methenamine\", \"methenamine silver\", \"methenaminum\", \"metramine\", \"naphthamine\", \"nocceler h\", \"preparation af\", \"resotropin\", \"sanceler h\", \"sanceler ht\", \"silver methenamine\", \"uramin\", \"uratrine\", \"urisol\", \"uritone\", \"urodeine\", \"urotropin\", \"urotropine\", \"vesaloin\", \"vesalvine\", \"xametrin\")"	3	"g"			"character(0)"
-"MET"	"J01CF03"	6087	"Methicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"meti"	"c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")"			4	"g"	"c(\"29492-6\", \"3788-7\")"
+"MET"	6087	"Methicillin"	"Beta-lactams/penicillins"	"J01CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"meti"	"c(\"dimocillin\", \"metacillin\", \"methcilline\", \"methicillin\", \"methicillinum\", \"methycillin\", \"meticilina\", \"meticillin\", \"meticillina\", \"meticilline\", \"meticillinum\", \"staphcillin\")"			4	"g"	"c(\"29492-6\", \"3788-7\")"
-"MTP"		68590	"Metioprim"	"Other antibacterials"			""	"c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")"					"character(0)"
+"MTP"	68590	"Metioprim"	"Other antibacterials"				""	"c(\"methioprim\", \"metioprim\", \"metioprima\", \"metioprime\", \"metioprimum\")"					"character(0)"
-"MXT"		3047729	"Metioxate"	"Quinolones"			""	"c(\"metioxate\", \"metioxato\", \"metioxatum\")"					"character(0)"
+"MXT"	3047729	"Metioxate"	"Quinolones"				""	"c(\"metioxate\", \"metioxato\", \"metioxatum\")"					"character(0)"
-"MTR"	"J01XD01"	4173	"Metronidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"	"c(\"metr\", \"mnz\")"	"c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\", 
+"MTR"	4173	"Metronidazole"	"Other antibacterials"	"c(\"A01AB17\", \"D06BX01\", \"G01AF01\", \"J01XD01\", \"P01AB01\")"	"Other antibacterials"	"Imidazole derivatives"	"c(\"metr\", \"mnz\")"	"c(\"acromona\", \"anagiardil\", \"arilin\", \"atrivyl\", \"danizol\", \"deflamon\", \"efloran\", \"elyzol\", \"entizol\", \"flagemona\", \"flagesol\", \"flagil\", \"flagyl\", \"flagyl er\", \"flagyl i.v.\", \"flagyl i.v. rtu\", \"flazol\", \"flegyl\", \"florazole\", \"fossyol\", \"giatricol\", \"ginefla vir\", \"gineflavir\", \"helidac\", \"mepagyl\", \"meronidal\", \"methronidazole\", \"metric\", \"metro cream\", \"metro gel\", \"metro i.v\", \"metro i.v.\", \"metro iv\", \"metrocream\", \"metrodzhil\", \"metrogel\", \"metrogyl\", \"metrolag\", \"metrolotion\", \"metrolyl\", 
 \"metromidol\", \"metronidaz\", \"metronidazol\", \"metronidazole\", \"metronidazole usp\", \"metronidazolo\", \"metronidazolum\", \"metrotop\", \"metrozine\", \"metryl\", \"mexibol\", \"mexibol 'silanes'\", \"monagyl\", \"monasin\", \"nidagel\", \"nidagyl\", \"noritate\", \"novonidazol\", \"orvagil\", \"polibiotic\", \"protostat\", \"rathimed\", \"rosased\", \"sanatrichom\", \"satric\", \"takimetol\", \"trichazol\", \"trichex\", \"tricho cordes\", \"trichobrol\", \"trichocide\", \"trichomol\", \"trichopal\", \"trichopol\", \"tricocet\", \"tricom\", \"tricowas b\", \"trikacide\", 
-\"trikamon\", \"trikhopol\", \"trikojol\", \"trikozol\", \"trimeks\", \"trivazol\", \"vagilen\", \"vagimid\", \"vandazole\", \"vertisal\", \"wagitran\", \"zadstat\", \"zidoval\")"			1.5	"g"	"10991-8"
+\"trikamon\", \"trikhopol\", \"trikojol\", \"trikozol\", \"trimeks\", \"trivazol\", \"vagilen\", \"vagimid\", \"vandazole\", \"vertisal\", \"wagitran\", \"zadstat\", \"zidoval\")"	2	"g"	1.5	"g"	"10991-8"
-"MEZ"	"J01CA10"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"mez\", \"mezl\", \"mz\")"	"c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")"			6	"g"	"3820-8"
+"MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"mez\", \"mezl\", \"mz\")"	"c(\"mezlin\", \"mezlocilina\", \"mezlocillin\", \"mezlocillin acid\", \"mezlocillin sodium\", \"mezlocilline\", \"mezlocillinum\", \"multocillin\")"			6	"g"	"3820-8"
-"MSU"			"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"			""	""					""
+"MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"				""	""					""
-"MIF"	"J02AX05"	477468	"Micafungin"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"c(\"\", \"mica\")"	"c(\"micafungin\", \"mycamine\")"			0.1	"g"	"58418-5"
+"MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"c(\"\", \"mica\")"	"c(\"micafungin\", \"mycamine\")"			0.1	"g"	"58418-5"
-"MCZ"	"J02AB01"	4189	"Miconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")"			1	"g"	"17278-3"
+"MCZ"	4189	"Miconazole"	"Antifungals/antimycotics"	"c(\"A01AB09\", \"A07AC01\", \"D01AC02\", \"G01AF04\", \"J02AB01\", \"S02AA13\")"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"c(\"aflorix\", \"albistat\", \"andergin\", \"brentan\", \"conofite\", \"dactarin\", \"daktarin\", \"daktarin iv\", \"florid\", \"lotrimin af\", \"micantin\", \"miconasil nitrate\", \"miconazol\", \"miconazole\", \"miconazole base\", \"miconazolo\", \"miconazolum\", \"micozole\", \"minostate\", \"monista\", \"monistat\", \"monistat iv\", \"oravig\", \"vusion\", \"zimybase\", \"zimycan\")"	0.2	"g"	1	"g"	"17278-3"
-"MCR"		3037206	"Micronomicin"	"Aminoglycosides"			""	"c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")"					"character(0)"
+"MCR"	3037206	"Micronomicin"	"Aminoglycosides"	"S01AA22"			""	"c(\"gentamicin c\", \"micromycin\", \"micronomicin\", \"micronomicina\", \"micronomicine\", \"micronomicinum\", \"sagamicin\", \"santemycin\")"					"character(0)"
-"MID"	"J01FA03"	5282169	"Midecamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")"	1.2		1	"g"	"character(0)"
+"MID"	5282169	"Midecamycin"	"Macrolides/lincosamides"	"J01FA03"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"aboren\", \"espinomycin a\", \"macropen\", \"madecacine\", \"medemycin\", \"midecamicina\", \"midecamycin\", \"midecamycin a\", \"midecamycine\", \"midecamycinum\", \"midecin\", \"momicine\", \"mydecamycin\", \"myoxam\", \"normicina\", \"rubimycin\", \"turimycin p\")"	1.2	"g"	1	"g"	"character(0)"
-"MIL"		37614	"Miloxacin"	"Quinolones"			""	"c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")"					"character(0)"
+"MIL"	37614	"Miloxacin"	"Quinolones"				""	"c(\"miloxacin\", \"miloxacine\", \"miloxacino\", \"miloxacinum\")"					"character(0)"
-"MNO"	"J01AA08"	54675783	"Minocycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")"	"c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")"	0.2	"g"	0.2	"g"	"c(\"34606-4\", \"3822-4\", \"49757-8\")"
+"MNO"	54675783	"Minocycline"	"Tetracyclines"	"c(\"A01AB23\", \"D10AF07\", \"J01AA08\")"	"Tetracyclines"	"Tetracyclines"	"c(\"mc\", \"mh\", \"mi\", \"min\", \"mino\", \"mn\", \"mno\")"	"c(\"akamin\", \"aknemin\", \"borymycin\", \"dynacin\", \"klinomycin\", \"minociclina\", \"minocin\", \"minocline\", \"minocyclin\", \"minocycline\", \"minocyclinum\", \"minocyn\", \"minoderm\", \"minomycin\", \"sebomin\", \"solodyn\", \"vectrin\")"	1	"mg"	0.2	"g"	"c(\"34606-4\", \"3822-4\", \"49757-8\")"
-"MCM"	"J01FA11"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")"	1.2	"g"			"character(0)"
+"MCM"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"J01FA11"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"acecamycin\", \"macroral\", \"midecamycin acetate\", \"miocamen\", \"miocamycine\", \"miokamycin\", \"myocamicin\", \"ponsinomycin\")"	1.2	"g"			"character(0)"
-"MON"		23667299	"Monensin sodium"	"Other antibacterials"			""	"c(\"monensin sodium\", \"sodium monensin\")"					"character(0)"
+"MON"	23667299	"Monensin sodium"	"Other antibacterials"				""	"c(\"monensin sodium\", \"sodium monensin\")"					"character(0)"
-"MRN"	"J04AK04"	70374	"Morinamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")"					"character(0)"
+"MRN"	70374	"Morinamide"	"Antimycobacterials"	"J04AK04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"c(\"morfazinamide\", \"morfazinammide\", \"morfgazinamide\", \"morinamida\", \"morinamide\", \"morinamidum\", \"morphazinamid\", \"morphazinamide\", \"piazofolina\", \"piazolin\", \"piazolina\")"					"character(0)"
-"MFX"	"J01MA14"	152946	"Moxifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"mox\", \"moxi\", \"mxf\")"	"c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")"	0.4	"g"	0.4	"g"	"c(\"43751-7\", \"45223-5\", \"80540-8\")"
+"MFX"	152946	"Moxifloxacin"	"Quinolones"	"c(\"J01MA14\", \"S01AE07\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"mox\", \"moxi\", \"mxf\")"	"c(\"actira\", \"avelox\", \"avelox i.v.\", \"avelox iv\", \"avolex\", \"izilox\", \"moxeza\", \"moxifloxacin\", \"moxifloxacine\", \"vigamox\")"	0.4	"g"	0.4	"g"	"c(\"43751-7\", \"45223-5\", \"80540-8\")"
-"MUP"	"R01AX06"	446596	"Mupirocin"	"Other antibacterials"			"c(\"mup\", \"mupi\")"	"c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")"					"character(0)"
+"MUP"	446596	"Mupirocin"	"Other antibacterials"	"c(\"D06AX09\", \"R01AX06\")"			"c(\"mup\", \"mupi\")"	"c(\"bactoderm\", \"bactroban\", \"bactroban nasal\", \"bactroban ointment\", \"centany\", \"mupirocin\", \"mupirocina\", \"mupirocine\", \"mupirocinum\", \"plasimine\", \"pseudomonic acid\", \"pseudomonic acid a\", \"turixin\")"					"character(0)"
-"NAC"		73386748	"Nacubactam"	"Beta-lactams/penicillins"			""	"nacubactam"					"character(0)"
+"NAC"	73386748	"Nacubactam"	"Beta-lactams/penicillins"				""	"nacubactam"					"character(0)"
-"NAD"		4410	"Nadifloxacin"	"Quinolones"			""	"c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")"					"character(0)"
+"NAD"	4410	"Nadifloxacin"	"Quinolones"	"D10AF05"			""	"c(\"acuatim\", \"nadifloxacin\", \"nadifloxacine\", \"nadifloxacino\", \"nadifloxacinum\", \"nadixa\", \"nadoxin\")"					"character(0)"
-"NAF"		8982	"Nafcillin"	"Beta-lactams/penicillins"			""	"c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")"					"c(\"10993-4\", \"25232-0\")"
+"NAF"	8982	"Nafcillin"	"Beta-lactams/penicillins"	"J01CF06"			""	"c(\"nafcilina\", \"nafcillin\", \"nafcillin sodium\", \"nafcilline\", \"nafcillinum\", \"nallpen\", \"naphcillin\", \"unipen\")"			3	"g"	"c(\"10993-4\", \"25232-0\")"
-"ZWK"		117587595	"Nafithromycin"	"Macrolides/lincosamides"			""	"nafithromycin"					"character(0)"
+"ZWK"	117587595	"Nafithromycin"	"Macrolides/lincosamides"				""	"nafithromycin"					"character(0)"
-"NAL"	"J01MB02"	4421	"Nalidixic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"c(\"na\", \"nal\", \"nali\")"	"c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\", 
+"NAL"	4421	"Nalidixic acid"	"Quinolones"	"J01MB02"	"Quinolone antibacterials"	"Other quinolones"	"c(\"na\", \"nal\", \"nali\")"	"c(\"acide nalidixico\", \"acide nalidixique\", \"acido nalidissico\", \"acido nalidixico\", \"acidum nalidixicum\", \"betaxina\", \"dixiben\", \"dixinal\", \"eucisten\", \"eucistin\", \"innoxalomn\", \"innoxalon\", \"jicsron\", \"kusnarin\", \"naldixic acid\", \"nalidic acid\", \"nalidicron\", \"nalidixan\", \"nalidixane\", \"nalidixate\", \"nalidixate sodium\", \"nalidixic\", \"nalidixic acid\", \"nalidixin\", \"nalidixinic acid\", \"nalidixinsaure\", \"nalitucsan\", \"nalurin\", \"narigix\", \"naxuril\", \"neggram\", \"negram\", \"nevigramon\", \"nicelate\", \"nogram\", 
 \"poleon\", \"sicmylon\", \"specifen\", \"specifin\", \"unaserus\", \"uralgin\", \"uriben\", \"uriclar\", \"urisal\", \"urodixin\", \"uroman\", \"uroneg\", \"uronidix\", \"uropan\", \"wintomylon\", \"wintron\")"	4	"g"			"character(0)"
-"NAR"		65452	"Narasin"	"Other antibacterials"			""	"c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")"					"87570-8"
+"NAR"	65452	"Narasin"	"Other antibacterials"				""	"c(\"monteban\", \"narasin\", \"narasin a\", \"narasine\", \"narasino\", \"narasinum\", \"narasul\")"					"87570-8"
-"NEO"	"J01GB05"	8378	"Neomycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom"	"c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", 
+"NEO"	8378	"Neomycin"	"Aminoglycosides"	"c(\"A01AB08\", \"A07AA01\", \"B05CA09\", \"D06AX04\", \"J01GB05\", \"R02AB01\", \"S01AA03\", \"S02AA07\", \"S03AA01\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom"	"c(\"actilin\", \"actiline\", \"antibiotique\", \"bycomycin\", \"endomixin\", \"enterfram\", \"fradiomycin\", \"fradiomycin b\", \"fradiomycinum\", \"framicetina\", \"framycetin\", \"framycetin sulfate\", \"framycetine\", \"framycetinum\", \"framygen\", \"fraquinol\", \"jernadex\", \"myacine\", \"myacyne\", \"mycerin\", \"mycifradin\", \"neobrettin\", \"neolate\", \"neomas\", \"neomcin\", \"neomicina\", \"neomin\", \"neomycin\", \"neomycin b\", \"neomycin b sulfate\", \"neomycin solution\", \"neomycin sulfate\", \"neomycin sulphate\", \"neomycinb\", \"neomycine\", \"neomycinum\", 
-\"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")"	1	"g"			"c(\"10995-9\", \"25262-7\")"
+\"nivemycin\", \"pimavecort\", \"soframycin\", \"soframycine\", \"tuttomycin\", \"vonamycin\", \"vonamycin powder v\")"	5	"g"			"c(\"10995-9\", \"25262-7\")"
-"NET"	"J01GB07"	441306	"Netilmicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti"	"c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")"	0.35	"g"	0.35	"g"	"c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")"
+"NET"	441306	"Netilmicin"	"Aminoglycosides"	"c(\"J01GB07\", \"S01AA23\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti"	"c(\"netillin\", \"netilmicin\", \"netilmicin sulfate\", \"netilmicina\", \"netilmicine\", \"netilmicinum\", \"netilyn\", \"netira\", \"vectacin\")"	0.35	"g"	0.35	"g"	"c(\"25263-5\", \"3848-9\", \"3849-7\", \"3850-5\", \"47385-0\", \"59565-2\", \"59566-0\", \"59567-8\")"
-"NIC"		9507	"Nicarbazin"	"Other antibacterials"			""	"c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")"					"character(0)"
+"NIC"	9507	"Nicarbazin"	"Other antibacterials"				""	"c(\"nicarb\", \"nicarbasin\", \"nicarbazin\", \"nicarbazine\", \"nicoxin\", \"nicrazin\", \"nicrazine\", \"nirazin\")"					"character(0)"
-"NIF"		71946	"Nifuroquine"	"Quinolones"			""	"c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")"					"character(0)"
+"NIF"	71946	"Nifuroquine"	"Quinolones"				""	"c(\"nifuroquina\", \"nifuroquine\", \"nifuroquinum\", \"quinaldofur\")"					"character(0)"
-"NFR"	"J01XE02"	9571062	"Nifurtoinol"	"Other antibacterials"	"Other antibacterials"	"Nitrofuran derivatives"	""	"c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")"	0.16	"g"			"character(0)"
+"NFR"	9571062	"Nifurtoinol"	"Other antibacterials"	"J01XE02"	"Other antibacterials"	"Nitrofuran derivatives"	""	"c(\"levantin\", \"nifurtoinol\", \"nifurtoinolo\", \"nifurtoinolum\", \"urfadin\", \"urfadine\", \"urfadyn\")"	0.16	"g"			"character(0)"
-"NTZ"		41684	"Nitazoxanide"	"Other antibacterials"			""	"c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")"					"character(0)"
+"NTZ"	41684	"Nitazoxanide"	"Other antibacterials"	"P01AX11"			""	"c(\"adrovet\", \"alinia\", \"azt + nitazoxanide\", \"colufase\", \"cryptaz\", \"dexidex\", \"heliton\", \"kidonax\", \"nitaxozanid\", \"nitaxozanide\", \"nitazox\", \"nitazoxamide\", \"nitazoxanid\", \"nitazoxanida\", \"nitazoxanide\", \"nitazoxanidum\", \"omniparax\", \"pacovanton\", \"paramix\", \"taenitaz\")"	1	"g"			"character(0)"
-"NIT"	"J01XE01"	6604200	"Nitrofurantoin"	"Other antibacterials"	"Other antibacterials"	"Nitrofuran derivatives"	"c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")"	"c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\", 
+"NIT"	6604200	"Nitrofurantoin"	"Other antibacterials"	"J01XE01"	"Other antibacterials"	"Nitrofuran derivatives"	"c(\"f\", \"f/m\", \"fd\", \"ft\", \"ni\", \"nit\", \"nitr\")"	"c(\"alfuran\", \"benkfuran\", \"berkfuran\", \"berkfurin\", \"ceduran\", \"chemiofuran\", \"cistofuran\", \"cyantin\", \"cystit\", \"dantafur\", \"fua med\", \"fuamed\", \"furabid\", \"furachel\", \"furadantin\", \"furadantin retard\", \"furadantina mc\", \"furadantine\", \"furadantine mc\", \"furadantoin\", \"furadoin\", \"furadoine\", \"furadonin\", \"furadonine\", \"furadoninum\", \"furadontin\", \"furadoxyl\", \"furalan\", \"furaloid\", \"furantoin\", \"furantoina\", \"furatoin\", \"furedan\", \"furina\", \"furobactina\", \"furodantin\", \"furophen t\", \"gerofuran\", 
 \"io>>uss>>a<<ixoo\", \"ituran\", \"ivadantin\", \"macpac\", \"macrobid\", \"macrodantin\", \"macrodantina\", \"macrofuran\", \"macrofurin\", \"nierofu\", \"nifurantin\", \"nifuretten\", \"nitoin\", \"nitrex\", \"nitrofuradantin\", \"nitrofurantion\", \"nitrofurantoin\", \"nitrofurantoin macro\", \"nitrofurantoina\", \"nitrofurantoine\", \"nitrofurantoinum\", \"novofuran\", \"orafuran\", \"parfuran\", \"phenurin\", \"piyeloseptyl\", \"siraliden\", \"trantoin\", \"uerineks\", \"urantoin\", \"urizept\", \"urodin\", \"urofuran\", \"urofurin\", \"urolisa\", \"urolong\", 
 \"uvamin\", \"welfurin\", \"zoofurin\")"	0.2	"g"			"3860-4"
-"NIZ"		5447130	"Nitrofurazone"	"Other antibacterials"			""	"c(\"acutol\", \"aldomycin\", \"alfucin\", \"amifur\", \"babrocid\", \"becafurazone\", \"biofuracina\", \"biofurea\", \"chemofuran\", \"chixin\", \"cocafurin\", \"coxistat\", \"dermofural\", \"dymazone\", \"dynazone\", \"eldezol\", \"fedacin\", \"flavazone\", \"fracine\", \"furacilin\", \"furacilinum\", \"furacillin\", \"furacin\", \"furacine\", \"furacinetten\", \"furacoccid\", \"furacort\", \"furacycline\", \"furaderm\", \"furagent\", \"furalcyn\", \"furaldon\", \"furalone\", \"furametral\", \"furaplast\", \"furaseptyl\", \"furaskin\", \"furatsilin\", \"furaziline\", \"furazin\", 
+"NIZ"	5447130	"Nitrofurazone"	"Other antibacterials"				""	"c(\"acutol\", \"aldomycin\", \"alfucin\", \"amifur\", \"babrocid\", \"becafurazone\", \"biofuracina\", \"biofurea\", \"chemofuran\", \"chixin\", \"cocafurin\", \"coxistat\", \"dermofural\", \"dymazone\", \"dynazone\", \"eldezol\", \"fedacin\", \"flavazone\", \"fracine\", \"furacilin\", \"furacilinum\", \"furacillin\", \"furacin\", \"furacine\", \"furacinetten\", \"furacoccid\", \"furacort\", \"furacycline\", \"furaderm\", \"furagent\", \"furalcyn\", \"furaldon\", \"furalone\", \"furametral\", \"furaplast\", \"furaseptyl\", \"furaskin\", \"furatsilin\", \"furaziline\", \"furazin\", 
 \"furazina\", \"furazol w\", \"furazone\", \"furazyme\", \"furesol\", \"furfurin\", \"furosem\", \"fuvacillin\", \"hemofuran\", \"ibiofural\", \"mammex\", \"mastofuran\", \"monafuracin\", \"monafuracis\", \"monofuracin\", \"nfz mix\", \"nifucin\", \"nifurid\", \"nifuzon\", \"nitrofural\", \"nitrofuralum\", \"nitrofuran\", \"nitrofurane\", \"nitrofurazan\", \"nitrofurazone\", \"nitrofurazonum\", \"nitrofurol\", \"nitrozone\", \"otofural\", \"otofuran\", \"rivafurazon\", \"sanfuran\", \"vabrocid\", \"vadrocid\", \"yatrocin\")"					"character(0)"
-"NTR"	"J01XX07"	19910	"Nitroxoline"	"Quinolones"	"Other antibacterials"	"Other antibacterials"	""	"c(\"galinok\", \"isinok\", \"nibiol\", \"nicene forte\", \"nitroxolin\", \"nitroxolina\", \"nitroxoline\", \"nitroxolinum\", \"notroxoline\", \"noxibiol\")"	1	"g"			"character(0)"
+"NTR"	19910	"Nitroxoline"	"Quinolones"	"J01XX07"	"Other antibacterials"	"Other antibacterials"	""	"c(\"galinok\", \"isinok\", \"nibiol\", \"nicene forte\", \"nitroxolin\", \"nitroxolina\", \"nitroxoline\", \"nitroxolinum\", \"notroxoline\", \"noxibiol\")"	1	"g"			"character(0)"
-"NOR"	"J01MA06"	4539	"Norfloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"nor\", \"norf\", \"nx\", \"nxn\")"	"c(\"baccidal\", \"barazan\", \"chibroxin\", \"chibroxine\", \"chibroxol\", \"fulgram\", \"gonorcin\", \"lexinor\", \"nolicin\", \"noracin\", \"noraxin\", \"norflo\", \"norfloxacin\", \"norfloxacine\", \"norfloxacino\", \"norfloxacinum\", \"norocin\", \"noroxin\", \"noroxine\", \"norxacin\", \"sebercim\", \"uroxacin\", \"utinor\", \"zoroxin\")"	0.8	"g"			"3867-9"
+"NOR"	4539	"Norfloxacin"	"Quinolones"	"c(\"J01MA06\", \"S01AE02\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"nor\", \"norf\", \"nx\", \"nxn\")"	"c(\"baccidal\", \"barazan\", \"chibroxin\", \"chibroxine\", \"chibroxol\", \"fulgram\", \"gonorcin\", \"lexinor\", \"nolicin\", \"noracin\", \"noraxin\", \"norflo\", \"norfloxacin\", \"norfloxacine\", \"norfloxacino\", \"norfloxacinum\", \"norocin\", \"noroxin\", \"noroxine\", \"norxacin\", \"sebercim\", \"uroxacin\", \"utinor\", \"zoroxin\")"	0.8	"g"			"3867-9"
-"NVA"		10419027	"Norvancomycin"	"Glycopeptides"			""	"norvancomycin"					"character(0)"
+"NVA"	10419027	"Norvancomycin"	"Glycopeptides"				""	"norvancomycin"					"character(0)"
-"NOV"	"QJ01XX95"	54675769	"Novobiocin"	"Other antibacterials"			"novo"	"c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")"					"17378-1"
+"NOV"	54675769	"Novobiocin"	"Other antibacterials"				"novo"	"c(\"albamix\", \"albamycin\", \"cardelmycin\", \"cathocin\", \"cathomycin\", \"crystallinic acid\", \"inamycin\", \"novobiocin\", \"novobiocina\", \"novobiocine\", \"novobiocinum\", \"robiocina\", \"sirbiocina\", \"spheromycin\", \"stilbiocina\", \"streptonivicin\")"					"17378-1"
-"NYS"	"G01AA01"	6433272	"Nystatin"	"Antifungals/antimycotics"			"nyst"	"c(\"biofanal\", \"candex lotion\", \"comycin\", \"diastatin\", \"herniocid\", \"moronal\", \"myconystatin\", \"mycostatin\", \"mycostatin pastilles\", \"mykinac\", \"mykostatyna\", \"nilstat\", \"nistatin\", \"nistatina\", \"nyamyc\", \"nyotran\", \"nyotrantrade mark\", \"nystaform\", \"nystan\", \"nystatin\", \"nystatin a\", \"nystatin g\", \"nystatin lf\", \"nystatine\", \"nystatinum\", \"nystatyna\", \"nystavescent\", \"nystex\", \"nystop\", \"stamycin\", \"terrastatin\", \"zydin e\")"					"character(0)"
+"NYS"	6433272	"Nystatin"	"Antifungals/antimycotics"	"c(\"A07AA02\", \"D01AA01\", \"G01AA01\")"			"nyst"	"c(\"biofanal\", \"candex lotion\", \"comycin\", \"diastatin\", \"herniocid\", \"moronal\", \"myconystatin\", \"mycostatin\", \"mycostatin pastilles\", \"mykinac\", \"mykostatyna\", \"nilstat\", \"nistatin\", \"nistatina\", \"nyamyc\", \"nyotran\", \"nyotrantrade mark\", \"nystaform\", \"nystan\", \"nystatin\", \"nystatin a\", \"nystatin g\", \"nystatin lf\", \"nystatine\", \"nystatinum\", \"nystatyna\", \"nystavescent\", \"nystex\", \"nystop\", \"stamycin\", \"terrastatin\", \"zydin e\")"	1.5	"MU"			"character(0)"
-"OFX"	"J01MA01"	4583	"Ofloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"of\", \"ofl\", \"oflo\", \"ofx\")"	"c(\"bactocin\", \"danoflox\", \"effexin\", \"exocin\", \"exocine\", \"flobacin\", \"flodemex\", \"flotavid\", \"flovid\", \"floxal\", \"floxil\", \"floxin\", \"floxin otic\", \"floxstat\", \"fugacin\", \"inoflox\", \"kinflocin\", \"kinoxacin\", \"levofloxacin hcl\", \"liflox\", \"loxinter\", \"marfloxacin\", \"medofloxine\", \"mergexin\", \"monoflocet\", \"novecin\", \"nufafloqo\", \"occidal\", \"ocuflox\", \"oflocee\", \"oflocet\", \"oflocin\", \"oflodal\", \"oflodex\", \"oflodura\", \"ofloxacin\", \"ofloxacin otic\", \"ofloxacina\", \"ofloxacine\", \"ofloxacino\", \"ofloxacinum\", 
+"OFX"	4583	"Ofloxacin"	"Quinolones"	"c(\"J01MA01\", \"S01AE01\", \"S02AA16\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"of\", \"ofl\", \"oflo\", \"ofx\")"	"c(\"bactocin\", \"danoflox\", \"effexin\", \"exocin\", \"exocine\", \"flobacin\", \"flodemex\", \"flotavid\", \"flovid\", \"floxal\", \"floxil\", \"floxin\", \"floxin otic\", \"floxstat\", \"fugacin\", \"inoflox\", \"kinflocin\", \"kinoxacin\", \"levofloxacin hcl\", \"liflox\", \"loxinter\", \"marfloxacin\", \"medofloxine\", \"mergexin\", \"monoflocet\", \"novecin\", \"nufafloqo\", \"occidal\", \"ocuflox\", \"oflocee\", \"oflocet\", \"oflocin\", \"oflodal\", \"oflodex\", \"oflodura\", \"ofloxacin\", \"ofloxacin otic\", \"ofloxacina\", \"ofloxacine\", \"ofloxacino\", \"ofloxacinum\", 
 \"ofloxin\", \"onexacin\", \"operan\", \"orocin\", \"otonil\", \"oxaldin\", \"pharflox\", \"praxin\", \"puiritol\", \"qinolon\", \"quinolon\", \"quotavil\", \"sinflo\", \"tabrin\", \"taravid\", \"tariflox\", \"tarivid\", \"telbit\", \"tructum\", \"uro tarivid\", \"viotisone\", \"visiren\", \"zanocin\")"	0.4	"g"	0.4	"g"	"c(\"25264-3\", \"3877-8\")"
-"OLE"	"J01FA05"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"amimycin\", \"landomycin\", \"matromycin\", \"oleandomycin a\", \"romicil\")"	1	"g"			"character(0)"
+"OLE"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"J01FA05"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"amimycin\", \"landomycin\", \"matromycin\", \"oleandomycin a\", \"romicil\")"	1	"g"			"character(0)"
-"OMC"		54697325	"Omadacycline"	"Tetracyclines"			""	"c(\"amadacycline\", \"omadacycline\")"					"character(0)"
+"OMC"	54697325	"Omadacycline"	"Tetracyclines"	"J01AA15"			""	"c(\"amadacycline\", \"omadacycline\")"	0.3	"g"	0.1	"g"	"character(0)"
-"OPT"		87880	"Optochin"	"Other antibacterials"			""	"c(\"numoquin\", \"optochin\", \"optoquine\")"					"character(0)"
+"OPT"	87880	"Optochin"	"Other antibacterials"				""	"c(\"numoquin\", \"optochin\", \"optoquine\")"					"character(0)"
-"ORB"		60605	"Orbifloxacin"	"Quinolones"			""	"orbifloxacin"					"character(0)"
+"ORB"	60605	"Orbifloxacin"	"Quinolones"				""	"orbifloxacin"					"character(0)"
-"ORI"	"J01XA05"	16136912	"Oritavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit"	"oritavancin"					"character(0)"
+"ORI"	16136912	"Oritavancin"	"Glycopeptides"	"J01XA05"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit"	"oritavancin"					"character(0)"
-"ORS"			"Ormetroprim/sulfamethoxazole"	"Other antibacterials"			""	""					""
+"ORS"		"Ormetroprim/sulfamethoxazole"	"Other antibacterials"				""	""					""
-"ORN"	"J01XD03"	28061	"Ornidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"	""	"c(\"madelen\", \"ornidal\", \"ornidazol\", \"ornidazole\", \"ornidazolum\", \"tiberal\")"			1	"g"	"character(0)"
+"ORN"	28061	"Ornidazole"	"Other antibacterials"	"c(\"G01AF06\", \"J01XD03\", \"P01AB03\")"	"Other antibacterials"	"Imidazole derivatives"	""	"c(\"madelen\", \"ornidal\", \"ornidazol\", \"ornidazole\", \"ornidazolum\", \"tiberal\")"	1.5	"g"	1	"g"	"character(0)"
-"OXA"	"J01CF04"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"ox\", \"oxa\", \"oxac\", \"oxal\", \"oxs\")"	"c(\"bactocill\", \"ossacillina\", \"oxacilina\", \"oxacillin\", \"oxacillin sodium\", \"oxacilline\", \"oxacillinum\", \"oxazocillin\", \"oxazocilline\", \"prostaphlin\", \"prostaphlyn\", \"sodium oxacillin\")"	2	"g"	2	"g"	"c(\"25265-0\", \"3882-8\")"
+"OXA"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"J01CF04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"c(\"ox\", \"oxa\", \"oxac\", \"oxal\", \"oxs\")"	"c(\"bactocill\", \"ossacillina\", \"oxacilina\", \"oxacillin\", \"oxacillin sodium\", \"oxacilline\", \"oxacillinum\", \"oxazocillin\", \"oxazocilline\", \"prostaphlin\", \"prostaphlyn\", \"sodium oxacillin\")"	2	"g"	2	"g"	"c(\"25265-0\", \"3882-8\")"
-"OXO"	"J01MB05"	4628	"Oxolinic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acide oxolinique\", \"acido ossolico\", \"acido oxolinico\", \"acidum oxolinicum\", \"aqualinic\", \"cistopax\", \"dioxacin\", \"emyrenil\", \"gramurin\", \"inoxyl\", \"nidantin\", \"oksaren\", \"orthurine\", \"ossian\", \"oxoboi\", \"oxolinic\", \"oxolinic acid\", \"pietil\", \"prodoxal\", \"prodoxol\", \"starner\", \"tiurasin\", \"ultibid\", \"urinox\", \"uritrate\", \"urotrate\", \"uroxol\", \"utibid\")"	1	"g"			"character(0)"
+"OXO"	4628	"Oxolinic acid"	"Quinolones"	"J01MB05"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acide oxolinique\", \"acido ossolico\", \"acido oxolinico\", \"acidum oxolinicum\", \"aqualinic\", \"cistopax\", \"dioxacin\", \"emyrenil\", \"gramurin\", \"inoxyl\", \"nidantin\", \"oksaren\", \"orthurine\", \"ossian\", \"oxoboi\", \"oxolinic\", \"oxolinic acid\", \"pietil\", \"prodoxal\", \"prodoxol\", \"starner\", \"tiurasin\", \"ultibid\", \"urinox\", \"uritrate\", \"urotrate\", \"uroxol\", \"utibid\")"	1	"g"			"character(0)"
-"OXY"	"J01AA06"	54675779	"Oxytetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"adamycin\", \"berkmycen\", \"biostat\", \"biostat pa\", \"dabicycline\", \"dalimycin\", \"embryostat\", \"fanterrin\", \"galsenomycin\", \"geomycin\", \"geotilin\", \"hydroxytetracyclinum\", \"imperacin\", \"lenocycline\", \"macocyn\", \"medamycin\", \"mepatar\", \"oksisyklin\", \"ossitetraciclina\", \"oxacycline\", \"oxitetraciclina\", \"oxitetracyclin\", \"oxitetracycline\", \"oxitetracyclinum\", \"oxydon\", \"oxymycin\", \"oxymykoin\", \"oxypam\", \"oxysteclin\", \"oxyterracin\", \"oxyterracine\", \"oxyterracyne\", \"oxytetracid\", \"oxytetracyclin\", \"oxytetracycline\", 
+"OXY"	54675779	"Oxytetracycline"	"Tetracyclines"	"c(\"D06AA03\", \"G01AA07\", \"J01AA06\", \"S01AA04\")"	"Tetracyclines"	"Tetracyclines"	""	"c(\"adamycin\", \"berkmycen\", \"biostat\", \"biostat pa\", \"dabicycline\", \"dalimycin\", \"embryostat\", \"fanterrin\", \"galsenomycin\", \"geomycin\", \"geotilin\", \"hydroxytetracyclinum\", \"imperacin\", \"lenocycline\", \"macocyn\", \"medamycin\", \"mepatar\", \"oksisyklin\", \"ossitetraciclina\", \"oxacycline\", \"oxitetraciclina\", \"oxitetracyclin\", \"oxitetracycline\", \"oxitetracyclinum\", \"oxydon\", \"oxymycin\", \"oxymykoin\", \"oxypam\", \"oxysteclin\", \"oxyterracin\", \"oxyterracine\", \"oxyterracyne\", \"oxytetracid\", \"oxytetracyclin\", \"oxytetracycline\", 
 \"oxytetracycline base\", \"oxytetracyclinum\", \"proteroxyna\", \"riomitsin\", \"ryomycin\", \"solkaciclina\", \"stecsolin\", \"stevacin\", \"tarocyn\", \"tarosin\", \"teravit\", \"terrafungine\", \"terramitsin\", \"terramycin\", \"terramycin im\", \"tetran\", \"unimycin\", \"ursocyclin\", \"ursocycline\", \"vendarcin\")"	1	"g"	1	"g"	"c(\"17396-3\", \"25266-8\", \"87595-5\")"
-"PAS"		4649	"P-aminosalicylic acid"	"Antimycobacterials"			""	"c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")"					"character(0)"
+"PAS"	4649	"P-aminosalicylic acid"	"Antimycobacterials"				""	"c(\"aminopar\", \"aminosalicylic\", \"aminosalicylic acid\", \"aminosalyl\", \"aminox\", \"apacil\", \"deapasil\", \"entepas\", \"ferrosan\", \"gabbropas\", \"helipidyl\", \"hellipidyl\", \"neopasalate\", \"osacyl\", \"pamacyl\", \"pamisyl\", \"paramycin\", \"parasal\", \"parasalicil\", \"parasalindon\", \"pasalon\", \"pasara\", \"pascorbic\", \"pasdium\", \"paser granules\", \"paskalium\", \"pasmed\", \"pasnodia\", \"pasolac\", \"propasa\", \"rezipas\", \"teebacin\", \"wln: zr cq dvq\")"					"character(0)"
-"PAN"		72015	"Panipenem"	"Carbapenems"			""	"c(\"panipenem\", \"panipenemum\", \"penipanem\")"					"character(0)"
+"PAN"	72015	"Panipenem"	"Carbapenems"				""	"c(\"panipenem\", \"panipenemum\", \"penipanem\")"					"character(0)"
-"PAR"		165580	"Paromomycin"	"Other antibacterials"			""	"c(\"aminosidin\", \"aminosidine\", \"aminosidine i\", \"aminosidine sulfate\", \"amminosidin\", \"crestomycin\", \"estomycin\", \"gabbromicina\", \"gabbromycin\", \"gabromycin\", \"humatin\", \"humycin\", \"hydroxymycin\", \"hydroxymycin sulfate\", \"monomycin\", \"monomycin a\", \"neomycin e\", \"paramomycin\", \"paramomycin sulfate\", \"paromomicina\", \"paromomycin\", \"paromomycin i\", \"paromomycine\", \"paromomycinum\", \"paucimycin\", \"paucimycinum\", \"quintomycin c\")"					"character(0)"
+"PAR"	165580	"Paromomycin"	"Other antibacterials"	"A07AA06"			""	"c(\"aminosidin\", \"aminosidine\", \"aminosidine i\", \"aminosidine sulfate\", \"amminosidin\", \"crestomycin\", \"estomycin\", \"gabbromicina\", \"gabbromycin\", \"gabromycin\", \"humatin\", \"humycin\", \"hydroxymycin\", \"hydroxymycin sulfate\", \"monomycin\", \"monomycin a\", \"neomycin e\", \"paramomycin\", \"paramomycin sulfate\", \"paromomicina\", \"paromomycin\", \"paromomycin i\", \"paromomycine\", \"paromomycinum\", \"paucimycin\", \"paucimycinum\", \"quintomycin c\")"	3	"g"			"character(0)"
-"PAZ"	"J01MA18"	65957	"Pazufloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")"			1	"g"	"character(0)"
+"PAZ"	65957	"Pazufloxacin"	"Quinolones"	"J01MA18"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"pazufloxacin\", \"pazufloxacine\", \"pazufloxacino\", \"pazufloxacinum\")"			1	"g"	"character(0)"
-"PEF"	"J01MA03"	51081	"Pefloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"pefl\")"	"c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")"	0.8	"g"	0.8	"g"	"3906-5"
+"PEF"	51081	"Pefloxacin"	"Quinolones"	"J01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"pefl\")"	"c(\"abactal\", \"labocton\", \"pefloxacin\", \"pefloxacine\", \"pefloxacino\", \"pefloxacinum\", \"perfloxacin\", \"silver pefloxacin\")"	0.8	"g"	0.8	"g"	"3906-5"
-"PNM"	"J01CE06"	10250769	"Penamecillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")"	1.05	"g"			"character(0)"
+"PNM"	10250769	"Penamecillin"	"Beta-lactams/penicillins"	"J01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"hydroxymethyl\", \"penamecilina\", \"penamecillin\", \"penamecillina\", \"penamecilline\", \"penamecillinum\")"	1.05	"g"			"character(0)"
-"PNO"			"Penicillin/novobiocin"	"Beta-lactams/penicillins"			""	""					""
+"PNO"		"Penicillin/novobiocin"	"Beta-lactams/penicillins"				""	""					""
-"PSU"			"Penicillin/sulbactam"	"Beta-lactams/penicillins"			""	""					""
+"PSU"		"Penicillin/sulbactam"	"Beta-lactams/penicillins"				""	""					""
-"PNM1"	"J01AA10"	54686187	"Penimepicycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")"					"character(0)"
+"PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10"	"Tetracyclines"	"Tetracyclines"	""	"c(\"duamine\", \"hydrocycline\", \"penetracyne\", \"penimepiciclina\", \"penimepicycline\", \"penimepicyclinum\")"					"character(0)"
-"PIM"		65453	"Pentisomicin"	"Aminoglycosides"			""	"c(\"pentisomicin\", \"pentisomicina\", \"pentisomicine\", \"pentisomicinum\")"					"character(0)"
+"PIM"	65453	"Pentisomicin"	"Aminoglycosides"				""	"c(\"pentisomicin\", \"pentisomicina\", \"pentisomicine\", \"pentisomicinum\")"					"character(0)"
-"PTZ"		55250256	"Pentizidone"	"Other antibacterials"			""	""					""
+"PTZ"	55250256	"Pentizidone"	"Other antibacterials"				""	""					""
-"PEX"		16132253	"Pexiganan"	"Other antibacterials"			""	"pexiganan"					"character(0)"
+"PEX"	16132253	"Pexiganan"	"Other antibacterials"				""	"pexiganan"					"character(0)"
-"PHE"	"J01CE05"	272833	"Phenethicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"c(\"\", \"fene\")"	"c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")"	1	"g"			"41471-4"
+"PHE"	272833	"Phenethicillin"	"Beta-lactams/penicillins"	"J01CE05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"c(\"\", \"fene\")"	"c(\"feneticilina\", \"feneticillina\", \"feneticilline\", \"k phenethicillin\", \"phenethicilin\", \"phenethicillinum\", \"pheneticillin\", \"pheneticilline\", \"pheneticillinum\", \"phenoxy pc\", \"potassium penicillin\")"	1	"g"			"41471-4"
-"PHN"	"J01CE02"	6869	"Phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")"	"c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")"	2	"g"			"character(0)"
+"PHN"	6869	"Phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"c(\"fepe\", \"peni v\", \"penicillin v\", \"pnv\", \"pv\")"	"c(\"acipen v\", \"apocillin\", \"apopen\", \"beromycin\", \"calcipen\", \"compocillin v\", \"crystapen v\", \"distaquaine v\", \"eskacillian v\", \"eskacillin v\", \"fenacilin\", \"fenospen\", \"meropenin\", \"oracillin\", \"oratren\", \"penicillin v\", \"phenocillin\", \"phenomycilline\", \"phenopenicillin\", \"robicillin\", \"rocilin\", \"stabicillin\", \"vebecillin\", \"veetids\", \"vegacillin\")"	2	"g"			"character(0)"
-"PMR"		5284447	"Pimaricin (Natamycin)"	"Antifungals/antimycotics"			""	"c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")"					"character(0)"
+"PMR"	5284447	"Pimaricin (Natamycin)"	"Antifungals/antimycotics"				""	"c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")"					"character(0)"
-"PPA"	"J01MB04"	4831	"Pipemidic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	"c(\"pipz\", \"pizu\")"	"c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")"	0.8	"g"			"character(0)"
+"PPA"	4831	"Pipemidic acid"	"Quinolones"	"J01MB04"	"Quinolone antibacterials"	"Other quinolones"	"c(\"pipz\", \"pizu\")"	"c(\"acide pipemidique\", \"acido pipemidico\", \"acidum pipemidicum\", \"deblaston\", \"dolcol\", \"pipedac\", \"pipemid\", \"pipemidic\", \"pipemidic acid\", \"pipemidicacid\", \"pipram\", \"uromidin\")"	0.8	"g"			"character(0)"
-"PIP"	"J01CA12"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")"	"c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")"			14	"g"	"c(\"25268-4\", \"3972-7\")"
+"PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"pi\", \"pip\", \"pipc\", \"pipe\", \"pp\")"	"c(\"isipen\", \"pentcillin\", \"peperacillin\", \"peracin\", \"piperacilina\", \"piperacillin\", \"piperacillin na\", \"piperacillin sodium\", \"piperacilline\", \"piperacillinum\", \"pipercillin\", \"pipracil\", \"pipril\")"			14	"g"	"c(\"25268-4\", \"3972-7\")"
-"PIS"			"Piperacillin/sulbactam"	"Beta-lactams/penicillins"			""	""					""
+"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"				""	""					""
-"TZP"	"J01CR05"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")"	"c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")"			14	"g"	"character(0)"
+"TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"p/t\", \"piptaz\", \"piptazo\", \"pit\", \"pita\", \"pt\", \"ptc\", \"ptz\", \"tzp\")"	"c(\"\", \"tazocel\", \"tazocillin\", \"tazocin\", \"zosyn\")"			14	"g"	"character(0)"
-"PRC"		71978	"Piridicillin"	"Beta-lactams/penicillins"			""	"piridicillin"					"character(0)"
+"PRC"	71978	"Piridicillin"	"Beta-lactams/penicillins"				""	"piridicillin"					"character(0)"
-"PRL"		157385	"Pirlimycin"	"Other antibacterials"			""	"c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")"					"character(0)"
+"PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"				""	"c(\"pirlimycin\", \"pirlimycina\", \"pirlimycine\", \"pirlimycinum\", \"pirsue\")"					"character(0)"
-"PIR"	"J01MB03"	4855	"Piromidic acid"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")"	2	"g"			"character(0)"
+"PIR"	4855	"Piromidic acid"	"Quinolones"	"J01MB03"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acide piromidique\", \"acido piromidico\", \"acidum piromidicum\", \"actrun c\", \"bactramyl\", \"enterol\", \"gastrurol\", \"panacid\", \"pirodal\", \"piromidic acid\", \"pyrido\", \"reelon\", \"septural\", \"urisept\", \"uropir\", \"zaomeal\")"	2	"g"			"character(0)"
-"PVM"	"J01CA02"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"berocillin\", \"pivaloylampicillin\", \"pivampicilina\", \"pivampicillin\", \"pivampicilline\", \"pivampicillinum\", \"pondocillin\")"	1.05	"g"			"character(0)"
+"PVM"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"J01CA02"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"berocillin\", \"pivaloylampicillin\", \"pivampicilina\", \"pivampicillin\", \"pivampicilline\", \"pivampicillinum\", \"pondocillin\")"	1.05	"g"			"character(0)"
-"PME"	"J01CA08"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"amdinocillin pivoxil\", \"coactabs\", \"hydroxymethyl\", \"pivmecilinamo\", \"pivmecillinam\", \"pivmecillinam hcl\", \"pivmecillinamum\")"	0.6	"g"			"character(0)"
+"PME"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"J01CA08"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"amdinocillin pivoxil\", \"coactabs\", \"hydroxymethyl\", \"pivmecilinamo\", \"pivmecillinam\", \"pivmecillinam hcl\", \"pivmecillinamum\")"	0.6	"g"			"character(0)"
-"PLZ"		42613186	"Plazomicin"	"Aminoglycosides"			""	"plazomicin"					"92024-9"
+"PLZ"	42613186	"Plazomicin"	"Aminoglycosides"	"J01GB14"			""	"plazomicin"					"92024-9"
-"PLB"	"J01XB02"	49800004	"Polymyxin B"	"Polymyxins"	"Other antibacterials"	"Polymyxins"	"c(\"pb\", \"pol\", \"polb\", \"poly\", \"poly b\", \"polymixin\", \"polymixin b\")"	"c(\"polimixina b\", \"polumyxin b\", \"polymixin b\", \"polymyxine b\")"			0.15	"g"	"c(\"17473-0\", \"25269-2\")"
+"PLB"	49800004	"Polymyxin B"	"Polymyxins"	"c(\"A07AA05\", \"J01XB02\", \"S01AA18\", \"S02AA11\", \"S03AA03\")"	"Other antibacterials"	"Polymyxins"	"c(\"pb\", \"pol\", \"polb\", \"poly\", \"poly b\", \"polymixin\", \"polymixin b\")"	"c(\"polimixina b\", \"polumyxin b\", \"polymixin b\", \"polymyxine b\")"	3	"MU"	0.15	"g"	"c(\"17473-0\", \"25269-2\")"
-"POP"			"Polymyxin B/polysorbate 80"	"Polymyxins"			""	""					""
+"POP"		"Polymyxin B/polysorbate 80"	"Polymyxins"				""	""					""
-"POS"	"J02AC04"	468595	"Posaconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa"	"c(\"noxafil\", \"posaconazole\", \"posaconazole sp\", \"posconazole\")"	0.3	"g"	0.3	"g"	"c(\"53731-6\", \"80545-7\")"
+"POS"	468595	"Posaconazole"	"Antifungals/antimycotics"	"J02AC04"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa"	"c(\"noxafil\", \"posaconazole\", \"posaconazole sp\", \"posconazole\")"	0.3	"g"	0.3	"g"	"c(\"53731-6\", \"80545-7\")"
-"PRA"		9802884	"Pradofloxacin"	"Quinolones"			""	"pradofloxacin"					"character(0)"
+"PRA"	9802884	"Pradofloxacin"	"Quinolones"				""	"pradofloxacin"					"character(0)"
-"PRX"		71455	"Premafloxacin"	"Quinolones"			""	"premafloxacin"					"character(0)"
+"PRX"	71455	"Premafloxacin"	"Quinolones"				""	"premafloxacin"					"character(0)"
-"PMD"	"J04AK08"	456199	"Pretomanid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	""					""
+"PMD"	456199	"Pretomanid"	"Antimycobacterials"	"J04AK08"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	""					""
-"PRM"		6446787	"Primycin"	"Macrolides/lincosamides"			""	""					""
+"PRM"	6446787	"Primycin"	"Macrolides/lincosamides"				""	""					""
-"PRI"	"J01FG01"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"c(\"\", \"pris\")"	"c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")"	2	"g"			"character(0)"
+"PRI"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"J01FG01"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"c(\"\", \"pris\")"	"c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")"	2	"g"			"character(0)"
-"PRB"	"J01CE09"	5903	"Procaine benzylpenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"depocillin\", \"duphapen\", \"hostacillin\", \"hydracillin\", \"jenacillin o\", \"nopcaine\", \"penicillin procaine\", \"retardillin\", \"vetspen\", \"vitablend\")"			0.6	"g"	"character(0)"
+"PRB"	5903	"Procaine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE09"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"depocillin\", \"duphapen\", \"hostacillin\", \"hydracillin\", \"jenacillin o\", \"nopcaine\", \"penicillin procaine\", \"retardillin\", \"vetspen\", \"vitablend\")"			0.6	"g"	"character(0)"
-"PRP"	"J01CE03"	92879	"Propicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"propicilina\", \"propicillin\", \"propicilline\", \"propicillinum\")"	0.9	"g"			"character(0)"
+"PRP"	92879	"Propicillin"	"Beta-lactams/penicillins"	"J01CE03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"c(\"propicilina\", \"propicillin\", \"propicilline\", \"propicillinum\")"	0.9	"g"			"character(0)"
-"PKA"		9872451	"Propikacin"	"Aminoglycosides"			""	"c(\"propikacin\", \"propikacina\", \"propikacine\", \"propikacinum\")"					"character(0)"
+"PKA"	9872451	"Propikacin"	"Aminoglycosides"				""	"c(\"propikacin\", \"propikacina\", \"propikacine\", \"propikacinum\")"					"character(0)"
-"PTH"	"J04AD01"	666418	"Prothionamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"prot"	"c(\"ektebin\", \"peteha\", \"prothionamide\", \"prothionamidum\", \"protion\", \"protionamid\", \"protionamida\", \"protionamide\", \"protionamidum\", \"protionizina\", \"tebeform\", \"trevintix\", \"tuberex\")"	0.75	"g"			"character(0)"
+"PTH"	666418	"Prothionamide"	"Antimycobacterials"	"J04AD01"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"prot"	"c(\"ektebin\", \"peteha\", \"prothionamide\", \"prothionamidum\", \"protion\", \"protionamid\", \"protionamida\", \"protionamide\", \"protionamidum\", \"protionizina\", \"tebeform\", \"trevintix\", \"tuberex\")"	0.75	"g"			"character(0)"
-"PRU"	"J01MA17"	65947	"Prulifloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"prulifloxacin\", \"pruvel\", \"pufloxacin dioxolil\", \"quisnon\")"	0.6	"g"			"character(0)"
+"PRU"	65947	"Prulifloxacin"	"Quinolones"	"J01MA17"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"prulifloxacin\", \"pruvel\", \"pufloxacin dioxolil\", \"quisnon\")"	0.6	"g"			"character(0)"
-"PZA"	"J04AK01"	1046	"Pyrazinamide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"c(\"aldinamid\", \"aldinamide\", \"braccopiral\", \"corsazinmid\", \"dipimide\", \"eprazin\", \"farmizina\", \"isopas\", \"lynamide\", \"novamid\", \"p ezetamid\", \"pezetamid\", \"pharozinamide\", \"piraldina\", \"pirazimida\", \"pirazinamid\", \"pirazinamida\", \"pirazinamide\", \"prazina\", \"pyrafat\", \"pyramide\", \"pyrazide\", \"pyrazinamdie\", \"pyrazinamid\", \"pyrazinamide\", \"pyrazinamidum\", \"pyrazine carboxamide\", \"pyrazineamide\", \"pyrizinamide\", \"rifafour\", \"rozide\", \"tebrazid\", \"tebrazio\", \"tisamid\", \"unipyranamide\", \"zinamide\", \"zinastat\"
+"PZA"	1046	"Pyrazinamide"	"Antimycobacterials"	"J04AK01"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"c(\"aldinamid\", \"aldinamide\", \"braccopiral\", \"corsazinmid\", \"dipimide\", \"eprazin\", \"farmizina\", \"isopas\", \"lynamide\", \"novamid\", \"p ezetamid\", \"pezetamid\", \"pharozinamide\", \"piraldina\", \"pirazimida\", \"pirazinamid\", \"pirazinamida\", \"pirazinamide\", \"prazina\", \"pyrafat\", \"pyramide\", \"pyrazide\", \"pyrazinamdie\", \"pyrazinamid\", \"pyrazinamide\", \"pyrazinamidum\", \"pyrazine carboxamide\", \"pyrazineamide\", \"pyrizinamide\", \"rifafour\", \"rozide\", \"tebrazid\", \"tebrazio\", \"tisamid\", \"unipyranamide\", \"zinamide\", \"zinastat\"
 )"	1.5	"g"			"c(\"11001-5\", \"25270-0\")"
-"QDA"	"J01FG02"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"c(\"q/d\", \"qda\", \"qida\", \"quda\", \"rp\", \"syn\")"	""			1.5	"g"	""
+"QDA"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"J01FG02"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"c(\"q/d\", \"qda\", \"qida\", \"quda\", \"rp\", \"syn\")"	""			1.5	"g"	""
-"RAC"		56052	"Ractopamine"	"Other antibacterials"			""	"c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")"					"character(0)"
+"RAC"	56052	"Ractopamine"	"Other antibacterials"				""	"c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")"					"character(0)"
-"RAM"		16132338	"Ramoplanin"	"Glycopeptides"			""	"ramoplanin"					"character(0)"
+"RAM"	16132338	"Ramoplanin"	"Glycopeptides"				""	"ramoplanin"					"character(0)"
-"RZM"		10993211	"Razupenem"	"Carbapenems"			""	"razupenem"					"character(0)"
+"RZM"	10993211	"Razupenem"	"Carbapenems"				""	"razupenem"					"character(0)"
-"RTP"	"A07AA11"	6918462	"Retapamulin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"	""	"c(\"altabax\", \"altargo\", \"retapamulin\")"	0.6	"g"			"character(0)"
+"RTP"	6918462	"Retapamulin"	"Other antibacterials"	"D06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	""	"c(\"altabax\", \"altargo\", \"retapamulin\")"					"character(0)"
-"RBC"	"J02AC05"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"c(\"kisqali\", \"ribociclib\")"	0.2		0.2		"character(0)"
+"RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"c(\"kisqali\", \"ribociclib\")"					"character(0)"
-"RST"	"J01GB10"	33042	"Ribostamycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")"			1	"g"	"character(0)"
+"RST"	33042	"Ribostamycin"	"Aminoglycosides"	"J01GB10"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"c(\"dekamycin iv\", \"hetangmycin\", \"ribastamin\", \"ribostamicina\", \"ribostamycin\", \"ribostamycine\", \"ribostamycinum\", \"vistamycin\", \"xylostatin\")"			1	"g"	"character(0)"
-"RID1"		16659285	"Ridinilazole"	"Other antibacterials"			""	"ridinilazole"					"character(0)"
+"RID1"	16659285	"Ridinilazole"	"Other antibacterials"				""	"ridinilazole"					"character(0)"
-"RIB"	"J04AB04"	135398743	"Rifabutin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifb"	"c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")"	0.15	"g"			"24032-5"
+"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifb"	"c(\"alfacid\", \"ansamicin\", \"ansamycin\", \"ansatipin\", \"ansatipine\", \"mycobutin\", \"rifabutin\", \"rifabutina\", \"rifabutine\", \"rifabutinum\")"	0.15	"g"			"24032-5"
-"RIF"	"J04AB02"	135398735	"Rifampicin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa"	"c(\"abrifam\", \"archidyn\", \"arficin\", \"arzide\", \"azt + rifampin\", \"benemicin\", \"benemycin\", \"dipicin\", \"doloresum\", \"eremfat\", \"famcin\", \"fenampicin\", \"rifadin\", \"rifadin i.v\", \"rifadin i.v.\", \"rifadine\", \"rifagen\", \"rifaldazin\", \"rifaldazine\", \"rifaldin\", \"rifamate\", \"rifamicin amp\", \"rifamor\", \"rifampicin\", \"rifampicin sv\", \"rifampicina\", \"rifampicine\", \"rifampicinum\", \"rifampin\", \"rifamsolin\", \"rifamycin amp\", \"rifaprodin\", \"rifcin\", \"rifobac\", \"rifoldin\", \"rifoldine\", \"riforal\", \"rimactan\", \"rimactane\", 
+"RIF"	135398735	"Rifampicin"	"Antimycobacterials"	"J04AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa"	"c(\"abrifam\", \"archidyn\", \"arficin\", \"arzide\", \"azt + rifampin\", \"benemicin\", \"benemycin\", \"dipicin\", \"doloresum\", \"eremfat\", \"famcin\", \"fenampicin\", \"rifadin\", \"rifadin i.v\", \"rifadin i.v.\", \"rifadine\", \"rifagen\", \"rifaldazin\", \"rifaldazine\", \"rifaldin\", \"rifamate\", \"rifamicin amp\", \"rifamor\", \"rifampicin\", \"rifampicin sv\", \"rifampicina\", \"rifampicine\", \"rifampicinum\", \"rifampin\", \"rifamsolin\", \"rifamycin amp\", \"rifaprodin\", \"rifcin\", \"rifobac\", \"rifoldin\", \"rifoldine\", \"riforal\", \"rimactan\", \"rimactane\", 
 \"rimactizid\", \"rimazid\", \"rimycin\", \"sinerdol\", \"tubocin\")"	0.6	"g"	0.6	"g"	"character(0)"
-"RFI"	"J04AM02"		"Rifampicin/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	"c(\"rifinah\", \"rimactazid\")"					"character(0)"
+"RFI"		"Rifampicin/isoniazid"	"Antimycobacterials"	"J04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	"c(\"rifinah\", \"rimactazid\")"					"character(0)"
-"RPEI"	"J04AM06"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
+"RPEI"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM06"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"RPI"	"J04AM05"		"Rifampicin/pyrazinamide/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
+"RPI"		"Rifampicin/pyrazinamide/isoniazid"	"Antimycobacterials"	"J04AM05"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"RFM"	"J04AB03"	6324616	"Rifamycin"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	""	"c(\"aemcolo\", \"rifacin\", \"rifamicina\", \"rifamicine sv\", \"rifamycin\", \"rifamycine\", \"rifamycinum\", \"rifocin\", \"rifocyn\", \"rifomycin\", \"rifomycin sv\", \"tuborin\")"			0.6	"g"	"character(0)"
+"RFM"	6324616	"Rifamycin"	"Antimycobacterials"	"c(\"A07AA13\", \"D06AX15\", \"J04AB03\", \"S01AA16\", \"S02AA12\")"	"Drugs for treatment of tuberculosis"	"Antibiotics"	""	"c(\"aemcolo\", \"rifacin\", \"rifamicina\", \"rifamicine sv\", \"rifamycin\", \"rifamycine\", \"rifamycinum\", \"rifocin\", \"rifocyn\", \"rifomycin\", \"rifomycin sv\", \"tuborin\")"			0.6	"g"	"character(0)"
-"RFP"	"J04AB05"	135403821	"Rifapentine"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp"	"c(\"cyclopentyl rifampin\", \"priftin\", \"rifapentin\", \"rifapentina\", \"rifapentine\", \"rifapentinum\")"	0.11	"g"			"character(0)"
+"RFP"	135403821	"Rifapentine"	"Antimycobacterials"	"J04AB05"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp"	"c(\"cyclopentyl rifampin\", \"priftin\", \"rifapentin\", \"rifapentina\", \"rifapentine\", \"rifapentinum\")"	0.11	"g"			"character(0)"
-"RFX"	"A07AA11"	6436173	"Rifaximin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"	""	"c(\"fatroximin\", \"flonorm\", \"lormyx\", \"lumenax\", \"normix\", \"redactiv\", \"rifacol\", \"rifamixin\", \"rifaxidin\", \"rifaximin\", \"rifaximina\", \"rifaximine\", \"rifaximinum\", \"rifaxin\", \"ritacol\", \"spiraxin\", \"xifaxan\", \"xifaxsan\")"	0.6	"g"			"character(0)"
+"RFX"	6436173	"Rifaximin"	"Other antibacterials"	"c(\"A07AA11\", \"D06AX11\")"	"Intestinal antiinfectives"	"Antibiotics"	""	"c(\"fatroximin\", \"flonorm\", \"lormyx\", \"lumenax\", \"normix\", \"redactiv\", \"rifacol\", \"rifamixin\", \"rifaxidin\", \"rifaximin\", \"rifaximina\", \"rifaximine\", \"rifaximinum\", \"rifaxin\", \"ritacol\", \"spiraxin\", \"xifaxan\", \"xifaxsan\")"	0.6	"g"			"character(0)"
-"RIT"		65633	"Ritipenem"	"Carbapenems"			""	"ritipenem"					"character(0)"
+"RIT"	65633	"Ritipenem"	"Carbapenems"				""	"ritipenem"					"character(0)"
-"RIA"		163692	"Ritipenem acoxil"	"Carbapenems"			""	"ritipenem acoxil"					"character(0)"
+"RIA"	163692	"Ritipenem acoxil"	"Carbapenems"				""	"ritipenem acoxil"					"character(0)"
-"ROK"	"J01FA12"	5282211	"Rokitamycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"propionylleucomycin\", \"ricamycin\", \"rokicid\", \"rokital\", \"rokitamicina\", \"rokitamycin\", \"rokitamycine\", \"rokitamycinum\")"	0.8	"g"			"character(0)"
+"ROK"	5282211	"Rokitamycin"	"Macrolides/lincosamides"	"J01FA12"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"propionylleucomycin\", \"ricamycin\", \"rokicid\", \"rokital\", \"rokitamicina\", \"rokitamycin\", \"rokitamycine\", \"rokitamycinum\")"	0.8	"g"			"character(0)"
-"RLT"	"J01AA09"	54682938	"Rolitetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bristacin\", \"kinteto\", \"reverin\", \"rolitetraciclina\", \"rolitetracycline\", \"rolitetracyclinum\", \"solvocillin\", \"superciclin\", \"synotodecin\", \"synterin\", \"syntetrex\", \"syntetrin\", \"velacicline\", \"velacycline\")"			0.35	"g"	"character(0)"
+"RLT"	54682938	"Rolitetracycline"	"Tetracyclines"	"J01AA09"	"Tetracyclines"	"Tetracyclines"	""	"c(\"bristacin\", \"kinteto\", \"reverin\", \"rolitetraciclina\", \"rolitetracycline\", \"rolitetracyclinum\", \"solvocillin\", \"superciclin\", \"synotodecin\", \"synterin\", \"syntetrex\", \"syntetrin\", \"velacicline\", \"velacycline\")"			0.35	"g"	"character(0)"
-"ROS"	"J01MB01"	287180	"Rosoxacin"	"Quinolones"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acrosoxacin\", \"eracine\", \"eradacil\", \"eradacin\", \"rosoxacin\", \"rosoxacine\", \"rosoxacino\", \"rosoxacinum\", \"roxadyl\", \"winuron\")"	0.3	"g"			"character(0)"
+"ROS"	287180	"Rosoxacin"	"Quinolones"	"J01MB01"	"Quinolone antibacterials"	"Other quinolones"	""	"c(\"acrosoxacin\", \"eracine\", \"eradacil\", \"eradacin\", \"rosoxacin\", \"rosoxacine\", \"rosoxacino\", \"rosoxacinum\", \"roxadyl\", \"winuron\")"	0.3	"g"			"character(0)"
-"RXT"	"J01FA06"		"Roxithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi"	""	0.3	"g"			""
+"RXT"		"Roxithromycin"	"Macrolides/lincosamides"	"J01FA06"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi"	""	0.3	"g"			""
-"RFL"	"J01MA10"	58258	"Rufloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"rufloxacin\", \"rufloxacin hcl\", \"rufloxacine\", \"rufloxacino\", \"rufloxacinum\")"	0.2	"g"			"character(0)"
+"RFL"	58258	"Rufloxacin"	"Quinolones"	"J01MA10"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"rufloxacin\", \"rufloxacin hcl\", \"rufloxacine\", \"rufloxacino\", \"rufloxacinum\")"	0.2	"g"			"character(0)"
-"SAL"		3085092	"Salinomycin"	"Other antibacterials"			""	"c(\"coxistac\", \"procoxacin\", \"salinomicina\", \"salinomycin\", \"salinomycine\", \"salinomycinum\")"					"87593-0"
+"SAL"	3085092	"Salinomycin"	"Other antibacterials"				""	"c(\"coxistac\", \"procoxacin\", \"salinomicina\", \"salinomycin\", \"salinomycine\", \"salinomycinum\")"					"87593-0"
-"SAR"		56208	"Sarafloxacin"	"Quinolones"			""	"c(\"difloxacine\", \"difloxacino\", \"difloxacinum\", \"saraflox\", \"sarafloxacin\", \"sarafloxacine\", \"sarafloxacino\", \"sarafloxacinum\")"					"character(0)"
+"SAR"	56208	"Sarafloxacin"	"Quinolones"				""	"c(\"difloxacine\", \"difloxacino\", \"difloxacinum\", \"saraflox\", \"sarafloxacin\", \"sarafloxacine\", \"sarafloxacino\", \"sarafloxacinum\")"					"character(0)"
-"SRX"		9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"			""	"sarmoxicillin"					"character(0)"
+"SRX"	9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"				""	"sarmoxicillin"					"character(0)"
-"SEC"		71815	"Secnidazole"	"Other antibacterials"			""	"c(\"flagentyl\", \"secnidal\", \"secnidazol\", \"secnidazole\", \"secnidazolum\", \"secnil\", \"sindose\", \"solosec\")"					"character(0)"
+"SEC"	71815	"Secnidazole"	"Other antibacterials"	"P01AB07"			""	"c(\"flagentyl\", \"secnidal\", \"secnidazol\", \"secnidazole\", \"secnidazolum\", \"secnil\", \"sindose\", \"solosec\")"	2	"g"			"character(0)"
-"SMF"	"J04AK05"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	""	86				""
+"SMF"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"C10BA04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	""					""
-"SIS"	"J01GB08"	36119	"Sisomicin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso"	"c(\"rickamicin\", \"salvamina\", \"siseptin sulfate\", \"sisomicin\", \"sisomicin sulfate\", \"sisomicina\", \"sisomicine\", \"sisomicinum\", \"sisomin\", \"sisomycin\", \"sissomicin\", \"sizomycin\")"			0.24	"g"	"character(0)"
+"SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso"	"c(\"rickamicin\", \"salvamina\", \"siseptin sulfate\", \"sisomicin\", \"sisomicin sulfate\", \"sisomicina\", \"sisomicine\", \"sisomicinum\", \"sisomin\", \"sisomycin\", \"sissomicin\", \"sizomycin\")"			0.24	"g"	"character(0)"
-"SIT"		461399	"Sitafloxacin"	"Quinolones"			""	"c(\"gracevit\", \"sitafloxacinisomer\")"					"character(0)"
+"SIT"	461399	"Sitafloxacin"	"Quinolones"	"J01MA21"			""	"c(\"gracevit\", \"sitafloxacinisomer\")"	0.1	"g"			"character(0)"
-"SDA"	"J04AA02"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	"c(\"bactylan\", \"decapasil\", \"lepasen\", \"monopas\", \"nippas\", \"p.a.s. sodium\", \"pamisyl sodium\", \"parasal sodium\", \"pas sodium\", \"pasade\", \"pasnal\", \"passodico\", \"salvis\", \"sanipirol\", \"sodiopas\", \"sodium p.a.s\", \"sodium pas\", \"teebacin\", \"tubersan\")"	14	"g"	14	"g"	"character(0)"
+"SDA"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"J04AA02"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	"c(\"bactylan\", \"decapasil\", \"lepasen\", \"monopas\", \"nippas\", \"p.a.s. sodium\", \"pamisyl sodium\", \"parasal sodium\", \"pas sodium\", \"pasade\", \"pasnal\", \"passodico\", \"salvis\", \"sanipirol\", \"sodiopas\", \"sodium p.a.s\", \"sodium pas\", \"teebacin\", \"tubersan\")"	14	"g"	14	"g"	"character(0)"
-"SOL"		25242512	"Solithromycin"	"Macrolides/lincosamides"			""	""					""
+"SOL"	25242512	"Solithromycin"	"Macrolides/lincosamides"	"J01FA16"			""	""					""
-"SPX"	"J01MA09"	60464	"Sparfloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"spa\", \"spar\")"	"c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")"	0.2	"g"			"character(0)"
+"SPX"	60464	"Sparfloxacin"	"Quinolones"	"J01MA09"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"spa\", \"spar\")"	"c(\"esparfloxacino\", \"sparfloxacin\", \"sparfloxacine\", \"sparfloxacinum\")"	0.2	"g"			"character(0)"
-"SPT"	"J01XX04"	15541	"Spectinomycin"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	"c(\"sc\", \"spe\", \"spec\", \"spt\")"	"c(\"actinospectacina\", \"adspec\", \"espectinomicina\", \"prospec\", \"specitinomycin\", \"spectam\", \"spectinomicina\", \"spectinomycin\", \"spectinomycin di hcl\", \"spectinomycine\", \"spectinomycinum\", \"stanilo\", \"togamycin\", \"trobicin\")"			3	"g"	"character(0)"
+"SPT"	15541	"Spectinomycin"	"Other antibacterials"	"J01XX04"	"Other antibacterials"	"Other antibacterials"	"c(\"sc\", \"spe\", \"spec\", \"spt\")"	"c(\"actinospectacina\", \"adspec\", \"espectinomicina\", \"prospec\", \"specitinomycin\", \"spectam\", \"spectinomicina\", \"spectinomycin\", \"spectinomycin di hcl\", \"spectinomycine\", \"spectinomycinum\", \"stanilo\", \"togamycin\", \"trobicin\")"			3	"g"	"character(0)"
-"SPI"	"J01FA02"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"\", \"spir\")"	"c(\"espiramicin\", \"provamycin\", \"rovamycin\", \"rovamycine\", \"sequamycin\", \"spiramycine\", \"spiramycinum\")"	3	"g"			"character(0)"
+"SPI"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"J01FA02"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"\", \"spir\")"	"c(\"espiramicin\", \"provamycin\", \"rovamycin\", \"rovamycine\", \"sequamycin\", \"spiramycine\", \"spiramycinum\")"	3	"g"			"character(0)"
-"SPM"	"J01RA04"		"Spiramycin/metronidazole"	"Other antibacterials"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
+"SPM"		"Spiramycin/metronidazole"	"Other antibacterials"	"J01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"STR"	"J01GA02"		"Streptoduocin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Streptomycins"	""	""			1	"g"	""
+"STR"		"Streptoduocin"	"Aminoglycosides"	"J01GA02"	"Aminoglycoside antibacterials"	"Streptomycins"	""	""			1	"g"	""
-"STR1"	"J01GA01"	19649	"Streptomycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Streptomycins"	"c(\"s\", \"stm\", \"str\", \"stre\")"	"c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")"			1	"g"	"4039-4"
+"STR1"	19649	"Streptomycin"	"Aminoglycosides"	"c(\"A07AA04\", \"J01GA01\")"	"Aminoglycoside antibacterials"	"Streptomycins"	"c(\"s\", \"stm\", \"str\", \"stre\")"	"c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")"			1	"g"	"4039-4"
-"STH"			"Streptomycin-high"	"Aminoglycosides"			"c(\"s_h\", \"sthl\", \"strepto high\", \"streptomycin high\")"	""					""
+"STH"		"Streptomycin-high"	"Aminoglycosides"				"c(\"s_h\", \"sthl\", \"strepto high\", \"streptomycin high\")"	""					""
-"STI"	"J04AM01"		"Streptomycin/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
+"STI"		"Streptomycin/isoniazid"	"Antimycobacterials"	"J04AM01"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"SUL"	"J01CG01"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	""	"c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")"			1	"g"	"character(0)"
+"SUL"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"J01CG01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	""	"c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")"			1	"g"	"character(0)"
-"SBC"	"J01CA16"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")"			15	"g"	"character(0)"
+"SBC"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"J01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")"			15	"g"	"character(0)"
-"SUC"		5318	"Sulconazole"	"Antifungals/antimycotics"			""	"c(\"sulconazol\", \"sulconazole\", \"sulconazolum\")"					"character(0)"
+"SUC"	5318	"Sulconazole"	"Antifungals/antimycotics"	"D01AC09"			""	"c(\"sulconazol\", \"sulconazole\", \"sulconazolum\")"					"character(0)"
-"SUP"		6634	"Sulfachlorpyridazine"	"Other antibacterials"			""	"c(\"cluricol\", \"cosulid\", \"cosumix\", \"durasulf\", \"nefrosul\", \"nsulfanilamide\", \"prinzone vet\", \"prinzone vet.\", \"solfaclorpiridazina\", \"sonilyn\", \"sulfachlorpyridazine\", \"sulfacloropiridazina\", \"vetisulid\")"					"character(0)"
+"SUP"	6634	"Sulfachlorpyridazine"	"Other antibacterials"				""	"c(\"cluricol\", \"cosulid\", \"cosumix\", \"durasulf\", \"nefrosul\", \"nsulfanilamide\", \"prinzone vet\", \"prinzone vet.\", \"solfaclorpiridazina\", \"sonilyn\", \"sulfachlorpyridazine\", \"sulfacloropiridazina\", \"vetisulid\")"					"character(0)"
-"SDI"	"J01EC02"	5215	"Sulfadiazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"c(\"adiazin\", \"adiazine\", \"cocodiazine\", \"codiazine\", \"cremodiazine\", \"cremotres\", \"debenal\", \"deltazina\", \"diazin\", \"diazolone\", \"diazovit\", \"diazyl\", \"eskadiazine\", \"honey diazine\", \"liquadiazine\", \"microsulfon\", \"neazine\", \"neotrizine\", \"nsulfanilamide\", \"palatrize\", \"piridisir\", \"pirimal\", \"pyrimal\", \"quadetts\", \"quadramoid\", \"sanodiazine\", \"sildaflo\", \"silvadene\", \"solfadiazina\", \"spofadrizine\", \"sterazine\", \"sulfacombin\", \"sulfadiazene\", \"sulfadiazin\", \"sulfadiazina\", \"sulfadiazine\", \"sulfadiazinum\", 
+"SDI"	5215	"Sulfadiazine"	"Trimethoprims"	"J01EC02"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"c(\"adiazin\", \"adiazine\", \"cocodiazine\", \"codiazine\", \"cremodiazine\", \"cremotres\", \"debenal\", \"deltazina\", \"diazin\", \"diazolone\", \"diazovit\", \"diazyl\", \"eskadiazine\", \"honey diazine\", \"liquadiazine\", \"microsulfon\", \"neazine\", \"neotrizine\", \"nsulfanilamide\", \"palatrize\", \"piridisir\", \"pirimal\", \"pyrimal\", \"quadetts\", \"quadramoid\", \"sanodiazine\", \"sildaflo\", \"silvadene\", \"solfadiazina\", \"spofadrizine\", \"sterazine\", \"sulfacombin\", \"sulfadiazene\", \"sulfadiazin\", \"sulfadiazina\", \"sulfadiazine\", \"sulfadiazinum\", 
 \"sulfapirimidin\", \"sulfapyrimidin\", \"sulfapyrimidine\", \"sulfatryl\", \"sulfazine\", \"sulfolex\", \"sulfonamides duplex\", \"sulfonsol\", \"sulfose\", \"sulphadiazine\", \"sulphadiazine e\", \"terfonyl\", \"theradiazine\", \"thermazene\", \"trifonamide\", \"triple sulfa\", \"triple sulfas\", \"trisem\", \"truozine\", \"zinc sulfadiazine\")"	0.6	"g"			"c(\"27216-1\", \"59742-7\", \"6907-0\")"
-"SLT"	"J01EE06"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
+"SLT"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims"	"J01EE06"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
-"SLT1"	"J01EE02"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	"c(\"antastmon\", \"cotrimazine\", \"diaziprim forte\", \"ditrim\", \"ditrivet\", \"sultrisan\", \"triglobe\", \"trimin\", \"tucoprim\", \"uniprim\")"					"character(0)"
+"SLT1"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims"	"J01EE02"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	"c(\"antastmon\", \"cotrimazine\", \"diaziprim forte\", \"ditrim\", \"ditrivet\", \"sultrisan\", \"triglobe\", \"trimin\", \"tucoprim\", \"uniprim\")"					"character(0)"
-"SUD"	"J01ED01"	5323	"Sulfadimethoxine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"agribon\", \"arnosulfan\", \"bactrovet\", \"deposul\", \"diasulfa\", \"diasulfyl\", \"dimetazina\", \"dinosol\", \"dorisul\", \"lasibon\", \"madribon\", \"madrigid\", \"madriqid\", \"madroxin\", \"madroxine\", \"maxulvet\", \"mecozine\", \"memcozine\", \"metoxidon\", \"neostrepal\", \"neostreptal\", \"nsulfanilamide\", \"omnibon\", \"persulfen\", \"primor\", \"radonin\", \"redifal\", \"rofenaid\", \"roscosulf\", \"scandisil\", \"solfadimetossina\", \"sudine\", \"suldixine\", \"sulfabon\", \"sulfadimethoxin\", \"sulfadimethoxine\", \"sulfadimethoxinum\", \"sulfadimetossina\", 
+"SUD"	5323	"Sulfadimethoxine"	"Trimethoprims"	"J01ED01"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"agribon\", \"arnosulfan\", \"bactrovet\", \"deposul\", \"diasulfa\", \"diasulfyl\", \"dimetazina\", \"dinosol\", \"dorisul\", \"lasibon\", \"madribon\", \"madrigid\", \"madriqid\", \"madroxin\", \"madroxine\", \"maxulvet\", \"mecozine\", \"memcozine\", \"metoxidon\", \"neostrepal\", \"neostreptal\", \"nsulfanilamide\", \"omnibon\", \"persulfen\", \"primor\", \"radonin\", \"redifal\", \"rofenaid\", \"roscosulf\", \"scandisil\", \"solfadimetossina\", \"sudine\", \"suldixine\", \"sulfabon\", \"sulfadimethoxin\", \"sulfadimethoxine\", \"sulfadimethoxinum\", \"sulfadimetossina\", 
 \"sulfadimetoxin\", \"sulfadimetoxina\", \"sulfadimetoxine\", \"sulfastop\", \"sulfdimethoxine\", \"sulfoplan\", \"sulphadimethoxine\", \"sulxin\", \"sumbio\", \"symbio\", \"theracanzan\", \"ultrasulfon\")"	0.5	"g"			"character(0)"
-"SDM"	"J01EB03"	5327	"Sulfadimidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\", 
+"SDM"	5327	"Sulfadimidine"	"Trimethoprims"	"J01EB03"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\", 
 \"sulfametazina\", \"sulfametazyny\", \"sulfamethazine\", \"sulfamethiazine\", \"sulfamezathine\", \"sulfamidine\", \"sulfasure sr bolus\", \"sulfodimesin\", \"sulfodimezine\", \"sulka k boluses\", \"sulka s boluses\", \"sulmet\", \"sulphadimidine\", \"sulphamethasine\", \"sulphamethazine\", \"sulphamezathine\", \"sulphamidine\", \"sulphodimezine\", \"superseptil\", \"superseptyl\", \"vertolan\")"	4	"g"			"character(0)"
-"SLT2"	"J01EE05"		"Sulfadimidine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
+"SLT2"		"Sulfadimidine/trimethoprim"	"Trimethoprims"	"J01EE05"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
-"SLF"	"J01EB05"	5344	"Sulfafurazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"c(\"\", \"sfsz\")"	"c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\", 
+"SLF"	5344	"Sulfafurazole"	"Trimethoprims"	"c(\"J01EB05\", \"S01AB02\")"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"c(\"\", \"sfsz\")"	"c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\", 
 \"soxamide\", \"soxazole\", \"soxisol\", \"soxitabs\", \"soxomide\", \"stansin\", \"sulbio\", \"sulfafuraz ole\", \"sulfafurazol\", \"sulfafurazole\", \"sulfafurazolum\", \"sulfagan\", \"sulfagen\", \"sulfaisoxazole\", \"sulfalar\", \"sulfapolar\", \"sulfasol\", \"sulfasoxazole\", \"sulfasoxizole\", \"sulfazin\", \"sulfisin\", \"sulfisonazole\", \"sulfisoxasole\", \"sulfisoxazol\", \"sulfisoxazole\", \"sulfisoxazolum\", \"sulfizin\", \"sulfizol\", \"sulfizole\", \"sulfofurazole\", \"sulfoxol\", \"suloxsol\", \"sulphafuraz\", \"sulphafurazol\", \"sulphafurazole\", \"sulphafurazolum\", 
 \"sulphaisoxazole\", \"sulphisoxazol\", \"sulphisoxazole\", \"sulphofurazole\", \"sulsoxin\", \"thiasin\", \"unisulf\", \"urisoxin\", \"uritrisin\", \"urogan\", \"vagilia\")"	4	"g"	4	"g"	"character(0)"
-"SLF1"	"J01EB01"	5343	"Sulfaisodimidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"aristamid\", \"aristamide\", \"aristogyn\", \"domain\", \"domian\", \"elcosin\", \"elcosine\", \"elkosil\", \"elkosin\", \"elkosine\", \"erycon\", \"isosulf\", \"mefenal\", \"nsulfanilamide\", \"solfisomidina\", \"sulfadimetine\", \"sulfaisodimerazine\", \"sulfaisodimidine\", \"sulfaisodimidinum\", \"sulfaisomidine\", \"sulfamethin\", \"sulfasomidine\", \"sulfisomidina\", \"sulfisomidine\", \"sulfisomidine sodium\", \"sulfisomidinum\", \"sulphasomidine\")"	4	"g"	4	"g"	"character(0)"
+"SLF1"	5343	"Sulfaisodimidine"	"Trimethoprims"	"J01EB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"aristamid\", \"aristamide\", \"aristogyn\", \"domain\", \"domian\", \"elcosin\", \"elcosine\", \"elkosil\", \"elkosin\", \"elkosine\", \"erycon\", \"isosulf\", \"mefenal\", \"nsulfanilamide\", \"solfisomidina\", \"sulfadimetine\", \"sulfaisodimerazine\", \"sulfaisodimidine\", \"sulfaisodimidinum\", \"sulfaisomidine\", \"sulfamethin\", \"sulfasomidine\", \"sulfisomidina\", \"sulfisomidine\", \"sulfisomidine sodium\", \"sulfisomidinum\", \"sulphasomidine\")"	4	"g"	4	"g"	"character(0)"
-"SLF2"	"J01ED02"	9047	"Sulfalene"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"dalysep\", \"kelfizin\", \"kelfizina\", \"kelfizine\", \"kelfizine w\", \"longum\", \"nsulfanilamide\", \"policydal\", \"polycidal\", \"solfametopirazina\", \"sulfalen\", \"sulfalene\", \"sulfaleno\", \"sulfalenum\", \"sulfamethopyrazine\", \"sulfamethoxypyrazine\", \"sulfametopyrazine\", \"sulfametoxypyridazin\", \"sulphalene\", \"sulphametopyrazine\", \"vetkelfizina\")"	0.1	"g"			"character(0)"
+"SLF2"	9047	"Sulfalene"	"Trimethoprims"	"J01ED02"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"dalysep\", \"kelfizin\", \"kelfizina\", \"kelfizine\", \"kelfizine w\", \"longum\", \"nsulfanilamide\", \"policydal\", \"polycidal\", \"solfametopirazina\", \"sulfalen\", \"sulfalene\", \"sulfaleno\", \"sulfalenum\", \"sulfamethopyrazine\", \"sulfamethoxypyrazine\", \"sulfametopyrazine\", \"sulfametoxypyridazin\", \"sulphalene\", \"sulphametopyrazine\", \"vetkelfizina\")"	0.1	"g"			"character(0)"
-"SZO"	"J01ED09"	187764	"Sulfamazone"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"sulfamazon\", \"sulfamazona\", \"sulfamazone\", \"sulfamazonum\")"	1.5	"g"			"character(0)"
+"SZO"	187764	"Sulfamazone"	"Trimethoprims"	"J01ED09"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"sulfamazon\", \"sulfamazona\", \"sulfamazone\", \"sulfamazonum\")"	1.5	"g"			"character(0)"
-"SLF3"	"J01ED07"	5325	"Sulfamerazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"cremomerazine\", \"kelamerazine\", \"mebacid\", \"mesulfa\", \"methylpyrimal\", \"methylsulfazin\", \"methylsulfazine\", \"metilsulfadiazin\", \"metilsulfazin\", \"nsulfanilamide\", \"percoccide\", \"pyralcid\", \"pyrimal m\", \"romezin\", \"septacil\", \"septosyl\", \"solfamerazina\", \"solumedin\", \"sulfameradine\", \"sulfamerazin\", \"sulfamerazina\", \"sulfamerazine\", \"sulfamerazinum\", \"sulfamethyldiazine\", \"sulphamerazine\", \"sumedine\", \"susfamerazine\")"	3	"g"			"character(0)"
+"SLF3"	5325	"Sulfamerazine"	"Trimethoprims"	"c(\"D06BA06\", \"J01ED07\")"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"cremomerazine\", \"kelamerazine\", \"mebacid\", \"mesulfa\", \"methylpyrimal\", \"methylsulfazin\", \"methylsulfazine\", \"metilsulfadiazin\", \"metilsulfazin\", \"nsulfanilamide\", \"percoccide\", \"pyralcid\", \"pyrimal m\", \"romezin\", \"septacil\", \"septosyl\", \"solfamerazina\", \"solumedin\", \"sulfameradine\", \"sulfamerazin\", \"sulfamerazina\", \"sulfamerazine\", \"sulfamerazinum\", \"sulfamethyldiazine\", \"sulphamerazine\", \"sumedine\", \"susfamerazine\")"	3	"g"			"character(0)"
-"SLT3"	"J01EE07"		"Sulfamerazine/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
+"SLT3"		"Sulfamerazine/trimethoprim"	"Trimethoprims"	"J01EE07"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
-"SUM"		5327	"Sulfamethazine"	"Other antibacterials"			""	"c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\", 
+"SUM"	5327	"Sulfamethazine"	"Other antibacterials"				""	"c(\"azolmetazin\", \"benzene sulfonamide\", \"calfspan\", \"calfspan tablets\", \"cremomethazine\", \"diazil\", \"diazilsulfadine\", \"dimezathine\", \"intradine\", \"kelametazine\", \"mermeth\", \"metazin\", \"neasina\", \"neazina\", \"nsulfanilamide\", \"panazin\", \"pirmazin\", \"primazin\", \"sa iii\", \"solfadimidina\", \"spanbolet\", \"sulfadimerazine\", \"sulfadimesin\", \"sulfadimesine\", \"sulfadimethyldiazine\", \"sulfadimezin\", \"sulfadimezine\", \"sulfadimezinum\", \"sulfadimidin\", \"sulfadimidina\", \"sulfadimidine\", \"sulfadimidinum\", \"sulfadine\", 
 \"sulfametazina\", \"sulfametazyny\", \"sulfamethazine\", \"sulfamethiazine\", \"sulfamezathine\", \"sulfamidine\", \"sulfasure sr bolus\", \"sulfodimesin\", \"sulfodimezine\", \"sulka k boluses\", \"sulka s boluses\", \"sulmet\", \"sulphadimidine\", \"sulphamethasine\", \"sulphamethazine\", \"sulphamezathine\", \"sulphamidine\", \"sulphodimezine\", \"superseptil\", \"superseptyl\", \"vertolan\")"					"87592-2"
-"SLF4"	"J01EB02"	5328	"Sulfamethizole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"c(\"\", \"sfmz\")"	"c(\"ayerlucil\", \"lucosil\", \"methazol\", \"microsul\", \"nsulfanilamide\", \"proklar\", \"renasul\", \"salimol\", \"solfametizolo\", \"sulamethizole\", \"sulfa gram\", \"sulfamethizol\", \"sulfamethizole\", \"sulfamethizolum\", \"sulfametizol\", \"sulfapyelon\", \"sulfstat\", \"sulfurine\", \"sulphamethizole\", \"tetracid\", \"thidicur\", \"thiosulfil\", \"thiosulfil forte\", \"ultrasul\", \"urocydal\", \"urodiaton\", \"urolucosil\", \"urosulfin\")"	4	"g"			"c(\"60175-7\", \"60176-5\", \"60177-3\")"
+"SLF4"	5328	"Sulfamethizole"	"Trimethoprims"	"c(\"B05CA04\", \"D06BA04\", \"J01EB02\", \"S01AB01\")"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"c(\"\", \"sfmz\")"	"c(\"ayerlucil\", \"lucosil\", \"methazol\", \"microsul\", \"nsulfanilamide\", \"proklar\", \"renasul\", \"salimol\", \"solfametizolo\", \"sulamethizole\", \"sulfa gram\", \"sulfamethizol\", \"sulfamethizole\", \"sulfamethizolum\", \"sulfametizol\", \"sulfapyelon\", \"sulfstat\", \"sulfurine\", \"sulphamethizole\", \"tetracid\", \"thidicur\", \"thiosulfil\", \"thiosulfil forte\", \"ultrasul\", \"urocydal\", \"urodiaton\", \"urolucosil\", \"urosulfin\")"	4	"g"			"c(\"60175-7\", \"60176-5\", \"60177-3\")"
-"SMX"	"J01EC01"	5329	"Sulfamethoxazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"c(\"sfmx\", \"sulf\")"	"c(\"azo gantanol\", \"eusaprim\", \"gamazole\", \"gantanol\", \"gantanol ds\", \"metoxal\", \"nsulfanilamide\", \"nsulphanilamide\", \"radonil\", \"septran\", \"septrin\", \"simsinomin\", \"sinomin\", \"solfametossazolo\", \"sulfamethalazole\", \"sulfamethoxazol\", \"sulfamethoxazole\", \"sulfamethoxazolum\", \"sulfamethoxizole\", \"sulfamethylisoxazole\", \"sulfametoxazol\", \"sulfisomezole\", \"sulphamethalazole\", \"sulphamethoxazol\", \"sulphamethoxazole\", \"sulphisomezole\", \"urobak\")"	2	"g"			"c(\"10342-4\", \"25271-8\", \"39772-9\", \"59971-2\", \"59972-0\", \"60333-2\", \"72674-5\", \"80549-9\", \"80974-9\")"
+"SMX"	5329	"Sulfamethoxazole"	"Trimethoprims"	"J01EC01"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"c(\"sfmx\", \"sulf\")"	"c(\"azo gantanol\", \"eusaprim\", \"gamazole\", \"gantanol\", \"gantanol ds\", \"metoxal\", \"nsulfanilamide\", \"nsulphanilamide\", \"radonil\", \"septran\", \"septrin\", \"simsinomin\", \"sinomin\", \"solfametossazolo\", \"sulfamethalazole\", \"sulfamethoxazol\", \"sulfamethoxazole\", \"sulfamethoxazolum\", \"sulfamethoxizole\", \"sulfamethylisoxazole\", \"sulfametoxazol\", \"sulfisomezole\", \"sulphamethalazole\", \"sulphamethoxazol\", \"sulphamethoxazole\", \"sulphisomezole\", \"urobak\")"	2	"g"			"c(\"10342-4\", \"25271-8\", \"39772-9\", \"59971-2\", \"59972-0\", \"60333-2\", \"72674-5\", \"80549-9\", \"80974-9\")"
-"SLF5"	"J01ED05"	5330	"Sulfamethoxypyridazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"altezol\", \"davosin\", \"depovernil\", \"kineks\", \"lederkyn\", \"lentac\", \"lisulfen\", \"longin\", \"medicel\", \"midicel\", \"midikel\", \"myasul\", \"nsulfanilamide\", \"opinsul\", \"paramid\", \"paramid supra\", \"petrisul\", \"piridolo\", \"quinoseptyl\", \"retamid\", \"retasulfin\", \"retasulphine\", \"slosul\", \"spofadazine\", \"sulfalex\", \"sulfapyridazine\", \"sulfdurazin\", \"sulfozona\", \"sultirene\", \"vinces\")"	0.5	"g"			"character(0)"
+"SLF5"	5330	"Sulfamethoxypyridazine"	"Trimethoprims"	"J01ED05"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"altezol\", \"davosin\", \"depovernil\", \"kineks\", \"lederkyn\", \"lentac\", \"lisulfen\", \"longin\", \"medicel\", \"midicel\", \"midikel\", \"myasul\", \"nsulfanilamide\", \"opinsul\", \"paramid\", \"paramid supra\", \"petrisul\", \"piridolo\", \"quinoseptyl\", \"retamid\", \"retasulfin\", \"retasulphine\", \"slosul\", \"spofadazine\", \"sulfalex\", \"sulfapyridazine\", \"sulfdurazin\", \"sulfozona\", \"sultirene\", \"vinces\")"	0.5	"g"			"character(0)"
-"SLF6"	"J01ED03"	19596	"Sulfametomidine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"duroprocin\", \"methofadin\", \"methofazine\", \"nsulfanilamide\", \"solfametomidina\", \"sulfamethomidine\", \"sulfametomidin\", \"sulfametomidina\", \"sulfametomidine\", \"sulfametomidinum\")"					"character(0)"
+"SLF6"	19596	"Sulfametomidine"	"Trimethoprims"	"J01ED03"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"duroprocin\", \"methofadin\", \"methofazine\", \"nsulfanilamide\", \"solfametomidina\", \"sulfamethomidine\", \"sulfametomidin\", \"sulfametomidina\", \"sulfametomidine\", \"sulfametomidinum\")"					"character(0)"
-"SLF7"	"J01ED04"	5326	"Sulfametoxydiazine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"bayrena\", \"berlicid\", \"dairena\", \"durenat\", \"juvoxin\", \"kinecid\", \"kirocid\", \"longasulf\", \"methoxypyrimal\", \"nsulfanilamide\", \"solfametossidiazina\", \"sulfameter\", \"sulfamethorine\", \"sulfamethoxine\", \"sulfamethoxydiazin\", \"sulfamethoxydiazine\", \"sulfamethoxydin\", \"sulfamethoxydine\", \"sulfametin\", \"sulfametinum\", \"sulfametorin\", \"sulfametorine\", \"sulfametorinum\", \"sulfametoxidiazina\", \"sulfametoxidine\", \"sulfametoxydiazine\", \"sulfametoxydiazinum\", \"sulphameter\", \"sulphamethoxydiazine\", \"supramid\", 
+"SLF7"	5326	"Sulfametoxydiazine"	"Trimethoprims"	"J01ED04"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"bayrena\", \"berlicid\", \"dairena\", \"durenat\", \"juvoxin\", \"kinecid\", \"kirocid\", \"longasulf\", \"methoxypyrimal\", \"nsulfanilamide\", \"solfametossidiazina\", \"sulfameter\", \"sulfamethorine\", \"sulfamethoxine\", \"sulfamethoxydiazin\", \"sulfamethoxydiazine\", \"sulfamethoxydin\", \"sulfamethoxydine\", \"sulfametin\", \"sulfametinum\", \"sulfametorin\", \"sulfametorine\", \"sulfametorinum\", \"sulfametoxidiazina\", \"sulfametoxidine\", \"sulfametoxydiazine\", \"sulfametoxydiazinum\", \"sulphameter\", \"sulphamethoxydiazine\", \"supramid\", 
 \"ultrax\")"	0.5	"g"			"character(0)"
-"SLT4"	"J01EE03"		"Sulfametrole/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"c(\"\", \"trsm\")"	""					""
+"SLT4"		"Sulfametrole/trimethoprim"	"Trimethoprims"	"J01EE03"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"c(\"\", \"trsm\")"	""					""
-"SLF8"	"J01EC03"	12894	"Sulfamoxole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"c(\"justamil\", \"nsulfanilamide\", \"oxasulfa\", \"solfamossolo\", \"sulfadimethyloxazole\", \"sulfamoxol\", \"sulfamoxole\", \"sulfamoxolum\", \"sulfano\", \"sulfavigor\", \"sulfmidil\", \"sulfono\", \"sulfune\", \"sulfuno\", \"sulphamoxole\", \"tardamid\", \"tardamide\")"	1	"g"	1	"g"	"character(0)"
+"SLF8"	12894	"Sulfamoxole"	"Trimethoprims"	"J01EC03"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"c(\"justamil\", \"nsulfanilamide\", \"oxasulfa\", \"solfamossolo\", \"sulfadimethyloxazole\", \"sulfamoxol\", \"sulfamoxole\", \"sulfamoxolum\", \"sulfano\", \"sulfavigor\", \"sulfmidil\", \"sulfono\", \"sulfune\", \"sulfuno\", \"sulphamoxole\", \"tardamid\", \"tardamide\")"	1	"g"	1	"g"	"character(0)"
-"SLT5"	"J01EE04"		"Sulfamoxole/trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
+"SLT5"		"Sulfamoxole/trimethoprim"	"Trimethoprims"	"J01EE04"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
-"SLF9"	"J01EB06"	5333	"Sulfanilamide"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"albexan\", \"albosal\", \"ambeside\", \"antistrept\", \"astreptine\", \"astrocid\", \"bacteramid\", \"bactesid\", \"collomide\", \"colsulanyde\", \"copticide\", \"deseptyl\", \"desseptyl\", \"dipron\", \"ergaseptine\", \"erysipan\", \"estreptocida\", \"exoseptoplix\", \"gerison\", \"gombardol\", \"infepan\", \"lysococcine\", \"neococcyl\", \"orgaseptine\", \"prontalbin\", \"prontosil album\", \"prontosil i\", \"prontosil white\", \"prontylin\", \"pronzin album\", \"proseptal\", \"proseptine\", \"proseptol\", \"pysococcine\", \"rubiazol a\", \"sanamid\", \"septamide album\", 
+"SLF9"	5333	"Sulfanilamide"	"Trimethoprims"	"c(\"D06BA05\", \"J01EB06\")"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"albexan\", \"albosal\", \"ambeside\", \"antistrept\", \"astreptine\", \"astrocid\", \"bacteramid\", \"bactesid\", \"collomide\", \"colsulanyde\", \"copticide\", \"deseptyl\", \"desseptyl\", \"dipron\", \"ergaseptine\", \"erysipan\", \"estreptocida\", \"exoseptoplix\", \"gerison\", \"gombardol\", \"infepan\", \"lysococcine\", \"neococcyl\", \"orgaseptine\", \"prontalbin\", \"prontosil album\", \"prontosil i\", \"prontosil white\", \"prontylin\", \"pronzin album\", \"proseptal\", \"proseptine\", \"proseptol\", \"pysococcine\", \"rubiazol a\", \"sanamid\", \"septamide album\", 
 \"septanilam\", \"septinal\", \"septolix\", \"septoplex\", \"septoplix\", \"solfanilamide\", \"stopton album\", \"stramid\", \"strepamide\", \"strepsan\", \"streptagol\", \"streptamid\", \"streptamin\", \"streptasol\", \"streptocid\", \"streptocid album\", \"streptocide\", \"streptocide white\", \"streptocidum\", \"streptoclase\", \"streptocom\", \"streptol\", \"strepton\", \"streptopan\", \"streptosil\", \"streptozol\", \"streptozone\", \"streptrocide\", \"sulfamidyl\", \"sulfamine\", \"sulfana\", \"sulfanalone\", \"sulfanidyl\", \"sulfanil\", \"sulfanilamida\", \"sulfanilamide\", 
 \"sulfanilamidum\", \"sulfanilimidic acid\", \"sulfanimide\", \"sulfocidin\", \"sulfocidine\", \"sulfonamide\", \"sulfonamide p\", \"sulfonylamide\", \"sulphanilamide\", \"sulphanilamide gr\", \"sulphonamide\", \"therapol\", \"tolder\", \"white streptocide\", \"wln: zswr dz\")"					"character(0)"
-"SLF10"	"J01ED06"	68933	"Sulfaperin"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"anastaf\", \"archisulfa\", \"avissul\", \"chemiopen\", \"demosulfan\", \"durisan saft\", \"ipersulfidin sirup\", \"isosulfamerazine\", \"methylsulfadiazin\", \"novosul\", \"nsulfanilamide\", \"orosulfan\", \"pallidin\", \"retardon\", \"risulfasens\", \"sulfaperin\", \"sulfaperina\", \"sulfaperine\", \"sulfaperinum\", \"sulfatreis\", \"sulfopirimidine\", \"sulpenta\", \"ultrasulfon sirup\")"	0.5	"g"			"character(0)"
+"SLF10"	68933	"Sulfaperin"	"Trimethoprims"	"J01ED06"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"anastaf\", \"archisulfa\", \"avissul\", \"chemiopen\", \"demosulfan\", \"durisan saft\", \"ipersulfidin sirup\", \"isosulfamerazine\", \"methylsulfadiazin\", \"novosul\", \"nsulfanilamide\", \"orosulfan\", \"pallidin\", \"retardon\", \"risulfasens\", \"sulfaperin\", \"sulfaperina\", \"sulfaperine\", \"sulfaperinum\", \"sulfatreis\", \"sulfopirimidine\", \"sulpenta\", \"ultrasulfon sirup\")"	0.5	"g"			"character(0)"
-"SLF11"	"J01ED08"	5335	"Sulfaphenazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"depocid\", \"depotsulfonamide\", \"eftolon\", \"firmazolo\", \"inamil\", \"isarol\", \"isarol v\", \"merian\", \"microtan pirazolo\", \"nsulfanilamide\", \"orisul\", \"orisulf\", \"paidazolo\", \"phenylsulfapyrazole\", \"plisulfan\", \"raziosulfa\", \"solfafenazolo\", \"sulfabid\", \"sulfafenazol\", \"sulfafenazolo\", \"sulfaphenazol\", \"sulfaphenazole\", \"sulfaphenazolum\", \"sulfaphenazon\", \"sulfaphenylpipazol\", \"sulfaphenylpyrazol\", \"sulfaphenylpyrazole\", \"sulfonylpyrazol\", \"sulphaphenazole\", \"sulphenazole\")"	1	"g"			"character(0)"
+"SLF11"	5335	"Sulfaphenazole"	"Trimethoprims"	"J01ED08"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"c(\"depocid\", \"depotsulfonamide\", \"eftolon\", \"firmazolo\", \"inamil\", \"isarol\", \"isarol v\", \"merian\", \"microtan pirazolo\", \"nsulfanilamide\", \"orisul\", \"orisulf\", \"paidazolo\", \"phenylsulfapyrazole\", \"plisulfan\", \"raziosulfa\", \"solfafenazolo\", \"sulfabid\", \"sulfafenazol\", \"sulfafenazolo\", \"sulfaphenazol\", \"sulfaphenazole\", \"sulfaphenazolum\", \"sulfaphenazon\", \"sulfaphenylpipazol\", \"sulfaphenylpyrazol\", \"sulfaphenylpyrazole\", \"sulfonylpyrazol\", \"sulphaphenazole\", \"sulphenazole\")"	1	"g"			"character(0)"
-"SLF12"	"J01EB04"	5336	"Sulfapyridine"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"adiplon\", \"coccoclase\", \"dagenan\", \"eubasin\", \"eubasinum\", \"haptocil\", \"piridazol\", \"plurazol\", \"pyriamid\", \"pyridazol\", \"relbapiridina\", \"septipulmon\", \"solfapiridina\", \"streptosilpyridine\", \"sulfapiridina\", \"sulfapyridin\", \"sulfapyridine\", \"sulfapyridinum\", \"sulfidin\", \"sulfidine\", \"sulphapyridin\", \"sulphapyridine\", \"thioseptal\", \"trianon\")"	1	"g"			"c(\"14075-6\", \"55580-5\")"
+"SLF12"	5336	"Sulfapyridine"	"Trimethoprims"	"J01EB04"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"adiplon\", \"coccoclase\", \"dagenan\", \"eubasin\", \"eubasinum\", \"haptocil\", \"piridazol\", \"plurazol\", \"pyriamid\", \"pyridazol\", \"relbapiridina\", \"septipulmon\", \"solfapiridina\", \"streptosilpyridine\", \"sulfapiridina\", \"sulfapyridin\", \"sulfapyridine\", \"sulfapyridinum\", \"sulfidin\", \"sulfidine\", \"sulphapyridin\", \"sulphapyridine\", \"thioseptal\", \"trianon\")"	1	"g"			"c(\"14075-6\", \"55580-5\")"
-"SNA"		60582	"Sulfasuccinamide"	"Other antibacterials"			""	"c(\"ambesid\", \"derganil\", \"sulfasuccinamid\", \"sulfasuccinamida\", \"sulfasuccinamide\", \"sulfasuccinamidum\")"					"character(0)"
+"SNA"	60582	"Sulfasuccinamide"	"Other antibacterials"				""	"c(\"ambesid\", \"derganil\", \"sulfasuccinamid\", \"sulfasuccinamida\", \"sulfasuccinamide\", \"sulfasuccinamidum\")"					"character(0)"
-"SUT"	"J01EB07"	5340	"Sulfathiazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"azoquimiol\", \"azoseptale\", \"cerazol\", \"cerazole\", \"chemosept\", \"cibazol\", \"duatok\", \"dulana\", \"eleudron\", \"enterobiocine\", \"estafilol\", \"formosulfathiazole\", \"neostrepsan\", \"norsulfasol\", \"norsulfazol\", \"norsulfazole\", \"norsulfazolum\", \"nsulfanilamide\", \"planomide\", \"poliseptil\", \"sanotiazol\", \"septozol\", \"solfatiazolo\", \"streptosilthiazole\", \"sulfamul\", \"sulfathiazol\", \"sulfathiazole\", \"sulfathiazolum\", \"sulfatiazol\", \"sulfavitina\", \"sulfocerol\", \"sulphathiazole\", \"sulzol\", \"thiacoccine\", \"thiasulfol\", 
+"SUT"	5340	"Sulfathiazole"	"Trimethoprims"	"c(\"D06BA02\", \"J01EB07\")"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"azoquimiol\", \"azoseptale\", \"cerazol\", \"cerazole\", \"chemosept\", \"cibazol\", \"duatok\", \"dulana\", \"eleudron\", \"enterobiocine\", \"estafilol\", \"formosulfathiazole\", \"neostrepsan\", \"norsulfasol\", \"norsulfazol\", \"norsulfazole\", \"norsulfazolum\", \"nsulfanilamide\", \"planomide\", \"poliseptil\", \"sanotiazol\", \"septozol\", \"solfatiazolo\", \"streptosilthiazole\", \"sulfamul\", \"sulfathiazol\", \"sulfathiazole\", \"sulfathiazolum\", \"sulfatiazol\", \"sulfavitina\", \"sulfocerol\", \"sulphathiazole\", \"sulzol\", \"thiacoccine\", \"thiasulfol\", 
 \"thiazamide\", \"thiozamide\", \"wintrazole\")"					"87591-4"
-"SLF13"	"J01EB08"	3000579	"Sulfathiourea"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"badional\", \"baldinol\", \"fontamide\", \"salvoseptyl\", \"solfatiourea\", \"solufontamide\", \"sulfanilthiourea\", \"sulfathiocarbamid\", \"sulfathiocarbamide\", \"sulfathiocarbamidum\", \"sulfathiourea\", \"sulfathiouree\", \"sulfatiourea\", \"sulphathiourea\")"	6	"g"			"character(0)"
+"SLF13"	3000579	"Sulfathiourea"	"Trimethoprims"	"J01EB08"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"c(\"badional\", \"baldinol\", \"fontamide\", \"salvoseptyl\", \"solfatiourea\", \"solufontamide\", \"sulfanilthiourea\", \"sulfathiocarbamid\", \"sulfathiocarbamide\", \"sulfathiocarbamidum\", \"sulfathiourea\", \"sulfathiouree\", \"sulfatiourea\", \"sulphathiourea\")"	6	"g"			"character(0)"
-"SOX"		5344	"Sulfisoxazole"	"Other antibacterials"			""	"c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\", 
+"SOX"	5344	"Sulfisoxazole"	"Other antibacterials"				""	"c(\"accuzole\", \"alphazole\", \"amidoxal\", \"astrazolo\", \"azo gantrisin\", \"azosulfizin\", \"bactesulf\", \"barazae\", \"chemouag\", \"cosoxazole\", \"dorsulfan\", \"dorsulfan warthausen\", \"entusil\", \"entusul\", \"eryzole\", \"gantrisin\", \"gantrisine\", \"gantrisona\", \"gantrizin\", \"gantrosan\", \"isoxamin\", \"neazolin\", \"neoxazoi\", \"neoxazol\", \"novazolo\", \"novosaxazole\", \"nsulfanilamide\", \"nsulphanilamide\", \"pancid\", \"pediazole\", \"renosulfan\", \"resoxol\", \"roxosul\", \"roxosul tablets\", \"roxoxol\", \"saxosozine\", \"sodizole\", \"solfafurazolo\", 
 \"soxamide\", \"soxazole\", \"soxisol\", \"soxitabs\", \"soxomide\", \"stansin\", \"sulbio\", \"sulfafuraz ole\", \"sulfafurazol\", \"sulfafurazole\", \"sulfafurazolum\", \"sulfagan\", \"sulfagen\", \"sulfaisoxazole\", \"sulfalar\", \"sulfapolar\", \"sulfasol\", \"sulfasoxazole\", \"sulfasoxizole\", \"sulfazin\", \"sulfisin\", \"sulfisonazole\", \"sulfisoxasole\", \"sulfisoxazol\", \"sulfisoxazole\", \"sulfisoxazolum\", \"sulfizin\", \"sulfizol\", \"sulfizole\", \"sulfofurazole\", \"sulfoxol\", \"suloxsol\", \"sulphafuraz\", \"sulphafurazol\", \"sulphafurazole\", \"sulphafurazolum\", 
 \"sulphaisoxazole\", \"sulphisoxazol\", \"sulphisoxazole\", \"sulphofurazole\", \"sulsoxin\", \"thiasin\", \"unisulf\", \"urisoxin\", \"uritrisin\", \"urogan\", \"vagilia\")"					"9701-4"
-"SSS"		86225	"Sulfonamide"	"Other antibacterials"			"c(\"\", \"sfna\")"	""					""
+"SSS"	86225	"Sulfonamide"	"Other antibacterials"				"c(\"\", \"sfna\")"	""					""
-"SLP"		9950244	"Sulopenem"	"Other antibacterials"			""	"sulopenem"					"character(0)"
+"SLP"	9950244	"Sulopenem"	"Other antibacterials"				""	"sulopenem"					"character(0)"
-"SLT6"	"J01CR04"	444022	"Sultamicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	""	"c(\"sultamicilina\", \"sultamicillin\", \"sultamicillinum\")"	1.5	"g"			"character(0)"
+"SLT6"	444022	"Sultamicillin"	"Beta-lactams/penicillins"	"J01CR04"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	""	"c(\"sultamicilina\", \"sultamicillin\", \"sultamicillinum\")"	1.5	"g"			"character(0)"
-"SUR"		46700778	"Surotomycin"	"Other antibacterials"			""	"surotomycin"					"character(0)"
+"SUR"	46700778	"Surotomycin"	"Other antibacterials"				""	"surotomycin"					"character(0)"
-"TAL"	"J01CA15"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"talampicilina\", \"talampicillin\", \"talampicilline\", \"talampicillinum\")"	2	"g"			"character(0)"
+"TAL"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"J01CA15"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"talampicilina\", \"talampicillin\", \"talampicilline\", \"talampicillinum\")"	2	"g"			"character(0)"
-"TLP"		163307	"Talmetoprim"	"Other antibacterials"			""	"talmetoprim"					"character(0)"
+"TLP"	163307	"Talmetoprim"	"Other antibacterials"				""	"talmetoprim"					"character(0)"
-"TAZ"	"J01CG02"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo"	"c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")"					"character(0)"
+"TAZ"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"J01CG02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo"	"c(\"tazobactam\", \"tazobactam acid\", \"tazobactamum\", \"tazobactum\")"					"character(0)"
-"TBP"		9800194	"Tebipenem"	"Carbapenems"			""	""					""
+"TBP"	9800194	"Tebipenem"	"Carbapenems"				""	""					""
-"TZD"	"J01XX11"	11234049	"Tedizolid"	"Oxazolidinones"	"Other antibacterials"	"Other antibacterials"	"tedi"	"c(\"tedizolid\", \"torezolid\")"	0.2		0.2		"character(0)"
+"TZD"	11234049	"Tedizolid"	"Oxazolidinones"	"J01XX11"	"Other antibacterials"	"Other antibacterials"	"tedi"	"c(\"tedizolid\", \"torezolid\")"	0.2	"g"	0.2	"g"	"character(0)"
-"TEC"	"J01XA02"	16131923	"Teicoplanin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")"	"c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")"			0.4	"g"	"c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
+"TEC"	16131923	"Teicoplanin"	"Glycopeptides"	"J01XA02"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"tec\", \"tei\", \"teic\", \"tp\", \"tpl\", \"tpn\")"	"c(\"targocid\", \"tecoplanina\", \"tecoplanine\", \"tecoplaninum\", \"teichomycin\", \"teicoplanina\", \"teicoplanine\", \"teicoplaninum\")"			0.4	"g"	"c(\"25534-9\", \"25535-6\", \"34378-0\", \"34379-8\", \"4043-6\", \"80968-1\")"
-"TCM"			"Teicoplanin-macromethod"	"Glycopeptides"			""	""					""
+"TCM"		"Teicoplanin-macromethod"	"Glycopeptides"				""	""					""
-"TLV"	"J01XA03"	3081362	"Telavancin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela"	"c(\"telavancin\", \"vibativ\")"					"character(0)"
+"TLV"	3081362	"Telavancin"	"Glycopeptides"	"J01XA03"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela"	"c(\"telavancin\", \"vibativ\")"					"character(0)"
-"TLT"	"J01FA15"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"\", \"teli\")"	"levviax"	0.8	"g"			"character(0)"
+"TLT"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"J01FA15"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"c(\"\", \"teli\")"	"levviax"	0.8	"g"			"character(0)"
-"TMX"	"J01MA05"	60021	"Temafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"tema\")"	"c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")"	0.8	"g"			"character(0)"
+"TMX"	60021	"Temafloxacin"	"Quinolones"	"J01MA05"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"tema\")"	"c(\"omniflox\", \"temafloxacin\", \"temafloxacina\", \"temafloxacine\", \"temafloxacinum\")"	0.8	"g"			"character(0)"
-"TEM"	"J01CA17"	171758	"Temocillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"\", \"temo\")"	"c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")"			4	"g"	"character(0)"
+"TEM"	171758	"Temocillin"	"Beta-lactams/penicillins"	"J01CA17"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"\", \"temo\")"	"c(\"temocilina\", \"temocillin\", \"temocillina\", \"temocilline\", \"temocillinum\")"			4	"g"	"character(0)"
-"TRB"	"D01BA02"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"Antifungals for systemic use"	"Antifungals for systemic use"	"c(\"\", \"terb\")"	"c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")"	0.25	"g"			"character(0)"
+"TRB"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"c(\"D01AE15\", \"D01BA02\")"	"Antifungals for systemic use"	"Antifungals for systemic use"	"c(\"\", \"terb\")"	"c(\"corbinal\", \"lamasil\", \"lamisil\", \"lamisil at\", \"lamisil tablet\", \"terbinafina\", \"terbinafine\", \"terbinafinum\", \"terbinex\")"	0.25	"g"			"character(0)"
-"TRC"		441383	"Terconazole"	"Antifungals/antimycotics"			""	"c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")"					"character(0)"
+"TRC"	441383	"Terconazole"	"Antifungals/antimycotics"	"G01AG02"			""	"c(\"fungistat\", \"panlomyc\", \"terazol\", \"terconazol\", \"terconazole\", \"terconazolum\", \"tercospor\", \"triaconazole\", \"zazole\")"					"character(0)"
-"TRZ"	"J04AK03"	65720	"Terizidone"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")"					"character(0)"
+"TRZ"	65720	"Terizidone"	"Antimycobacterials"	"J04AK03"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"c(\"terivalidin\", \"terizidon\", \"terizidona\", \"terizidone\", \"terizidonum\")"					"character(0)"
-"TCY"	"J01AA07"	54675776	"Tetracycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"tc\", \"te\", \"tet\", \"tetr\")"	"c(\"abramycin\", \"abricycline\", \"achromycin\", \"achromycin v\", \"actisite\", \"agromicina\", \"ambramicina\", \"ambramycin\", \"amycin\", \"biocycline\", \"bristaciclin\", \"bristaciclina\", \"bristacycline\", \"cefracycline\", \"centet\", \"ciclibion\", \"copharlan\", \"criseociclina\", \"cyclomycin\", \"cyclopar\", \"cytome\", \"democracin\", \"deschlorobiomycin\", \"dumocyclin\", \"enterocycline\", \"hostacyclin\", \"lexacycline\", \"limecycline\", \"liquamycin\", \"medocycline\", \"mericycline\", \"micycline\", \"neocycline\", \"oletetrin\", \"omegamycin\", 
+"TCY"	54675776	"Tetracycline"	"Tetracyclines"	"c(\"A01AB13\", \"D06AA04\", \"J01AA07\", \"S01AA09\", \"S02AA08\", \"S03AA02\")"	"Tetracyclines"	"Tetracyclines"	"c(\"tc\", \"te\", \"tet\", \"tetr\")"	"c(\"abramycin\", \"abricycline\", \"achromycin\", \"achromycin v\", \"actisite\", \"agromicina\", \"ambramicina\", \"ambramycin\", \"amycin\", \"biocycline\", \"bristaciclin\", \"bristaciclina\", \"bristacycline\", \"cefracycline\", \"centet\", \"ciclibion\", \"copharlan\", \"criseociclina\", \"cyclomycin\", \"cyclopar\", \"cytome\", \"democracin\", \"deschlorobiomycin\", \"dumocyclin\", \"enterocycline\", \"hostacyclin\", \"lexacycline\", \"limecycline\", \"liquamycin\", \"medocycline\", \"mericycline\", \"micycline\", \"neocycline\", \"oletetrin\", \"omegamycin\", 
 \"orlycycline\", \"panmycin\", \"piracaps\", \"polycycline\", \"polyotic\", \"purocyclina\", \"resteclin\", \"robitet\", \"roviciclina\", \"sigmamycin\", \"solvocin\", \"sumycin\", \"sumycin syrup\", \"tetrabon\", \"tetrachel\", \"tetraciclina\", \"tetracycl\", \"tetracyclin\", \"tetracycline\", \"tetracycline base\", \"tetracycline i\", \"tetracycline ii\", \"tetracyclinum\", \"tetracyn\", \"tetradecin\", \"tetrafil\", \"tetramed\", \"tetrasure\", \"tetraverine\", \"tetrazyklin\", \"tetrex\", \"topicycline\", \"tsiklomistsin\", \"tsiklomitsin\", \"veracin\", \"vetacyclinum\"
 )"	1	"g"	1	"g"	"c(\"25272-6\", \"4045-1\", \"87590-6\")"
-"TET"		65450	"Tetroxoprim"	"Other antibacterials"			""	"c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")"					"character(0)"
+"TET"	65450	"Tetroxoprim"	"Other antibacterials"				""	"c(\"tetroxoprim\", \"tetroxoprima\", \"tetroxoprime\", \"tetroxoprimum\")"					"character(0)"
-"THA"		9568512	"Thiacetazone"	"Oxazolidinones"			""	"c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\", 
+"THA"	9568512	"Thiacetazone"	"Oxazolidinones"				""	"c(\"aktivan\", \"ambathizon\", \"amithiozone\", \"amithizone\", \"amitiozon\", \"benthiozone\", \"benzothiozane\", \"benzothiozon\", \"berculon a\", \"berkazon\", \"citazone\", \"conteben\", \"diasan\", \"diazan\", \"domakol\", \"ilbion\", \"livazone\", \"mirizone neustab\", \"mivizon\", \"myvizone\", \"neotibil\", \"neustab\", \"novakol\", \"nuclon argentinian\", \"panrone\", \"parazone\", \"seroden\", \"siocarbazone\", \"tebalon\", \"tebecure\", \"tebemar\", \"tebesone i\", \"tebethion\", \"tebethione\", \"tebezon\", \"thiacetazone\", \"thiacetone\", \"thiacetozone\", 
 \"thibon\", \"thibone\", \"thioacetazon\", \"thioacetazone\", \"thioacetazonum\", \"thioazetazone\", \"thiocarbazil\", \"thiomicid\", \"thionicid\", \"thioparamizon\", \"thioparamizone\", \"thiosemicarbarzone\", \"thiosemicarbazone\", \"thiotebesin\", \"thiotebezin\", \"thiotebicina\", \"thizone\", \"tiacetazon\", \"tibicur\", \"tibion\", \"tibione\", \"tibizan\", \"tibone\", \"tioacetazon\", \"tioacetazona\", \"tioatsetazon\", \"tiobicina\", \"tiocarone\", \"tiosecolo\", \"tubercazon\", \"tubigal\")"					"character(0)"
-"THI"	"J01BA02"	27200	"Thiamphenicol"	"Amphenicols"	"Amphenicols"	"Amphenicols"	""	"c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")"	1.5	"g"	1.5	"g"	"character(0)"
+"THI"	27200	"Thiamphenicol"	"Amphenicols"	"J01BA02"	"Amphenicols"	"Amphenicols"	""	"c(\"descocin\", \"dexawin\", \"dextrosulfenidol\", \"dextrosulphenidol\", \"efnicol\", \"hyrazin\", \"igralin\", \"macphenicol\", \"masatirin\", \"neomyson\", \"racefenicol\", \"racefenicolo\", \"racefenicolum\", \"raceophenidol\", \"racephenicol\", \"rincrol\", \"thiamcol\", \"thiamphenicol\", \"thiamphenicolum\", \"thiocymetin\", \"thiomycetin\", \"thiophenicol\", \"tiamfenicol\", \"tiamfenicolo\", \"urfamicina\", \"urfamycine\", \"vicemycetin\")"	1.5	"g"	1.5	"g"	"character(0)"
-"THI1"	"J04AM04"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
+"THI1"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"J04AM04"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"TIA"		656958	"Tiamulin"	"Other antibacterials"			""	"c(\"denagard\", \"tiamulin\", \"tiamulin pamoate\", \"tiamulina\", \"tiamuline\", \"tiamulinum\")"					"87589-8"
+"TIA"	656958	"Tiamulin"	"Other antibacterials"				""	"c(\"denagard\", \"tiamulin\", \"tiamulin pamoate\", \"tiamulina\", \"tiamuline\", \"tiamulinum\")"					"87589-8"
-"TIC"	"J01CA13"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"tc\", \"ti\", \"tic\", \"tica\")"	"c(\"ticarcilina\", \"ticarcillin\", \"ticarcilline\", \"ticarcillinum\", \"ticillin\")"			15	"g"	"c(\"25254-4\", \"4054-3\", \"4055-0\")"
+"TIC"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"J01CA13"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"tc\", \"ti\", \"tic\", \"tica\")"	"c(\"ticarcilina\", \"ticarcillin\", \"ticarcilline\", \"ticarcillinum\", \"ticillin\")"			15	"g"	"c(\"25254-4\", \"4054-3\", \"4055-0\")"
-"TCC"	"J01CR03"	6437075	"Ticarcillin/clavulanic acid"	"Beta-lactams/penicillins"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"t/c\", \"tcc\", \"ticl\", \"tim\", \"tlc\")"	"timentin"			15	"g"	"character(0)"
+"TCC"	6437075	"Ticarcillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR03"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"c(\"t/c\", \"tcc\", \"ticl\", \"tim\", \"tlc\")"	"timentin"			15	"g"	"character(0)"
-"TGC"	"J01AA12"	54686904	"Tigecycline"	"Tetracyclines"	"Tetracyclines"	"Tetracyclines"	"c(\"tgc\", \"tig\", \"tige\")"	"c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")"			0.1	"g"	"character(0)"
+"TGC"	54686904	"Tigecycline"	"Tetracyclines"	"J01AA12"	"Tetracyclines"	"Tetracyclines"	"c(\"tgc\", \"tig\", \"tige\")"	"c(\"haizheng li xing\", \"tigeciclina\", \"tigecyclin\", \"tigecycline\", \"tigecycline hydrate\", \"tigecyclinum\", \"tigilcycline\", \"tygacil\")"			0.1	"g"	"character(0)"
-"TBQ"		65592	"Tilbroquinol"	"Quinolones"			""	"c(\"tilbroquinol\", \"tilbroquinolum\")"					"character(0)"
+"TBQ"	65592	"Tilbroquinol"	"Quinolones"	"P01AA05"			""	"c(\"tilbroquinol\", \"tilbroquinolum\")"					"character(0)"
-"TIP"		24860548	"Tildipirosin"	"Macrolides/lincosamides"			""	"c(\"tildipirosin\", \"zuprevo\")"					"character(0)"
+"TIP"	24860548	"Tildipirosin"	"Macrolides/lincosamides"				""	"c(\"tildipirosin\", \"zuprevo\")"					"character(0)"
-"TIL"		5282521	"Tilmicosin"	"Macrolides/lincosamides"			""	"c(\"micotil\", \"pulmotil\", \"tilmicosin\", \"tilmicosina\", \"tilmicosine\", \"tilmicosinum\")"					"87588-0"
+"TIL"	5282521	"Tilmicosin"	"Macrolides/lincosamides"				""	"c(\"micotil\", \"pulmotil\", \"tilmicosin\", \"tilmicosina\", \"tilmicosine\", \"tilmicosinum\")"					"87588-0"
-"TIN"	"J01XD02"	5479	"Tinidazole"	"Other antibacterials"	"Other antibacterials"	"Imidazole derivatives"	"c(\"\", \"tini\")"	"c(\"amtiba\", \"bioshik\", \"ethyl sulfone\", \"fasigin\", \"fasigyn\", \"fasigyntrade mark\", \"fasygin\", \"glongyn\", \"haisigyn\", \"pletil\", \"simplotan\", \"simplotantrade mark\", \"sorquetan\", \"tindamax\", \"tindamaxtrade mark\", \"tinidazol\", \"tinidazole\", \"tinidazolum\", \"tricolam\", \"trimonase\")"			1.5	"g"	"character(0)"
+"TIN"	5479	"Tinidazole"	"Other antibacterials"	"c(\"J01XD02\", \"P01AB02\")"	"Other antibacterials"	"Imidazole derivatives"	"c(\"\", \"tini\")"	"c(\"amtiba\", \"bioshik\", \"ethyl sulfone\", \"fasigin\", \"fasigyn\", \"fasigyntrade mark\", \"fasygin\", \"glongyn\", \"haisigyn\", \"pletil\", \"simplotan\", \"simplotantrade mark\", \"sorquetan\", \"tindamax\", \"tindamaxtrade mark\", \"tinidazol\", \"tinidazole\", \"tinidazolum\", \"tricolam\", \"trimonase\")"	2	"g"	1.5	"g"	"character(0)"
-"TCR"	"J04AD02"	3001386	"Tiocarlide"	"Antimycobacterials"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	""	"c(\"amixyl\", \"datanil\", \"disocarban\", \"disoxyl\", \"thiocarlide\", \"tiocarlid\", \"tiocarlida\", \"tiocarlide\", \"tiocarlidum\")"	7	"g"			"character(0)"
+"TCR"	3001386	"Tiocarlide"	"Antimycobacterials"	"J04AD02"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	""	"c(\"amixyl\", \"datanil\", \"disocarban\", \"disoxyl\", \"thiocarlide\", \"tiocarlid\", \"tiocarlida\", \"tiocarlide\", \"tiocarlidum\")"	7	"g"			"character(0)"
-"TDC"		10247721	"Tiodonium chloride"	"Other antibacterials"			""	"c(\"cloruro de tiodonio\", \"tiodonii chloridum\", \"tiodonium chloride\")"					"character(0)"
+"TDC"	10247721	"Tiodonium chloride"	"Other antibacterials"				""	"c(\"cloruro de tiodonio\", \"tiodonii chloridum\", \"tiodonium chloride\")"					"character(0)"
-"TXC"		65788	"Tioxacin"	"Quinolones"			""	"c(\"tioxacin\", \"tioxacine\", \"tioxacino\", \"tioxacinum\", \"tioxic acid\")"					"character(0)"
+"TXC"	65788	"Tioxacin"	"Quinolones"				""	"c(\"tioxacin\", \"tioxacine\", \"tioxacino\", \"tioxacinum\", \"tioxic acid\")"					"character(0)"
-"TIZ"		394397	"Tizoxanide"	"Other antibacterials"			""	"ntzdes"					"character(0)"
+"TIZ"	394397	"Tizoxanide"	"Other antibacterials"				""	"ntzdes"					"character(0)"
-"TOB"	"J01GB01"	36294	"Tobramycin"	"Aminoglycosides"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"nn\", \"tm\", \"to\", \"tob\", \"tobr\")"	"c(\"bethkis\", \"brulamycin\", \"deoxykanamycin b\", \"distobram\", \"gernebcin\", \"gotabiotic\", \"kitabis pak\", \"nebcin\", \"nebicin\", \"nebramycin\", \"nebramycin vi\", \"obramycin\", \"sybryx\", \"tenebrimycin\", \"tenemycin\", \"tobacin\", \"tobi podhaler\", \"tobracin\", \"tobradex\", \"tobradistin\", \"tobralex\", \"tobramaxin\", \"tobramicin\", \"tobramicina\", \"tobramitsetin\", \"tobramycetin\", \"tobramycin\", \"tobramycin base\", \"tobramycin sulfate\", \"tobramycine\", \"tobramycinum\", \"tobrased\", \"tobrasone\", \"tobrex\")"			0.24	"g"	"c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")"
+"TOB"	36294	"Tobramycin"	"Aminoglycosides"	"c(\"J01GB01\", \"S01AA12\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"nn\", \"tm\", \"to\", \"tob\", \"tobr\")"	"c(\"bethkis\", \"brulamycin\", \"deoxykanamycin b\", \"distobram\", \"gernebcin\", \"gotabiotic\", \"kitabis pak\", \"nebcin\", \"nebicin\", \"nebramycin\", \"nebramycin vi\", \"obramycin\", \"sybryx\", \"tenebrimycin\", \"tenemycin\", \"tobacin\", \"tobi podhaler\", \"tobracin\", \"tobradex\", \"tobradistin\", \"tobralex\", \"tobramaxin\", \"tobramicin\", \"tobramicina\", \"tobramitsetin\", \"tobramycetin\", \"tobramycin\", \"tobramycin base\", \"tobramycin sulfate\", \"tobramycine\", \"tobramycinum\", \"tobrased\", \"tobrasone\", \"tobrex\")"			0.24	"g"	"c(\"13584-8\", \"17808-7\", \"22750-4\", \"22751-2\", \"22752-0\", \"31094-6\", \"31095-3\", \"31096-1\", \"35239-3\", \"35670-9\", \"4057-6\", \"4058-4\", \"4059-2\", \"50927-3\", \"52962-8\", \"59380-6\", \"80966-5\")"
-"TOH"			"Tobramycin-high"	"Aminoglycosides"			"c(\"tobra high\", \"tobramycin high\", \"tohl\")"	""					""
+"TOH"		"Tobramycin-high"	"Aminoglycosides"				"c(\"tobra high\", \"tobramycin high\", \"tohl\")"	""					""
-"TFX"		5517	"Tosufloxacin"	"Quinolones"			""	"tosufloxacin"					"character(0)"
+"TFX"	5517	"Tosufloxacin"	"Quinolones"	"J01MA22"			""	"tosufloxacin"	0.45	"g"			"character(0)"
-"TMP"	"J01EA01"	5578	"Trimethoprim"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"c(\"t\", \"tmp\", \"tr\", \"tri\", \"trim\", \"w\")"	"c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\", 
+"TMP"	5578	"Trimethoprim"	"Trimethoprims"	"J01EA01"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"c(\"t\", \"tmp\", \"tr\", \"tri\", \"trim\", \"w\")"	"c(\"abaprim\", \"alprim\", \"anitrim\", \"antrima\", \"antrimox\", \"bacdan\", \"bacidal\", \"bacide\", \"bacterial\", \"bacticel\", \"bactifor\", \"bactin\", \"bactoprim\", \"bactramin\", \"bactrim\", \"bencole\", \"bethaprim\", \"biosulten\", \"briscotrim\", \"chemotrin\", \"colizole\", \"colizole ds\", \"conprim\", \"cotrimel\", \"cotrimoxizole\", \"deprim\", \"dosulfin\", \"duocide\", \"esbesul\", \"espectrin\", \"euctrim\", \"exbesul\", \"fermagex\", \"fortrim\", \"idotrim\", \"ikaprim\", \"instalac\", \"kombinax\", \"lagatrim\", \"lagatrim forte\", \"lastrim\", \"lescot\", 
 \"methoprim\", \"metoprim\", \"monoprim\", \"monotrim\", \"monotrimin\", \"novotrimel\", \"omstat\", \"oraprim\", \"pancidim\", \"polytrim\", \"priloprim\", \"primosept\", \"primsol\", \"proloprim\", \"protrin\", \"purbal\", \"resprim\", \"resprim forte\", \"roubac\", \"roubal\", \"salvatrim\", \"septrin ds\", \"septrin forte\", \"septrin s\", \"setprin\", \"sinotrim\", \"stopan\", \"streptoplus\", \"sugaprim\", \"sulfamar\", \"sulfamethoprim\", \"sulfoxaprim\", \"sulthrim\", \"sultrex\", \"syraprim\", \"tiempe\", \"tmp smx\", \"toprim\", \"trimanyl\", \"trimethioprim\", \"trimethopim\", 
 \"trimethoprim\", \"trimethoprime\", \"trimethoprimum\", \"trimethopriom\", \"trimetoprim\", \"trimetoprima\", \"trimexazole\", \"trimexol\", \"trimezol\", \"trimogal\", \"trimono\", \"trimopan\", \"trimpex\", \"triprim\", \"trisul\", \"trisulcom\", \"trisulfam\", \"trisural\", \"uretrim\", \"urobactrim\", \"utetrin\", \"velaten\", \"wellcoprim\", \"wellcoprin\", \"xeroprim\", \"zamboprim\")"	0.4	"g"	0.4	"g"	"c(\"11005-6\", \"17747-7\", \"25273-4\", \"32342-8\", \"4079-0\", \"4080-8\", \"4081-6\", \"55584-7\", \"80552-3\", \"80973-1\")"
-"SXT"	"J01EE01"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"c(\"cot\", \"cotrim\", \"sxt\", \"t/s\", \"trsu\", \"trsx\", \"ts\")"	"c(\"bactrim\", \"bactrimel\", \"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"cotrimazole\", \"cotrimoxazole\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"septra\", \"totazina\")"					"character(0)"
+"SXT"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"J01EE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"c(\"cot\", \"cotrim\", \"sxt\", \"t/s\", \"trsu\", \"trsx\", \"ts\")"	"c(\"bactrim\", \"bactrimel\", \"belcomycine\", \"colimycin\", \"colimycin sulphate\", \"colisticin\", \"colistimethate\", \"colistimethate sodium\", \"colistin sulfate\", \"colistin sulphate\", \"colomycin\", \"coly-mycin\", \"cotrimazole\", \"cotrimoxazole\", \"polymyxin e\", \"polymyxin e. sulfate\", \"promixin\", \"septra\", \"totazina\")"					"character(0)"
-"TRL"	"J01FA08"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"acetyloleandomycin\", \"aovine\", \"cyclamycin\", \"evramicina\", \"matromicina\", \"matromycin t\", \"oleandocetine\", \"t.a.o.\", \"treolmicina\", \"tribiocillina\", \"triocetin\", \"triolan\", \"troleandomicina\", \"troleandomycin\", \"troleandomycine\", \"troleandomycinum\", \"viamicina\", \"wytrion\")"	1	"g"			"character(0)"
+"TRL"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"J01FA08"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"c(\"acetyloleandomycin\", \"aovine\", \"cyclamycin\", \"evramicina\", \"matromicina\", \"matromycin t\", \"oleandocetine\", \"t.a.o.\", \"treolmicina\", \"tribiocillina\", \"triocetin\", \"triolan\", \"troleandomicina\", \"troleandomycin\", \"troleandomycine\", \"troleandomycinum\", \"viamicina\", \"wytrion\")"	1	"g"			"character(0)"
-"TRO"		55886	"Trospectomycin"	"Other antibacterials"			""	"c(\"trospectinomycin\", \"trospectomicina\", \"trospectomycin\", \"trospectomycine\", \"trospectomycinum\")"					"character(0)"
+"TRO"	55886	"Trospectomycin"	"Other antibacterials"				""	"c(\"trospectinomycin\", \"trospectomicina\", \"trospectomycin\", \"trospectomycine\", \"trospectomycinum\")"					"character(0)"
-"TVA"	"J01MA13"	62959	"Trovafloxacin"	"Quinolones"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"trov\")"	"c(\"trovafloxacin\", \"trovan\")"	0.2	"g"	0.2	"g"	"character(0)"
+"TVA"	62959	"Trovafloxacin"	"Quinolones"	"J01MA13"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"trov\")"	"c(\"trovafloxacin\", \"trovan\")"	0.2	"g"	0.2	"g"	"character(0)"
-"TUL"		9832301	"Tulathromycin"	"Macrolides/lincosamides"			""	"c(\"draxxin\", \"tulathrmycin a\", \"tulathromycin\", \"tulathromycin a\")"					"character(0)"
+"TUL"	9832301	"Tulathromycin"	"Macrolides/lincosamides"				""	"c(\"draxxin\", \"tulathrmycin a\", \"tulathromycin\", \"tulathromycin a\")"					"character(0)"
-"TYL"		5280440	"Tylosin"	"Macrolides/lincosamides"			""	"c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")"					"87587-2"
+"TYL"	5280440	"Tylosin"	"Macrolides/lincosamides"				""	"c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")"					"87587-2"
-"TYL1"	"A07AA11"	6441094	"Tylvalosin"	"Other antibacterials"	"Intestinal antiinfectives"	"Antibiotics"	""	""	0.6	"g"			""
+"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"				""	""					""
-"PRU1"		124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"			""	"ulifloxacin"					"character(0)"
+"PRU1"	124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"				""	"ulifloxacin"					"character(0)"
-"VAN"	"J01XA01"	14969	"Vancomycin"	"Glycopeptides"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"va\", \"van\", \"vanc\")"	"c(\"vancocin\", \"vancocin hcl\", \"vancoled\", \"vancomicina\", \"vancomycin\", \"vancomycin hcl\", \"vancomycine\", \"vancomycinum\", \"vancor\", \"viomycin derivative\")"			2	"g"	"c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
+"VAN"	14969	"Vancomycin"	"Glycopeptides"	"c(\"A07AA09\", \"J01XA01\", \"S01AA28\")"	"Other antibacterials"	"Glycopeptide antibacterials"	"c(\"va\", \"van\", \"vanc\")"	"c(\"vancocin\", \"vancocin hcl\", \"vancoled\", \"vancomicina\", \"vancomycin\", \"vancomycin hcl\", \"vancomycine\", \"vancomycinum\", \"vancor\", \"viomycin derivative\")"	2	"g"	2	"g"	"c(\"13586-3\", \"13587-1\", \"20578-1\", \"31012-8\", \"39092-2\", \"39796-8\", \"39797-6\", \"4089-9\", \"4090-7\", \"4091-5\", \"4092-3\", \"50938-0\", \"59381-4\")"
-"VAM"			"Vancomycin-macromethod"	"Glycopeptides"			""	""					""
+"VAM"		"Vancomycin-macromethod"	"Glycopeptides"				""	""					""
-"VIO"		135398671	"Viomycin"	"Antimycobacterials"			""	"c(\"celiomycin\", \"florimycin\", \"floromycin\", \"viomicina\", \"viomycin\", \"viomycine\", \"viomycinum\")"					"character(0)"
+"VIO"	135398671	"Viomycin"	"Antimycobacterials"				""	"c(\"celiomycin\", \"florimycin\", \"floromycin\", \"viomicina\", \"viomycin\", \"viomycine\", \"viomycinum\")"					"character(0)"
-"VIR"		11979535	"Virginiamycine"	"Other antibacterials"			""	"c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")"					"character(0)"
+"VIR"	11979535	"Virginiamycine"	"Other antibacterials"				""	"c(\"eskalin v\", \"mikamycin\", \"mikamycine\", \"mikamycinum\", \"ostreogrycinum\", \"pristinamycine\", \"pristinamycinum\", \"stafac\", \"stafytracine\", \"staphylomycin\", \"starfac\", \"streptogramin\", \"vernamycin\", \"virgimycin\", \"virgimycine\", \"virginiamycina\", \"virginiamycine\", \"virginiamycinum\")"					"character(0)"
-"VOR"	"J02AC03"	71616	"Voriconazole"	"Antifungals/antimycotics"	"Antimycotics for systemic use"	"Triazole derivatives"	"c(\"vori\", \"vrc\")"	"c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")"	0.4	"g"	0.4	"g"	"c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")"
+"VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"c(\"vori\", \"vrc\")"	"c(\"pfizer\", \"vfend i.v.\", \"voriconazol\", \"voriconazole\", \"voriconazolum\", \"vorikonazole\")"	0.4	"g"	0.4	"g"	"c(\"38370-3\", \"53902-3\", \"73676-9\", \"80553-1\", \"80651-3\")"
-"XBR"	"J01XX02"	72144	"Xibornol"	"Other antibacterials"	"Other antibacterials"	"Other antibacterials"	""	"c(\"bactacine\", \"bracen\", \"nanbacine\", \"xibornol\", \"xibornolo\", \"xibornolum\")"					"character(0)"
+"XBR"	72144	"Xibornol"	"Other antibacterials"	"J01XX02"	"Other antibacterials"	"Other antibacterials"	""	"c(\"bactacine\", \"bracen\", \"nanbacine\", \"xibornol\", \"xibornolo\", \"xibornolum\")"					"character(0)"
-"ZID"		77846445	"Zidebactam"	"Other antibacterials"			""	"zidebactam"					"character(0)"
+"ZID"	77846445	"Zidebactam"	"Other antibacterials"				""	"zidebactam"					"character(0)"

data-raw/exploratory_data_analysis_test.R

@@ -0,0 +1,28 @@
+library(dplyr)
+example_isolates %>% 
+  select(mo, where(is.rsi)) %>% 
+  tidyr::pivot_longer(cols = where(is.rsi)) %>% 
+  # remove intrisic R
+  filter(!paste(mo, name) %in% AMR:::INTRINSIC_R) %>% 
+  mutate(name = as.ab(name),
+         value = ifelse(value == "R", 1, 0),
+         class = ab_group(name)) %>% 
+  group_by(mo, class) %>% 
+  summarise(n = n(),
+            res = mean(value, na.rm = TRUE)) %>% 
+  filter(n > 30, !is.na(res))
+
+
+
+df <- example_isolates
+search_mo <- "B_ESCHR_COLI"
+intrinsic_res <- INTRINSIC_R[INTRINSIC_R %like% search_mo]
+intrinsic_res <- gsub(".* (.*)", "\\1", intrinsic_res)
+
+x <- df %>%
+  select(mo, where(is.rsi)) %>% 
+  filter(mo == search_mo) %>%
+  # at least 30 results available
+  select(function(x) sum(!is.na(x)) >= 30) %>% 
+  # remove intrisic R
+  select(!matches(paste(intrinsic_res, collapse = "|")))

data-raw/read_EUCAST.R

@@ -118,7 +118,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
                                       seq(from = 41, to = 49, by = 1),
                                       seq(from = 81, to = 89, by = 1))
   has_superscript <- function(x) {
-    # because due to floating point error 0.1252 is not in: 
+    # because due to floating point error, 0.1252 is not in: 
     # seq(from = 0.1251, to = 0.1259, by = 0.0001)
     sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
   }
@@ -242,3 +242,21 @@ for (i in 2:length(sheets_to_analyse)) {
                                          guideline_name = guideline_name))
     , error = function(e) message(e$message))
 }
+
+# 2021-07-12 fix for Morganellaceae (check other lines too next time)
+morg <- rsi_translation %>%
+  as_tibble() %>%
+  filter(ab == "IPM",
+         guideline == "EUCAST 2021",
+         mo == as.mo("Enterobacterales")) %>% 
+  mutate(mo = as.mo("Morganellaceae"))
+morg[which(morg$method == "MIC"), "breakpoint_S"] <- 0.001
+morg[which(morg$method == "MIC"), "breakpoint_R"] <- 4
+morg[which(morg$method == "DISK"), "breakpoint_S"] <- 50
+morg[which(morg$method == "DISK"), "breakpoint_R"] <- 19
+
+rsi_translation <- rsi_translation %>%
+  bind_rows(morg) %>%
+  bind_rows(morg %>%
+              mutate(guideline = "EUCAST 2020")) %>%
+  arrange(desc(guideline), ab, mo, method)

data-raw/reproduction_of_antibiotics.R

@@ -646,28 +646,104 @@ antibiotics <- antibiotics %>%
                      oral_ddd = NA_real_))
 
 
-# update DDDs from WHOCC website
+
-ddd_oral <- double(length = nrow(antibiotics))
+# update ATC codes from WHOCC website -------------------------------------
-ddd_iv <- double(length = nrow(antibiotics))
+
+# last time checked: 2021-08-16
+
+updated_atc <- as.list(antibiotics$atc)
+
+get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
+  
+  ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
+  
+  # we will do a search on their website, which means:
+  
+  # go to the url
+  atc_tbl <- read_html(url) %>% 
+    # get all forms
+    html_form() %>%
+    # get the second form (the first form is a global website form)
+    .[[2]] %>% 
+    # set the name input box to our search parameter
+    html_form_set(name = ab_name) %>% 
+    # hit Submit
+    html_form_submit() %>% 
+    # read the resulting page
+    read_html() %>% 
+    # retrieve the table on it
+    html_node("table") %>% 
+    # transform it to an R data set
+    html_table(header = FALSE)
+  # and get the ATCs (first column) of only exact hits
+  unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE]))
+}
+
+# this takes around 4 minutes (some are skipped and go faster)
+for (i in seq_len(nrow(antibiotics))) {
+  message(percentage(i / nrow(antibiotics), digits = 1), 
+          " - Downloading ", antibiotics$name[i],
+          appendLF = FALSE)
+  atcs <- get_atcs(antibiotics$name[i])
+  if (length(atcs) > 0) {
+    updated_atc[[i]] <- atcs
+    message(" (", length(atcs), " results)")
+    # let the WHO server rest for a second - they might have a limitation on the queries per second
+    Sys.sleep(1)
+  } else {
+    message(" (skipping)")
+  }
+}
+
+antibiotics$atc <- updated_atc
+
+# update DDDs from WHOCC website ------------------------------------------
+
+# last time checked: 2021-08-19
+ddd_oral <- rep(NA_real_, nrow(antibiotics))
+ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
+ddd_iv <- rep(NA_real_, nrow(antibiotics))
+ddd_iv_units <- rep(NA_character_, nrow(antibiotics))
 progress <- progress_ticker(nrow(antibiotics))
 for (i in seq_len(nrow(antibiotics))) {
   on.exit(close(progress))
   progress$tick()
-  if (!is.na(antibiotics$atc[i])) {
+  atcs <- antibiotics$atc[[i]]
-    ddd_oral[i] <- atc_online_ddd(antibiotics$atc[i], administration = "O")
+  if (!all(is.na(atcs))) {
-    ddd_iv[i] <- atc_online_ddd(antibiotics$atc[i], administration = "P") # parenteral
+    for (j in seq_len(length(atcs))) {
-    Sys.sleep(1)
+      # oral
+      if (is.na(ddd_oral[i])) {
+        ddd_oral[i] <- atc_online_ddd(atcs[j], administration = "O")
+        if (!is.na(ddd_oral[i])) {
+          ddd_oral_units[i] <- atc_online_ddd_units(atcs[j], administration = "O")
+        }
+      }
+      # parenteral
+      if (is.na(ddd_iv[i])) {
+        ddd_iv[i] <- atc_online_ddd(atcs[j], administration = "P")
+        if (!is.na(ddd_iv[i])) {
+          ddd_iv_units[i] <- atc_online_ddd_units(atcs[j], administration = "P")
+        }
+      }
+    }
+  }
+  if (!is.na(ddd_oral[i]) | !is.na(ddd_iv[i])) {
+    # let the WHO server rest for 0.25 second - they might have a limitation on the queries per second
+    Sys.sleep(0.25)
   }
 }
-ddd_oral[ddd_oral == 0] <- NA_real_
+
-ddd_iv[ddd_iv == 0] <- NA_real_
 antibiotics$oral_ddd <- ddd_oral
+antibiotics$oral_units <- ddd_oral_units
 antibiotics$iv_ddd <- ddd_iv
+antibiotics$iv_units <- ddd_iv_units
+
+# Wrap up -----------------------------------------------------------------
 
 # set as data.frame again
 antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
 class(antibiotics$ab) <- c("ab", "character")
-antibiotics <- antibiotics %>% dplyr::arrange(name)
+antibiotics <- dplyr::arrange(antibiotics, name)
 
 # make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
 for (i in 1:nrow(antibiotics)) {
@@ -683,5 +759,5 @@ for (i in 1:nrow(antibiotics)) {
 
 # REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
 
-usethis::use_data(antibiotics, overwrite = TRUE, version = 2)
+usethis::use_data(antibiotics, overwrite = TRUE, version = 2, compress = "xz")
 rm(antibiotics)

data-raw/reproduction_of_intrinsic_resistant.R

@@ -32,7 +32,7 @@ for (i in seq_len(nrow(antibiotics))) {
 }
 
 int_resis <- eucast_rules(int_resis, 
-                          eucast_rules_df = subset(AMR:::eucast_rules_file,
+                          eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
                                                    is.na(have_these_values) & reference.version == 3.2),
                           info = FALSE)
 

data-raw/rsi.md5

@@ -1 +1 @@
-1a7fe52f8185c9bb2c470712863d1887
+67a83b234f25a303c7944222bea47d73

data-raw/rsi_translation.txt

@@ -754,6 +754,8 @@
 "EUCAST 2021"	"MIC"		"Staphylococcus saccharolyticus"	"Imipenem/relebactam"	"Anaerobes, Grampositive"		2	2	FALSE
 "EUCAST 2021"	"MIC"		"Viridans Group Streptococcus (VGS)"	"Imipenem/relebactam"	"Viridans group streptococci"		2	2	FALSE
 "EUCAST 2021"	"MIC"		"(unknown name)"	"Imipenem/relebactam"	"PK PD breakpoints"		2	2	FALSE
+"EUCAST 2021"	"DISK"		"Morganellaceae"	"Imipenem"	"Enterobacterales"	"10ug"	50	19	FALSE
+"EUCAST 2021"	"MIC"		"Morganellaceae"	"Imipenem"	"Enterobacterales"		0.001	4	FALSE
 "EUCAST 2021"	"DISK"		"Enterobacterales"	"Imipenem"	"Enterobacterales"	"10ug"	22	19	FALSE
 "EUCAST 2021"	"MIC"		"Enterobacterales"	"Imipenem"	"Enterobacterales"		2	4	FALSE
 "EUCAST 2021"	"DISK"		"Acinetobacter"	"Imipenem"	"Acinetobacter"	"10ug"	24	21	FALSE
@@ -2542,6 +2544,8 @@
 "EUCAST 2020"	"MIC"		"Staphylococcus saccharolyticus"	"Imipenem/relebactam"	"Anaerobes, Grampositive"		2	2	FALSE
 "EUCAST 2020"	"MIC"		"Viridans Group Streptococcus (VGS)"	"Imipenem/relebactam"	"Viridans group streptococci"		2	2	FALSE
 "EUCAST 2020"	"MIC"		"(unknown name)"	"Imipenem/relebactam"	"PK PD breakpoints"		2	2	FALSE
+"EUCAST 2020"	"DISK"		"Morganellaceae"	"Imipenem"	"Enterobacterales"	"10ug"	50	19	FALSE
+"EUCAST 2020"	"MIC"		"Morganellaceae"	"Imipenem"	"Enterobacterales"		0.001	4	FALSE
 "EUCAST 2020"	"DISK"		"Enterobacterales"	"Imipenem"	"Enterobacterales"	"10ug"	22	17	FALSE
 "EUCAST 2020"	"MIC"		"Enterobacterales"	"Imipenem"	"Enterobacterales"		2	4	FALSE
 "EUCAST 2020"	"DISK"		"Acinetobacter"	"Imipenem"	"Acinetobacter"	"10ug"	24	21	FALSE

data-raw/translations.tsv

@@ -1,266 +1,269 @@
-pattern	regular_expr	case_sensitive	affect_ab_name	affect_mo_name	de	nl	es	it	fr	pt
+pattern	regular_expr	case_sensitive	affect_ab_name	affect_mo_name	de	nl	es	it	fr	pt	da
-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
+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
-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
+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
-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-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
-unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	unbekannte Gramnegativen	onbekende Gram-negatieven	Gram negativos desconocidos	Gram negativi sconosciuti	Gram négatifs inconnus	Gram negativos desconhecidos
+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
-unknown Gram-positives	TRUE	TRUE	FALSE	TRUE	unbekannte Grampositiven	onbekende Gram-positieven	Gram positivos desconocidos	Gram positivi sconosciuti	Gram positifs inconnus	Gram positivos desconhecidos
+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
-unknown fungus	TRUE	TRUE	FALSE	TRUE	unbekannter Pilze	onbekende schimmel	hongo desconocido	fungo sconosciuto	champignon inconnu	fungo desconhecido
+unknown fungus	TRUE	TRUE	FALSE	TRUE	unbekannter Pilze	onbekende schimmel	hongo desconocido	fungo sconosciuto	champignon inconnu	fungo desconhecido	ukendt svamp
-unknown yeast	TRUE	TRUE	FALSE	TRUE	unbekannte Hefe	onbekende gist	levadura desconocida	lievito sconosciuto	levure inconnue	levedura desconhecida
+unknown yeast	TRUE	TRUE	FALSE	TRUE	unbekannte Hefe	onbekende gist	levadura desconocida	lievito sconosciuto	levure inconnue	levedura desconhecida	ukendt gær
-unknown name	TRUE	TRUE	FALSE	TRUE	unbekannte Name	onbekende naam	nombre desconocido	nome sconosciuto	nom inconnu	nome desconhecido
+unknown name	TRUE	TRUE	FALSE	TRUE	unbekannte Name	onbekende naam	nombre desconocido	nome sconosciuto	nom inconnu	nome desconhecido	ukendt navn
-unknown kingdom	TRUE	TRUE	FALSE	TRUE	unbekanntes Reich	onbekend koninkrijk	reino desconocido	regno sconosciuto	règme inconnu	reino desconhecido
+unknown kingdom	TRUE	TRUE	FALSE	TRUE	unbekanntes Reich	onbekend koninkrijk	reino desconocido	regno sconosciuto	règme inconnu	reino desconhecido	ukendt kongerige
-unknown phylum	TRUE	TRUE	FALSE	TRUE	unbekannter Stamm	onbekend fylum	filo desconocido	phylum sconosciuto	embranchement inconnu	filo desconhecido
+unknown phylum	TRUE	TRUE	FALSE	TRUE	unbekannter Stamm	onbekend fylum	filo desconocido	phylum sconosciuto	embranchement inconnu	filo desconhecido	ukendt stamme
-unknown class	TRUE	TRUE	FALSE	TRUE	unbekannte Klasse	onbekende klasse	clase desconocida	classe sconosciuta	classe inconnue	classe desconhecida
+unknown class	TRUE	TRUE	FALSE	TRUE	unbekannte Klasse	onbekende klasse	clase desconocida	classe sconosciuta	classe inconnue	classe desconhecida	ukendt klasse
-unknown order	TRUE	TRUE	FALSE	TRUE	unbekannte Ordnung	onbekende orde	orden desconocido	ordine sconosciuto	ordre inconnu	ordem desconhecido
+unknown order	TRUE	TRUE	FALSE	TRUE	unbekannte Ordnung	onbekende orde	orden desconocido	ordine sconosciuto	ordre inconnu	ordem desconhecido	ukendt orden
-unknown family	TRUE	TRUE	FALSE	TRUE	unbekannte Familie	onbekende familie	familia desconocida	famiglia sconosciuta	famille inconnue	família desconhecida
+unknown family	TRUE	TRUE	FALSE	TRUE	unbekannte Familie	onbekende familie	familia desconocida	famiglia sconosciuta	famille inconnue	família desconhecida	ukendt familie
-unknown genus	TRUE	TRUE	FALSE	TRUE	unbekannte Gattung	onbekend geslacht	género desconocido	genere sconosciuto	genre inconnu	gênero desconhecido
+unknown genus	TRUE	TRUE	FALSE	TRUE	unbekannte Gattung	onbekend geslacht	género desconocido	genere sconosciuto	genre inconnu	gênero desconhecido	ukendt slægt
-unknown species	TRUE	TRUE	FALSE	TRUE	unbekannte Art	onbekende soort	especie desconocida	specie sconosciute	espèce inconnue	espécies desconhecida
+unknown species	TRUE	TRUE	FALSE	TRUE	unbekannte Art	onbekende soort	especie desconocida	specie sconosciute	espèce inconnue	espécies desconhecida	ukendt art
-unknown subspecies	TRUE	TRUE	FALSE	TRUE	unbekannte Unterart	onbekende ondersoort	subespecie desconocida	sottospecie sconosciute	sous-espèce inconnue	subespécies desconhecida
+unknown subspecies	TRUE	TRUE	FALSE	TRUE	unbekannte Unterart	onbekende ondersoort	subespecie desconocida	sottospecie sconosciute	sous-espèce inconnue	subespécies desconhecida	ukendt underart
-unknown rank	TRUE	TRUE	FALSE	TRUE	unbekannter Rang	onbekende rang	rango desconocido	grado sconosciuto	rang inconnu	classificação desconhecido
+unknown rank	TRUE	TRUE	FALSE	TRUE	unbekannter Rang	onbekende rang	rango desconocido	grado sconosciuto	rang inconnu	classificação desconhecido	ukendt rang
+ group 	TRUE	TRUE	FALSE	TRUE	 Gruppe 	 groep 	 grupo 	 gruppo 	 groupe 	 grupo 	 gruppe 
 CoNS	FALSE	TRUE	FALSE	TRUE	KNS	CNS	SCN				
 CoPS	FALSE	TRUE	FALSE	TRUE	KPS	CPS	SCP				
-Gram-negative	TRUE	TRUE	FALSE	FALSE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo
+Gram-negative	TRUE	TRUE	FALSE	FALSE	Gramnegativ	Gram-negatief	Gram negativo	Gram negativo	Gram négatif	Gram negativo	Gram-negativ
-Gram-positive	TRUE	TRUE	FALSE	FALSE	Grampositiv	Gram-positief	Gram positivo	Gram positivo	Gram positif	Gram positivo
+Gram-positive	TRUE	TRUE	FALSE	FALSE	Grampositiv	Gram-positief	Gram positivo	Gram positivo	Gram positif	Gram positivo	Gram-positiv
-^Bacteria$	TRUE	TRUE	FALSE	FALSE	Bakterien	Bacteriën	Bacterias	Batteri	Bactéries	Bactérias
+^Bacteria$	TRUE	TRUE	FALSE	FALSE	Bakterien	Bacteriën	Bacterias	Batteri	Bactéries	Bactérias	Bakterier
-^Fungi$	TRUE	TRUE	FALSE	FALSE	Pilze	Schimmels	Hongos	Funghi	Champignons	Fungos
+^Fungi$	TRUE	TRUE	FALSE	FALSE	Pilze	Schimmels	Hongos	Funghi	Champignons	Fungos	Støbeforme
-^Yeasts$	TRUE	TRUE	FALSE	FALSE	Hefen	Gisten	Levaduras	Lieviti	Levures	Leveduras
+^Yeasts$	TRUE	TRUE	FALSE	FALSE	Hefen	Gisten	Levaduras	Lieviti	Levures	Leveduras	Gær
-^Protozoa$	TRUE	TRUE	FALSE	FALSE	Protozoen	Protozoën	Protozoarios	Protozoi	Protozoaires	Protozoários
+^Protozoa$	TRUE	TRUE	FALSE	FALSE	Protozoen	Protozoën	Protozoarios	Protozoi	Protozoaires	Protozoários	Protozoer
-biogroup	TRUE	TRUE	FALSE	FALSE	Biogruppe	biogroep	biogrupo	biogruppo	biogroupe	biogrupo
+biogroup	TRUE	TRUE	FALSE	FALSE	Biogruppe	biogroep	biogrupo	biogruppo	biogroupe	biogrupo	biogruppe
 biotype	TRUE	TRUE	FALSE	FALSE	Biotyp		biotipo	biotipo		biótipo	
 vegetative	TRUE	TRUE	FALSE	FALSE	vegetativ	vegetatief	vegetativo	vegetativo	végétatif	vegetativo	
 ([([ ]*?)group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1groep	\\1grupo	\\1gruppo	\\1groupe	\\1grupo	
 ([([ ]*?)Group	TRUE	TRUE	FALSE	FALSE	\\1Gruppe	\\1Groep	\\1Grupo	\\1Gruppo	\\1Groupe	\\1Grupo	
 no .*growth	TRUE	FALSE	FALSE	FALSE	keine? .*wachstum	geen .*groei	no .*crecimientonon	sem .*crescimento	pas .*croissance	sem .*crescimento	
 no|not	TRUE	FALSE	FALSE	FALSE	keine?	geen|niet	no|sin	sem	non	sem	
-Susceptible	TRUE	FALSE	FALSE	FALSE	Empfindlich	Gevoelig	Susceptible			
 Intermediate	TRUE	FALSE	FALSE	FALSE	Mittlere	Intermediair	Intermedio				
+Susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	Empfindlich, erh Belastung	Gevoelig, hoge dosis					
+susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	empfindlich, erh Belastung	gevoelig, hoge dosis					
+Susceptible	TRUE	FALSE	FALSE	FALSE	Empfindlich	Gevoelig	Susceptible				
 Incr. exposure	TRUE	FALSE	FALSE	FALSE	Empfindlich, erh Belastung	'Incr. exposure'	'Incr. exposure'				
 Resistant	TRUE	FALSE	FALSE	FALSE	Resistent	Resistent	Resistente				
-antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	antibioticum	antibiótico			
+antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	antibioticum	antibiótico	antibiotico	antibiotique	antibiótico	antibiotikum
-Antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	Antibioticum	Antibiótico			
+Antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotikum	Antibioticum	Antibiótico	Antibiotico	Antibiotique	Antibiótico	Antibiotikum
-Drug	TRUE	TRUE	FALSE	FALSE	Medikament	Middel	Fármaco			
+Drug	TRUE	TRUE	FALSE	FALSE	Medikament	Middel	Fármaco	Droga	Médicament	Droga	Lægemiddel
-drug	TRUE	TRUE	FALSE	FALSE	Medikament	middel	fármaco			
+drug	TRUE	TRUE	FALSE	FALSE	Medikament	middel	fármaco	droga	médicament	droga	lægemiddel
-Frequency	FALSE	TRUE	FALSE	FALSE	Zahl	Aantal				
+Frequency	FALSE	TRUE	FALSE	FALSE	Zahl	Aantal	Frecuencia	Frequenza	Fréquence	Frequência	Frekvens
-Minimum Inhibitory Concentration (mg/L)	FALSE	FALSE	FALSE	FALSE	Minimale Hemm-Konzentration (mg/L)	Minimale inhiberende concentratie (mg/L)				
+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)
-Disk diffusion diameter (mm)	FALSE	FALSE	FALSE	FALSE	Durchmesser der Scheibenzone (mm)	Diameter diskzone (mm)				
+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)
-Antimicrobial Interpretation	FALSE	FALSE	FALSE	FALSE	Antimikrobielle Auswertung	Antimicrobiële interpretatie				
+Antimicrobial Interpretation	FALSE	FALSE	FALSE	FALSE	Antimikrobielle Auswertung	Antimicrobiële interpretatie	Interpretación antimicrobiana	Interpretazione antimicrobica	Interprétation antimicrobienne	Interpretação Antimicrobiana	Antimikrobiel fortolkning
-4-aminosalicylic acid	FALSE	TRUE	TRUE	FALSE	4-Aminosalicylsäure	4-aminosalicylzuur	Ácido 4-aminosalicílico			
+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
-Adefovir dipivoxil	FALSE	TRUE	TRUE	FALSE	Adefovir Dipivoxil	Adefovir	Adefovir dipivoxil			
+Adefovir dipivoxil	FALSE	TRUE	TRUE	FALSE	Adefovir Dipivoxil	Adefovir	Adefovir dipivoxil	Adefovir dipivoxil	Adéfovir dipivoxil	Adefovir dipivoxil	Adefovir dipivoxil
-Aldesulfone sodium	FALSE	TRUE	TRUE	FALSE	Aldesulfon-Natrium	Aldesulfon	Aldesulfona sódica			
+Aldesulfone sodium	FALSE	TRUE	TRUE	FALSE	Aldesulfon-Natrium	Aldesulfon	Aldesulfona sódica	Aldesulfone sodio	Aldésulfone sodique	Aldesulfona de sódio	Aldesulfon-natrium
-Amikacin	FALSE	TRUE	TRUE	FALSE	Amikacin	Amikacine	Amikacina			
+Amikacin	FALSE	TRUE	TRUE	FALSE	Amikacin	Amikacine	Amikacina	Amikacin	Amikacine	Amikacin	Amikacin
-Amoxicillin	FALSE	TRUE	TRUE	FALSE	Amoxicillin	Amoxicilline	Amoxicilina			
+Amoxicillin	FALSE	TRUE	TRUE	FALSE	Amoxicillin	Amoxicilline	Amoxicilina	Amoxicillina	Amoxicilline	Amoxicilina	Amoxicillin
-Amoxicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Amoxicillin/Beta-Lactamase-Hemmer	Amoxicilline/enzymremmer	amoxicilina/inhib. de la beta-lactamasa			
+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
-Amphotericin B	FALSE	TRUE	TRUE	FALSE	Amphotericin B	Amfotericine B	Anfotericina B			
+Amphotericin B	FALSE	TRUE	TRUE	FALSE	Amphotericin B	Amfotericine B	Anfotericina B	Amfotericina B	Amphotéricine B	Anfotericina B	Amfotericin B
-Ampicillin	FALSE	TRUE	TRUE	FALSE	Ampicillin	Ampicilline	Ampicilina			
+Ampicillin	FALSE	TRUE	TRUE	FALSE	Ampicillin	Ampicilline	Ampicilina	Ampicillina	Ampicilline	Ampicilina	Ampicillin
-Ampicillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Ampicillin/Beta-Laktamase-Hemmer	Ampicilline/enzymremmer	Ampicilina/inhib. de la betalactamasa			
+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
-Anidulafungin	FALSE	TRUE	TRUE	FALSE	Anidulafungin	Anidulafungine	Anidulafungina			
+Anidulafungin	FALSE	TRUE	TRUE	FALSE	Anidulafungin	Anidulafungine	Anidulafungina	Anidulafungin	Anidulafungine	Anidulafungin	Anidulafungin
-Azidocillin	FALSE	TRUE	TRUE	FALSE	Azidocillin	Azidocilline	Azidocilina			
+Azidocillin	FALSE	TRUE	TRUE	FALSE	Azidocillin	Azidocilline	Azidocilina	Azidocillina	Azidocilline	Azidocillin	Azidocillin
-Azithromycin	FALSE	TRUE	TRUE	FALSE	Azithromycin	Azitromycine	Azitromicina			
+Azithromycin	FALSE	TRUE	TRUE	FALSE	Azithromycin	Azitromycine	Azitromicina	Azitromicina	Azithromycine	Azitromicina	Azithromycin
-Azlocillin	FALSE	TRUE	TRUE	FALSE	Azlocillin	Azlocilline	Azlocilina			
+Azlocillin	FALSE	TRUE	TRUE	FALSE	Azlocillin	Azlocilline	Azlocilina	Azlocillina	Azlocilline	Azlocillin	Azlocillin
-Bacampicillin	FALSE	TRUE	TRUE	FALSE	Bacampicillin	Bacampicilline	Bacampicilina			
+Bacampicillin	FALSE	TRUE	TRUE	FALSE	Bacampicillin	Bacampicilline	Bacampicilina	Bacampicillina	Bacampicilline	Bacampicilina	Bacampicillin
-Bacitracin	FALSE	TRUE	TRUE	FALSE	Bacitracin	Bacitracine	Bacitracina			
+Bacitracin	FALSE	TRUE	TRUE	FALSE	Bacitracin	Bacitracine	Bacitracina	Bacitracina	Bacitracine	Bacitracin	Bacitracin
-Benzathine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Benzylpenicillin	Benzylpenicillinebenzathine	Bencilpenicilina benzatínica			
+Benzathine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Benzylpenicillin	Benzylpenicillinebenzathine	Bencilpenicilina benzatínica	Benzatina benzilpenicillina	Benzathine benzylpénicilline	Benzatina benzatina benzilpenicilina	Benzathinbenzylpenicillin
-Benzathine phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Phenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine	Fenoximetilpenicilina benzatínica			
+Benzathine phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzathin-Phenoxymethylpenicillin	Fenoxymethylpenicillinebenzathine	Fenoximetilpenicilina benzatínica	Benzatina fenossimetilpenicillina	Phénoxyméthylpénicilline benzathine	Benzatina fenoximetilpenicilina	Benzathinfenoxymethylpenicillin
-Benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzylpenicillin	Benzylpenicilline	Bencilpenicilina			
+Benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Benzylpenicillin	Benzylpenicilline	Bencilpenicilina	Benzilpenicillina	Benzylpénicilline	Benzilpenicilina	Benzylpenicillin
-Calcium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Kalzium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de calcio			
+Calcium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Kalzium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de calcio	Calcio aminosalicilato	Aminosalicylate de calcium	Aminosalicilato de cálcio	Calciumaminosalicylat
-Capreomycin	FALSE	TRUE	TRUE	FALSE	Capreomycin	Capreomycine	Capreomicina			
+Capreomycin	FALSE	TRUE	TRUE	FALSE	Capreomycin	Capreomycine	Capreomicina	Capreomicina	Capréomycine	Capreomicina	Capreomycin
-Carbenicillin	FALSE	TRUE	TRUE	FALSE	Carbenicillin	Carbenicilline	Carbenicilina			
+Carbenicillin	FALSE	TRUE	TRUE	FALSE	Carbenicillin	Carbenicilline	Carbenicilina	Carbenicillina	Carbénicilline	Carbenicilina	Carbenicillin
-Carindacillin	FALSE	TRUE	TRUE	FALSE	Carindacillin	Carindacilline	Carindacilina			
+Carindacillin	FALSE	TRUE	TRUE	FALSE	Carindacillin	Carindacilline	Carindacilina	Carindacillina	Carindacilline	Carindacillin	Carindacillin
-Caspofungin	FALSE	TRUE	TRUE	FALSE	Caspofungin	Caspofungine	Caspofungina			
+Caspofungin	FALSE	TRUE	TRUE	FALSE	Caspofungin	Caspofungine	Caspofungina	Caspofungin	Caspofungine	Caspofungin	Caspofungin
-Ce(f|ph)acetrile	TRUE	TRUE	TRUE	FALSE	Cefacetril	Cefacetril	Cefacetrilo			
+Ce(f|ph)acetrile	TRUE	TRUE	TRUE	FALSE	Cefacetril	Cefacetril	Cefacetrilo	Cefacetrile	Céphacétrile	Cephacetrile	Cephacetril
-Ce(f|ph)alotin	TRUE	TRUE	TRUE	FALSE	Cefalotin	Cefalotine	Cefalotina			
+Ce(f|ph)alotin	TRUE	TRUE	TRUE	FALSE	Cefalotin	Cefalotine	Cefalotina	Cefalotina	Céphalotine	Cefalotina	Cephalotin
-Ce(f|ph)amandole	TRUE	TRUE	TRUE	FALSE	Cefamandol	Cefamandol	Cefamandole			
+Ce(f|ph)amandole	TRUE	TRUE	TRUE	FALSE	Cefamandol	Cefamandol	Cefamandole	Cephamandole	Céphamandole	Cephamandole	Cephamandol
-Ce(f|ph)apirin	TRUE	TRUE	TRUE	FALSE	Cefapirin	Cefapirine	Cefapirina			
+Ce(f|ph)apirin	TRUE	TRUE	TRUE	FALSE	Cefapirin	Cefapirine	Cefapirina	Cefapirina	Céphapirine	Cephapirin	Cephapirin
-Ce(f|ph)azedone	TRUE	TRUE	TRUE	FALSE	Cefazedon	Cefazedon	Cefazedona			
+Ce(f|ph)azedone	TRUE	TRUE	TRUE	FALSE	Cefazedon	Cefazedon	Cefazedona	Cefazedone	Céphazédone	Cephazedone	Cephazedon
-Ce(f|ph)azolin	TRUE	TRUE	TRUE	FALSE	Cefazolin	Cefazoline	Cefazolina			
+Ce(f|ph)azolin	TRUE	TRUE	TRUE	FALSE	Cefazolin	Cefazoline	Cefazolina	Cephazolin	Céphazoline	Cephazolin	Cephazolin
-Ce(f|ph)alothin	TRUE	TRUE	TRUE	FALSE	Cefalothin	Cefalotine	Cefalotina			
+Ce(f|ph)alothin	TRUE	TRUE	TRUE	FALSE	Cefalothin	Cefalotine	Cefalotina	Cefalotina	Céphalothine	Cephalothin	Cephalothin
-Ce(f|ph)alexin	TRUE	TRUE	TRUE	FALSE	Cefalexin	Cefalexine	Cefalexina			
+Ce(f|ph)alexin	TRUE	TRUE	TRUE	FALSE	Cefalexin	Cefalexine	Cefalexina	Cephalexin	Céphalexine	Cephalexin	Cephalexin
-Ce(f|ph)epime	TRUE	TRUE	TRUE	FALSE	Cefepim	Cefepim	Cefepime			
+Ce(f|ph)epime	TRUE	TRUE	TRUE	FALSE	Cefepim	Cefepim	Cefepime	Cephepime	Céphépime	Cephepime	Cephepime
-Ce(f|ph)ixime	TRUE	TRUE	TRUE	FALSE	Cefixim	Cefixim	Cefixima			
+Ce(f|ph)ixime	TRUE	TRUE	TRUE	FALSE	Cefixim	Cefixim	Cefixima	Cephixime	Céphixime	Cephixime	Cephixim
-Ce(f|ph)menoxime	TRUE	TRUE	TRUE	FALSE	Cefmenoxim	Cefmenoxim	Cefmenoxima			
+Ce(f|ph)menoxime	TRUE	TRUE	TRUE	FALSE	Cefmenoxim	Cefmenoxim	Cefmenoxima	Cephmenoxime	Céphénoxime	Cephmenoxime	Cephmenoxim
-Ce(f|ph)metazole	TRUE	TRUE	TRUE	FALSE	Cefmetazol	Cefmetazol	Cefmetazol			
+Ce(f|ph)metazole	TRUE	TRUE	TRUE	FALSE	Cefmetazol	Cefmetazol	Cefmetazol	Cephmetazole	Céphmétazole	Cefmetazole	Cephmetazol
-Ce(f|ph)odizime	TRUE	TRUE	TRUE	FALSE	Cefodizim	Cefodizim	Cefodizima			
+Ce(f|ph)odizime	TRUE	TRUE	TRUE	FALSE	Cefodizim	Cefodizim	Cefodixima	Cephodizime	Céphodizime	Cephodizime	Cephodizim
-Ce(f|ph)onicid	TRUE	TRUE	TRUE	FALSE	Cefonicid	Cefonicide	Cefonicid			
+Ce(f|ph)onicid	TRUE	TRUE	TRUE	FALSE	Cefonicid	Cefonicide	Cefonicida	Cephonicid	Céphonicide	Cefonicid	Cephonicid
-Ce(f|ph)operazone	TRUE	TRUE	TRUE	FALSE	Cefoperazon	Cefoperazon	Cefoperazona			
+Ce(f|ph)operazone	TRUE	TRUE	TRUE	FALSE	Cefoperazon	Cefoperazon	Cefoperazona	Cephoperazone	Céphopérazone	Cephoperazone	Cephoperazon
-Ce(f|ph)operazone/beta-lactamase inhibitor	TRUE	TRUE	TRUE	FALSE	Cefoperazon/Beta-Lactamase-Hemmer	Cefoperazon/enzymremmer	Cefoperazona/inhib. de la betalactamasa			
+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
-Ce(f|ph)otaxime	TRUE	TRUE	TRUE	FALSE	Cefotaxim	Cefotaxim	Cefotaxima			
+Ce(f|ph)otaxime	TRUE	TRUE	TRUE	FALSE	Cefotaxim	Cefotaxim	Cefotaxima	Cephotaxime	Céphotaxime	Cephotaxime	Cephotaxim
-Ce(f|ph)oxitin	TRUE	TRUE	TRUE	FALSE	Cefoxitin	Cefoxitine	Cefoxitina			
+Ce(f|ph)oxitin	TRUE	TRUE	TRUE	FALSE	Cefoxitin	Cefoxitine	Cefoxitina	Cefossitina	Céphoxitine	Cephoxitin	Cephoxitin
-Ce(f|ph)pirome	TRUE	TRUE	TRUE	FALSE	Cefpirom	Cefpirom	Cefpirome			
+Ce(f|ph)pirome	TRUE	TRUE	TRUE	FALSE	Cefpirom	Cefpirom	Cephpirome	Cephpirome	Céphpirome	Cefpirome	Cephpirom
-Ce(f|ph)podoxime	TRUE	TRUE	TRUE	FALSE	Cefpodoxim	Cefpodoxim	Cefpodoxima			
+Ce(f|ph)podoxime	TRUE	TRUE	TRUE	FALSE	Cefpodoxim	Cefpodoxim	Cefpodoxima	Cephpodoxime	Céphpodoxime	Cephpodoxime	Cephpodoxim
-Ce(f|ph)radine	TRUE	TRUE	TRUE	FALSE	Cefradin	Cefradine	Cefradina			
+Ce(f|ph)radine	TRUE	TRUE	TRUE	FALSE	Cefradin	Cefradine	Cefradina	Cefradina	Céphradine	Cephradine	Cephradin
-Ce(f|ph)sulodin	TRUE	TRUE	TRUE	FALSE	Cefsulodin	Cefsulodine	Cefsulodina			
+Ce(f|ph)sulodin	TRUE	TRUE	TRUE	FALSE	Cefsulodin	Cefsulodine	Cefsulodina	Cephsulodin	Céphsulodine	Cephsulodin	Cephsulodin
-Ce(f|ph)tazidime	TRUE	TRUE	TRUE	FALSE	Ceftazidim	Ceftazidim	Ceftazidima			
+Ce(f|ph)tazidime	TRUE	TRUE	TRUE	FALSE	Ceftazidim	Ceftazidim	Ceftazidima	Ceftazidima	Céphtazidime	Ceftazidima	Cephtazidim
-Ce(f|ph)tezole	TRUE	TRUE	TRUE	FALSE	Ceftezol	Ceftezol	Ceftezol			
+Ce(f|ph)tezole	TRUE	TRUE	TRUE	FALSE	Ceftezol	Ceftezol	Ceftezol	Cephtezole	Céphtézole	Ceftezole	Cephtezol
-Ce(f|ph)tizoxime	TRUE	TRUE	TRUE	FALSE	Ceftizoxim	Ceftizoxim	Ceftizoxima			
+Ce(f|ph)tizoxime	TRUE	TRUE	TRUE	FALSE	Ceftizoxim	Ceftizoxim	Ceftizoxima	Cephtizoxime	Céphtizoxime	Cephtizoxime	Cephtizoxim
-Ce(f|ph)triaxone	TRUE	TRUE	TRUE	FALSE	Ceftriaxon	Ceftriaxon	Ceftriaxona			
+Ce(f|ph)triaxone	TRUE	TRUE	TRUE	FALSE	Ceftriaxon	Ceftriaxon	Ceftriaxona	Ceftriaxone	Céphtriaxone	Cefhtriaxone	Cephtriaxon
-Ce(f|ph)uroxime	TRUE	TRUE	TRUE	FALSE	Cefuroxim	Cefuroxim	Cefuroxima			
+Ce(f|ph)uroxime	TRUE	TRUE	TRUE	FALSE	Cefuroxim	Cefuroxim	Cefuroxima	Cefuroxima	Céphuroxime	Cephuroxime	Cephuroxim
-Ce(f|ph)uroxime/metronidazole	TRUE	TRUE	TRUE	FALSE	Cefuroxim/Metronidazol	Cefuroxim/andere antibacteriele middelen	Cefuroxima/metronidazol			
+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
-Chloramphenicol	FALSE	TRUE	TRUE	FALSE	Chloramphenicol	Chlooramfenicol	Cloranfenicol			
+Chloramphenicol	FALSE	TRUE	TRUE	FALSE	Chloramphenicol	Chlooramfenicol	Cloranfenicol	Cloramfenicolo	Chloramphénicol	Cloranfenicol	Kloramfenicol
-Chlortetracycline	FALSE	TRUE	TRUE	FALSE	Chlortetracyclin	Chloortetracycline	Clortetraciclina			
+Chlortetracycline	FALSE	TRUE	TRUE	FALSE	Chlortetracyclin	Chloortetracycline	Clortetraciclina	Clorotetraciclina	Chlortétracycline	Chlortetracycline	Chlortetracyclin
-Cinoxacin	FALSE	TRUE	TRUE	FALSE	Cinoxacin	Cinoxacine	Cinoxacina			
+Cinoxacin	FALSE	TRUE	TRUE	FALSE	Cinoxacin	Cinoxacine	Cinoxacina	Cinoxacina	Cinoxacine	Cinoxacin	Cinoxacin
-Ciprofloxacin	FALSE	TRUE	TRUE	FALSE	Ciprofloxacin	Ciprofloxacine	Ciprofloxacina			
+Ciprofloxacin	FALSE	TRUE	TRUE	FALSE	Ciprofloxacin	Ciprofloxacine	Ciprofloxacina	Ciprofloxacina	Ciprofloxacine	Ciprofloxacin	Ciprofloxacin
-Clarithromycin	FALSE	TRUE	TRUE	FALSE	Clarithromycin	Claritromycine	Claritromicina			
+Clarithromycin	FALSE	TRUE	TRUE	FALSE	Clarithromycin	Claritromycine	Claritromicina	Claritromicina	Clarithromycine	Claritromicina	Clarithromycin
-Clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	Clavulaanzuur	Ácido clavulánico			
+Clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	Clavulaanzuur	Ácido clavulánico	Acido clavulanico	Acide clavulanique	Ácido clavulânico	Clavulansyre
-clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	clavulaanzuur	ácido clavulánico			
+clavulanic acid	FALSE	TRUE	TRUE	FALSE	Clavulansäure	clavulaanzuur	ácido clavulánico	acido clavulanico	acide clavulanique	ácido clavulânico	clavulansyre
-Clindamycin	FALSE	TRUE	TRUE	FALSE	Clindamycin	Clindamycine	Clindamicina			
+Clindamycin	FALSE	TRUE	TRUE	FALSE	Clindamycin	Clindamycine	Clindamicina	Clindamicina	Clindamycine	Clindamicina	Clindamycin
-Clometocillin	FALSE	TRUE	TRUE	FALSE	Clometocillin	Clometocilline	Clometocilina			
+Clometocillin	FALSE	TRUE	TRUE	FALSE	Clometocillin	Clometocilline	Clometocilina	Clometocillina	Clométocilline	Clometocillin	Clometocillin
-Clotrimazole	FALSE	TRUE	TRUE	FALSE	Clotrimazol	Clotrimazol	Clotrimazol			
+Clotrimazole	FALSE	TRUE	TRUE	FALSE	Clotrimazol	Clotrimazol	Clotrimazol	Clotrimazolo	Clotrimazole	Clotrimazole	Clotrimazol
-Cloxacillin	FALSE	TRUE	TRUE	FALSE	Cloxacillin	Cloxacilline	Cloxacilina			
+Cloxacillin	FALSE	TRUE	TRUE	FALSE	Cloxacillin	Cloxacilline	Cloxacilina	Cloxacillina	Cloxacilline	Cloxacillin	Cloxacillin
-Colistin	FALSE	TRUE	TRUE	FALSE	Colistin	Colistine	Colistina			
+Colistin	FALSE	TRUE	TRUE	FALSE	Colistin	Colistine	Colistina	Colistina	Colistine	Colistin	Colistin
-Dapsone	FALSE	TRUE	TRUE	FALSE	Dapson	Dapson	Dapsona			
+Dapsone	FALSE	TRUE	TRUE	FALSE	Dapson	Dapson	Dapsona	Dapsone	Dapsone	Dapsone	Dapson
-Daptomycin	FALSE	TRUE	TRUE	FALSE	Daptomycin	Daptomycine	Daptomicina			
+Daptomycin	FALSE	TRUE	TRUE	FALSE	Daptomycin	Daptomycine	Daptomicina	Daptomicina	Daptomycine	Daptomicina	Daptomycin
-Dibekacin	FALSE	TRUE	TRUE	FALSE	Dibekacin	Dibekacine	Dibekacina			
+Dibekacin	FALSE	TRUE	TRUE	FALSE	Dibekacin	Dibekacine	Dibekacina	Dibekacin	Dibekacine	Dibekacin	Dibekacin
-Dicloxacillin	FALSE	TRUE	TRUE	FALSE	Dicloxacillin	Dicloxacilline	Dicloxacilina			
+Dicloxacillin	FALSE	TRUE	TRUE	FALSE	Dicloxacillin	Dicloxacilline	Dicloxacilina	Dicloxacillina	Dicloxacilline	Dicloxacilina	Dicloxacillin
-Dirithromycin	FALSE	TRUE	TRUE	FALSE	Dirithromycin	Diritromycine	Diritromicina			
+Dirithromycin	FALSE	TRUE	TRUE	FALSE	Dirithromycin	Diritromycine	Diritromicina	Diritromicina	Dirithromycine	Diritromicina	Dirithromycin
-Econazole	FALSE	TRUE	TRUE	FALSE	Econazol	Econazol	Econazol			
+Econazole	FALSE	TRUE	TRUE	FALSE	Econazol	Econazol	Econazol	Econazolo	Econazole	Econazole	Econazol
-Enoxacin	FALSE	TRUE	TRUE	FALSE	Enoxacin	Enoxacine	Enoxacina			
+Enoxacin	FALSE	TRUE	TRUE	FALSE	Enoxacin	Enoxacine	Enoxacina	Enoxacina	Enoxacine	Enoxacin	Enoxacin
-Epicillin	FALSE	TRUE	TRUE	FALSE	Epicillin	Epicilline	Epicilina			
+Epicillin	FALSE	TRUE	TRUE	FALSE	Epicillin	Epicilline	Epicilina	Epicillina	Epicilline	Epicilina	Epicillin
-Erythromycin	FALSE	TRUE	TRUE	FALSE	Erythromycin	Erytromycine	Eritromicina			
+Erythromycin	FALSE	TRUE	TRUE	FALSE	Erythromycin	Erytromycine	Eritromicina	Eritromicina	Erythromycine	Eritromicina	Erythromycin
-Ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	Ethambutol/Isoniazid	Ethambutol/isoniazide	Etambutol/isoniazida			
+Ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	Ethambutol/Isoniazid	Ethambutol/isoniazide	Etambutol/isoniazida	Etambutolo/isoniazide	Ethambutol/isoniazide	Ethambutol/isoniazid	Ethambutol/isoniazid
-Fleroxacin	FALSE	TRUE	TRUE	FALSE	Fleroxacin	Fleroxacine	Fleroxacina			
+Fleroxacin	FALSE	TRUE	TRUE	FALSE	Fleroxacin	Fleroxacine	Fleroxacina	Fleroxacina	Fléroxacine	Fleroxacina	Fleroxacin
-Flucloxacillin	FALSE	TRUE	TRUE	FALSE	Flucloxacillin	Flucloxacilline	Flucloxacilina			
+Flucloxacillin	FALSE	TRUE	TRUE	FALSE	Flucloxacillin	Flucloxacilline	Flucloxacilina	Flucloxacillina	Flucloxacilline	Flucloxacillin	Flucloxacillin
-Fluconazole	FALSE	TRUE	TRUE	FALSE	Fluconazol	Fluconazol	Fluconazol			
+Fluconazole	FALSE	TRUE	TRUE	FALSE	Fluconazol	Fluconazol	Fluconazol	Fluconazolo	Fluconazole	Fluconazole	Fluconazol
-Flucytosine	FALSE	TRUE	TRUE	FALSE	Flucytosin	Fluorocytosine	Flucitosina			
+Flucytosine	FALSE	TRUE	TRUE	FALSE	Flucytosin	Fluorocytosine	Flucitosina	Flucytosine	Flucytosine	Flucytosine	Flucytosin
-Flurithromycin	FALSE	TRUE	TRUE	FALSE	Flurithromycin	Fluritromycine	Fluritromicina			
+Flurithromycin	FALSE	TRUE	TRUE	FALSE	Flurithromycin	Fluritromycine	Fluritromicina	Fluritromicina	Flurithromycine	Fluritromicina	Flurithromycin
-Fosfomycin	FALSE	TRUE	TRUE	FALSE	Fosfomycin	Fosfomycine	Fosfomicina			
+Fosfomycin	FALSE	TRUE	TRUE	FALSE	Fosfomycin	Fosfomycine	Fosfomicina	Fosfomicina	Fosfomycine	Fosfomycin	Fosfomycin
-Fusidic acid	FALSE	TRUE	TRUE	FALSE	Fusidinsäure	Fusidinezuur	Ácido fusídico			
+Fusidic acid	FALSE	TRUE	TRUE	FALSE	Fusidinsäure	Fusidinezuur	Ácido fusídico	Acido fusidico	Acide fusidique	Ácido fusídico	Fusidinsyre
-Gatifloxacin	FALSE	TRUE	TRUE	FALSE	Gatifloxacin	Gatifloxacine	Gatifloxacina			
+Gatifloxacin	FALSE	TRUE	TRUE	FALSE	Gatifloxacin	Gatifloxacine	Gatifloxacina	Gatifloxacina	Gatifloxacine	Gatifloxacin	Gatifloxacin
-Gemifloxacin	FALSE	TRUE	TRUE	FALSE	Gemifloxacin	Gemifloxacine	Gemifloxacina			
+Gemifloxacin	FALSE	TRUE	TRUE	FALSE	Gemifloxacin	Gemifloxacine	Gemifloxacina	Gemifloxacina	Gemifloxacine	Gemifloxacin	Gemifloxacin
-Gentamicin	FALSE	TRUE	TRUE	FALSE	Gentamicin	Gentamicine	Gentamicina			
+Gentamicin	FALSE	TRUE	TRUE	FALSE	Gentamicin	Gentamicine	Gentamicina	Gentamicina	Gentamicine	Gentamicina	Gentamicin
-Grepafloxacin	FALSE	TRUE	TRUE	FALSE	Grepafloxacin	Grepafloxacine	Grepafloxacina			
+Grepafloxacin	FALSE	TRUE	TRUE	FALSE	Grepafloxacin	Grepafloxacine	Grepafloxacina	Grepafloxacina	Grepafloxacine	Grepafloxacin	Grepafloxacin
-Hachimycin	FALSE	TRUE	TRUE	FALSE	Hachimycin	Hachimycine	Hachimycin			
+Hachimycin	FALSE	TRUE	TRUE	FALSE	Hachimycin	Hachimycine	Hachimycin	Hachimycin	Hachimycine	Hachimycin	Hachimycin
-Hetacillin	FALSE	TRUE	TRUE	FALSE	Hetacillin	Hetacilline	Hetacilina			
+Hetacillin	FALSE	TRUE	TRUE	FALSE	Hetacillin	Hetacilline	Hetacilina	Hetacillin	Hétacilline	Hetacillin	Hetacillin
-Imipenem/cilastatin	FALSE	TRUE	TRUE	FALSE	Imipenem/Cilastatin	Imipenem/enzymremmer	Imipenem/cilastatina			
+Imipenem/cilastatin	FALSE	TRUE	TRUE	FALSE	Imipenem/Cilastatin	Imipenem/enzymremmer	Imipenem/cilastatina	Imipenem/cilastatina	Imipénème/cilastatine	Imipenem/coteltelatina	Imipenem/cilastatin
-Inosine pranobex	FALSE	TRUE	TRUE	FALSE	Inosin-Pranobex	Inosiplex	Inosina pranobex			
+Inosine pranobex	FALSE	TRUE	TRUE	FALSE	Inosin-Pranobex	Inosiplex	Inosina pranobex	Inosina pranobex	Inosine pranobex	Pranobex inosine	Inosin pranobex
-Isepamicin	FALSE	TRUE	TRUE	FALSE	Isepamicin	Isepamicine	Isepamicina			
+Isepamicin	FALSE	TRUE	TRUE	FALSE	Isepamicin	Isepamicine	Isepamicina	Isepamicina	Isepamicine	Isepamicina	Isepamicin
-Isoconazole	FALSE	TRUE	TRUE	FALSE	Isoconazol	Isoconazol	Isoconazol			
+Isoconazole	FALSE	TRUE	TRUE	FALSE	Isoconazol	Isoconazol	Isoconazol	Isoconazolo	Isoconazole	Isoconazole	Isoconazol
-Isoniazid	FALSE	TRUE	TRUE	FALSE	Isoniazid	Isoniazide	Isoniazida			
+Isoniazid	FALSE	TRUE	TRUE	FALSE	Isoniazid	Isoniazide	Isoniazida	Isoniazide	Isoniazide	Isoniazid	Isoniazid
-Itraconazole	FALSE	TRUE	TRUE	FALSE	Itraconazol	Itraconazol	Itraconazol			
+Itraconazole	FALSE	TRUE	TRUE	FALSE	Itraconazol	Itraconazol	Itraconazol	Itraconazolo	Itraconazole	Itraconazole	Itraconazol
-Josamycin	FALSE	TRUE	TRUE	FALSE	Josamycin	Josamycine	Josamicina			
+Josamycin	FALSE	TRUE	TRUE	FALSE	Josamycin	Josamycine	Josamicina	Josamicina	Josamycine	Josamycin	Josamycin
-Kanamycin	FALSE	TRUE	TRUE	FALSE	Kanamycin	Kanamycine	Kanamicina			
+Kanamycin	FALSE	TRUE	TRUE	FALSE	Kanamycin	Kanamycine	Kanamicina	Kanamicina	Kanamycine	Kanamycin	Kanamycin
-Ketoconazole	FALSE	TRUE	TRUE	FALSE	Ketoconazol	Ketoconazol	Ketoconazol			
+Ketoconazole	FALSE	TRUE	TRUE	FALSE	Ketoconazol	Ketoconazol	Ketoconazol	Ketoconazolo	Kétoconazole	Ketoconazole	Ketoconazol
-Levofloxacin	FALSE	TRUE	TRUE	FALSE	Levofloxacin	Levofloxacine	Levofloxacina			
+Levofloxacin	FALSE	TRUE	TRUE	FALSE	Levofloxacin	Levofloxacine	Levofloxacina	Levofloxacina	Lévofloxacine	Levofloxacin	Levofloxacin
-Lincomycin	FALSE	TRUE	TRUE	FALSE	Lincomycin	Lincomycine	Lincomicina			
+Lincomycin	FALSE	TRUE	TRUE	FALSE	Lincomycin	Lincomycine	Lincomicina	Lincomicina	Lincomycine	Lincomycin	Lincomycin
-Lomefloxacin	FALSE	TRUE	TRUE	FALSE	Lomefloxacin	Lomefloxacine	Lomefloxacina			
+Lomefloxacin	FALSE	TRUE	TRUE	FALSE	Lomefloxacin	Lomefloxacine	Lomefloxacina	Lomefloxacina	Loméfloxacine	Lomefloxacin	Lomefloxacin
-Lysozyme	FALSE	TRUE	TRUE	FALSE	Lysozym	Lysozym	Lisozima			
+Lysozyme	FALSE	TRUE	TRUE	FALSE	Lysozym	Lysozym	Lisozima	Lisozima	Lysozyme	Lysozyme	Lysozym
-Mandelic acid	FALSE	TRUE	TRUE	FALSE	Mandelsäure	Amandelzuur	Ácido mandélico			
+Mandelic acid	FALSE	TRUE	TRUE	FALSE	Mandelsäure	Amandelzuur	Ácido mandélico	Acido mandelico	Acide mandélique	Ácido mandélico	Mandelinsyre
-Metampicillin	FALSE	TRUE	TRUE	FALSE	Metampicillin	Metampicilline	Metampicilina			
+Metampicillin	FALSE	TRUE	TRUE	FALSE	Metampicillin	Metampicilline	Metampicilina	Metampicillina	Métampicilline	Metampicilina	Metampicillin
-Meticillin	FALSE	TRUE	TRUE	FALSE	Meticillin	Meticilline	Meticilina			
+Meticillin	FALSE	TRUE	TRUE	FALSE	Meticillin	Meticilline	Meticilina	Meticillina	Méticilline	Meticillin	Meticillin
-Metisazone	FALSE	TRUE	TRUE	FALSE	Metisazon	Metisazon	Metisazona			
+Metisazone	FALSE	TRUE	TRUE	FALSE	Metisazon	Metisazon	Metisazona	Metisazone	Métisazone	Metisazone	Metisazon
-Metronidazole	FALSE	TRUE	TRUE	FALSE	Metronidazol	Metronidazol	Metronidazol			
+Metronidazole	FALSE	TRUE	TRUE	FALSE	Metronidazol	Metronidazol	Metronidazol	Metronidazolo	Métronidazole	Metronidazol	Metronidazol
-Mezlocillin	FALSE	TRUE	TRUE	FALSE	Mezlocillin	Mezlocilline	Mezlocilina			
+Mezlocillin	FALSE	TRUE	TRUE	FALSE	Mezlocillin	Mezlocilline	Mezlocilina	Mezlocillina	Mezlocilline	Mezlocillin	Mezlocillin
-Micafungin	FALSE	TRUE	TRUE	FALSE	Micafungin	Micafungine	Micafungina			
+Micafungin	FALSE	TRUE	TRUE	FALSE	Micafungin	Micafungine	Micafungina	Micafungin	Micafungine	Micafungin	Micafungin
-Miconazole	FALSE	TRUE	TRUE	FALSE	Miconazol	Miconazol	Miconazol			
+Miconazole	FALSE	TRUE	TRUE	FALSE	Miconazol	Miconazol	Miconazol	Miconazolo	Miconazole	Miconazole	Miconazol
-Midecamycin	FALSE	TRUE	TRUE	FALSE	Midecamycin	Midecamycine	Midecamicina			
+Midecamycin	FALSE	TRUE	TRUE	FALSE	Midecamycin	Midecamycine	Midecamicina	Midecamicina	Midecamycine	Midecamycin	Midecamycin
-Miocamycin	FALSE	TRUE	TRUE	FALSE	Miocamycin	Miocamycine	Miocamycin			
+Miocamycin	FALSE	TRUE	TRUE	FALSE	Miocamycin	Miocamycine	Miocamycin	Miocamicina	Miocamycine	Miocamicina	Miocamycin
-Moxifloxacin	FALSE	TRUE	TRUE	FALSE	Moxifloxacin	Moxifloxacine	Moxifloxacina			
+Moxifloxacin	FALSE	TRUE	TRUE	FALSE	Moxifloxacin	Moxifloxacine	Moxifloxacina	Moxifloxacin	Moxifloxacine	Moxifloxacina	Moxifloxacin
-Mupirocin	FALSE	TRUE	TRUE	FALSE	Mupirocin	Mupirocine	Mupirocina			
+Mupirocin	FALSE	TRUE	TRUE	FALSE	Mupirocin	Mupirocine	Mupirocina	Mupirocina	Mupirocine	Mupirocina	Mupirocin
-Nalidixic acid	FALSE	TRUE	TRUE	FALSE	Nalidixinsäure	Nalidixinezuur	Ácido nalidíxico			
+Nalidixic acid	FALSE	TRUE	TRUE	FALSE	Nalidixinsäure	Nalidixinezuur	Ácido nalidíxico	Acido nalidixico	Acide nalidixique	Ácido nalidíxico	Nalidixinsyre
-Neomycin	FALSE	TRUE	TRUE	FALSE	Neomycin	Neomycine	Neomicina			
+Neomycin	FALSE	TRUE	TRUE	FALSE	Neomycin	Neomycine	Neomicina	Neomicina	Néomycine	Neomicina	Neomycin
-Netilmicin	FALSE	TRUE	TRUE	FALSE	Netilmicin	Netilmicine	Netilmicina			
+Netilmicin	FALSE	TRUE	TRUE	FALSE	Netilmicin	Netilmicine	Netilmicina	Netilmicin	Netilmicine	Netilmicin	Netilmicin
-Nitrofurantoin	FALSE	TRUE	TRUE	FALSE	Nitrofurantoin	Nitrofurantoine	Nitrofurantoína			
+Nitrofurantoin	FALSE	TRUE	TRUE	FALSE	Nitrofurantoin	Nitrofurantoine	Nitrofurantoína	Nitrofurantoina	Nitrofurantoïne	Nitrofurantoína	Nitrofurantoin
-Norfloxacin	FALSE	TRUE	TRUE	FALSE	Norfloxacin	Norfloxacine	Norfloxacina			
+Norfloxacin	FALSE	TRUE	TRUE	FALSE	Norfloxacin	Norfloxacine	Norfloxacina	Norfloxacina	Norfloxacine	Norfloxacin	Norfloxacin
-Novobiocin	FALSE	TRUE	TRUE	FALSE	Novobiocin	Novobiocine	Novobiocina			
+Novobiocin	FALSE	TRUE	TRUE	FALSE	Novobiocin	Novobiocine	Novobiocina	Novobiocin	Novobiocine	Novobiocin	Novobiocin
-Nystatin	FALSE	TRUE	TRUE	FALSE	Nystatin	Nystatine	Nistatina			
+Nystatin	FALSE	TRUE	TRUE	FALSE	Nystatin	Nystatine	Nistatina	Nystatin	Nystatine	Nystatin	Nystatin
-Ofloxacin	FALSE	TRUE	TRUE	FALSE	Ofloxacin	Ofloxacine	Ofloxacina			
+Ofloxacin	FALSE	TRUE	TRUE	FALSE	Ofloxacin	Ofloxacine	Ofloxacina	Ofloxacin	Ofloxacine	Ofloxacin	Ofloxacin
-Oleandomycin	FALSE	TRUE	TRUE	FALSE	Oleandomycin	Oleandomycine	Oleandomicina			
+Oleandomycin	FALSE	TRUE	TRUE	FALSE	Oleandomycin	Oleandomycine	Oleandomicina	Oleandomicina	Oleandomycine	Oleandomicina	Oleandomycin
-Ornidazole	FALSE	TRUE	TRUE	FALSE	Ornidazol	Ornidazol	Ornidazol			
+Ornidazole	FALSE	TRUE	TRUE	FALSE	Ornidazol	Ornidazol	Ornidazol	Ornidazolo	Ornidazole	Ornidazole	Ornidazol
-Oxacillin	FALSE	TRUE	TRUE	FALSE	Oxacillin	Oxacilline	Oxacilina			
+Oxacillin	FALSE	TRUE	TRUE	FALSE	Oxacillin	Oxacilline	Oxacilina	Oxacillina	Oxacilline	Oxacillin	Oxacillin
-Oxolinic acid	FALSE	TRUE	TRUE	FALSE	Oxolinsäure	Oxolinezuur	Ácido oxolínico			
+Oxolinic acid	FALSE	TRUE	TRUE	FALSE	Oxolinsäure	Oxolinezuur	Ácido oxolínico	Acido ossolinico	Acide oxolinique	Ácido oxolínico	Oxolinsyre
-Oxytetracycline	FALSE	TRUE	TRUE	FALSE	Oxytetracyclin	Oxytetracycline	Oxitetraciclina			
+Oxytetracycline	FALSE	TRUE	TRUE	FALSE	Oxytetracyclin	Oxytetracycline	Oxitetraciclina	Ossitetraciclina	Oxytétracycline	Oxitetraciclina	Oxytetracyclin
-Pazufloxacin	FALSE	TRUE	TRUE	FALSE	Pazufloxacin	Pazufloxacine	Pazufloxacina			
+Pazufloxacin	FALSE	TRUE	TRUE	FALSE	Pazufloxacin	Pazufloxacine	Pazufloxacina	Pazufloxacin	Pazufloxacine	Pazufloxacin	Pazufloxacin
-Pefloxacin	FALSE	TRUE	TRUE	FALSE	Pefloxacin	Pefloxacine	Pefloxacina			
+Pefloxacin	FALSE	TRUE	TRUE	FALSE	Pefloxacin	Pefloxacine	Pefloxacina	Pefloxacina	Péfloxacine	Pefloxacin	Pefloxacin
-Penamecillin	FALSE	TRUE	TRUE	FALSE	Penamecillin	Penamecilline	Penamecilina			
+Penamecillin	FALSE	TRUE	TRUE	FALSE	Penamecillin	Penamecilline	Penamecilina	Penamecillina	Pénamécilline	Penamecilina	Penamecillin
-Penicillin	FALSE	TRUE	TRUE	FALSE	Penicillin	Penicilline	Penicilina			
+Penicillin	FALSE	TRUE	TRUE	FALSE	Penicillin	Penicilline	Penicilina	Penicillina	Pénicilline	Penicilina	Penicillin
-Pheneticillin	FALSE	TRUE	TRUE	FALSE	Pheneticillin	Feneticilline	Feneticilina			
+Pheneticillin	FALSE	TRUE	TRUE	FALSE	Pheneticillin	Feneticilline	Feneticilina	Feneticillina	Phénéticilline	Pheneticillin	Pheneticillin
-Phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Phenoxymethylpenicillin	Fenoxymethylpenicilline	Fenoximetilpenicilina			
+Phenoxymethylpenicillin	FALSE	TRUE	TRUE	FALSE	Phenoxymethylpenicillin	Fenoxymethylpenicilline	Fenoximetilpenicilina	Fenossimetilpenicillina	Phénoxyméthylpénicilline	Fenoximetilpenicilina	Phenoxymethylpenicillin
-Pipemidic acid	FALSE	TRUE	TRUE	FALSE	Pipemidinsäure	Pipemidinezuur	Ácido pipemídico			
+Pipemidic acid	FALSE	TRUE	TRUE	FALSE	Pipemidinsäure	Pipemidinezuur	Ácido pipemídico	Acido pipemidico	Acide pipémidique	Ácido pipemídico	Pipemidinsyre
-Piperacillin	FALSE	TRUE	TRUE	FALSE	Piperacillin	Piperacilline	Piperacilina			
+Piperacillin	FALSE	TRUE	TRUE	FALSE	Piperacillin	Piperacilline	Piperacilina	Piperacillina	Pipéracilline	Piperacilina	Piperacillin
-Piperacillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Piperacillin/Beta-Lactamase-Hemmer	Piperacilline/enzymremmer	Piperacilina/inhib. de la betalactamasa			
+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
-Piromidic acid	FALSE	TRUE	TRUE	FALSE	Piromidinsäure	Piromidinezuur	Ácido piromídico			
+Piromidic acid	FALSE	TRUE	TRUE	FALSE	Piromidinsäure	Piromidinezuur	Ácido piromídico	Acido piromidico	Acide piromidique	Ácido piromídico	Piromidinsyre
-Pivampicillin	FALSE	TRUE	TRUE	FALSE	Pivampicillin	Pivampicilline	Pivampicilina			
+Pivampicillin	FALSE	TRUE	TRUE	FALSE	Pivampicillin	Pivampicilline	Pivampicilina	Pivampicillina	Pivampicilline	Pivampicilina	Pivampicillin
-Polymyxin B	FALSE	TRUE	TRUE	FALSE	Polymyxin B	Polymyxine B	Polimixina B			
+Polymyxin B	FALSE	TRUE	TRUE	FALSE	Polymyxin B	Polymyxine B	Polimixina B	Polimixina B	Polymyxine B	Polimixina B	Polymyxin B
-Posaconazole	FALSE	TRUE	TRUE	FALSE	Posaconazol	Posaconazol	Posaconazol			
+Posaconazole	FALSE	TRUE	TRUE	FALSE	Posaconazol	Posaconazol	Posaconazol	Posaconazolo	Posaconazole	Posaconazole	Posaconazol
-Pristinamycin	FALSE	TRUE	TRUE	FALSE	Pristinamycin	Pristinamycine	Pristinamicina			
+Pristinamycin	FALSE	TRUE	TRUE	FALSE	Pristinamycin	Pristinamycine	Pristinamicina	Pristinamicina	Pristinamycine	Pristinamicina	Pristinamycin
-Procaine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Procain-Benzylpenicillin	Benzylpenicillineprocaine	Bencilpenicilina procaína			
+Procaine benzylpenicillin	FALSE	TRUE	TRUE	FALSE	Procain-Benzylpenicillin	Benzylpenicillineprocaine	Bencilpenicilina procaína	Procaina benzilpenicillina	Procaïne benzylpénicilline	Procaína benzilpenicilina	Prokainbenzylpenicillin
-Propicillin	FALSE	TRUE	TRUE	FALSE	Propicillin	Propicilline	Propicilina			
+Propicillin	FALSE	TRUE	TRUE	FALSE	Propicillin	Propicilline	Propicilina	Propicillina	Propicilline	Propicilina	Propicillin
-Prulifloxacin	FALSE	TRUE	TRUE	FALSE	Prulifloxacin	Prulifloxacine	Prulifloxacina			
+Prulifloxacin	FALSE	TRUE	TRUE	FALSE	Prulifloxacin	Prulifloxacine	Prulifloxacina	Prulifloxacina	Prulifloxacine	Prulifloxacina	Prulifloxacin
-Quinupristin/dalfopristin	FALSE	TRUE	TRUE	FALSE	Quinupristin/Dalfopristin	Quinupristine/dalfopristine	Quinupristina/dalfopristina			
+Quinupristin/dalfopristin	FALSE	TRUE	TRUE	FALSE	Quinupristin/Dalfopristin	Quinupristine/dalfopristine	Quinupristina/dalfopristina	Quinupristina/dalfopristina	Quinupristine/dalfopristine	Quinupristin/dalfopristin	Quinupristin/dalfopristin
-Ribostamycin	FALSE	TRUE	TRUE	FALSE	Ribostamycin	Ribostamycine	Ribostamicina			
+Ribostamycin	FALSE	TRUE	TRUE	FALSE	Ribostamycin	Ribostamycine	Ribostamicina	Ribostamicina	Ribostamycine	Ribostamicina	Ribostamycin
-Rifabutin	FALSE	TRUE	TRUE	FALSE	Rifabutin	Rifabutine	Rifabutina			
+Rifabutin	FALSE	TRUE	TRUE	FALSE	Rifabutin	Rifabutine	Rifabutina	Rifabutina	Rifabutine	Rifabutin	Rifabutin
-Rifampicin	FALSE	TRUE	TRUE	FALSE	Rifampicin	Rifampicine	Rifampicina			
+Rifampicin	FALSE	TRUE	TRUE	FALSE	Rifampicin	Rifampicine	Rifampicina	Rifampicina	Rifampicine	Rifampicina	Rifampicin
-Rifampicin/pyrazinamide/ethambutol/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Pyrazinamid/Ethambutol/Isoniazid	Rifampicine/pyrazinamide/ethambutol/isoniazide	Rifampicina/pirazinamida/etambutol/isoniazida			
+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/pyrazinamide/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Pyrazinamid/Isoniazid	Rifampicine/pyrazinamide/isoniazide	Rifampicina/pirazinamida/isoniazida			
+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/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Isoniazid	Rifampicine/isoniazide	Rifampicina/isoniazida			
+Rifampicin/isoniazid	FALSE	TRUE	TRUE	FALSE	Rifampicin/Isoniazid	Rifampicine/isoniazide	Rifampicina/isoniazida	Rifampicina/isoniazide	Rifampicine/isoniazide	Rifampicina/isoniazida	Rifampicin/isoniazid
-Rifamycin	FALSE	TRUE	TRUE	FALSE	Rifamycin	Rifamycine	Rifamicina			
+Rifamycin	FALSE	TRUE	TRUE	FALSE	Rifamycin	Rifamycine	Rifamicina	Rifamicina	Rifamycine	Rifamycin	Rifamycin
-Rifaximin	FALSE	TRUE	TRUE	FALSE	Rifaximin	Rifaximine	Rifaximina			
+Rifaximin	FALSE	TRUE	TRUE	FALSE	Rifaximin	Rifaximine	Rifaximina	Rifaximina	Rifaximine	Rifaximin	Rifaximin
-Rokitamycin	FALSE	TRUE	TRUE	FALSE	Rokitamycin	Rokitamycine	Rokitamicina			
+Rokitamycin	FALSE	TRUE	TRUE	FALSE	Rokitamycin	Rokitamycine	Rokitamicina	Rokitamicina	Rokitamycine	Rokitamycin	Rokitamycin
-Rosoxacin	FALSE	TRUE	TRUE	FALSE	Rosoxacin	Rosoxacine	Rosoxacina			
+Rosoxacin	FALSE	TRUE	TRUE	FALSE	Rosoxacin	Rosoxacine	Rosoxacina	Rosoxacina	Rosoxacine	Rosoxacina	Rosoxacin
-Roxithromycin	FALSE	TRUE	TRUE	FALSE	Roxithromycin	Roxitromycine	Roxitromicina			
+Roxithromycin	FALSE	TRUE	TRUE	FALSE	Roxithromycin	Roxitromycine	Roxitromicina	Roxitromicina	Roxithromycine	Roxitromicina	Roxithromycin
-Rufloxacin	FALSE	TRUE	TRUE	FALSE	Rufloxacin	Rufloxacine	Rufloxacina			
+Rufloxacin	FALSE	TRUE	TRUE	FALSE	Rufloxacin	Rufloxacine	Rufloxacina	Rufloxacina	Rufloxacine	Rufloxacin	Rufloxacin
-Sisomicin	FALSE	TRUE	TRUE	FALSE	Sisomicin	Sisomicine	Sisomicina			
+Sisomicin	FALSE	TRUE	TRUE	FALSE	Sisomicin	Sisomicine	Sisomicina	Sisomicina	Sisomicine	Sisomicina	Sisomicin
-Sodium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Natrium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de sodio			
+Sodium aminosalicylate	FALSE	TRUE	TRUE	FALSE	Natrium-Aminosalicylat	Aminosalicylzuur	Aminosalicilato de sodio	Sodio aminosalicilato	Aminosalicylate de sodium	Aminosalicilato de sódio	Natriumaminosalicylat
-Sparfloxacin	FALSE	TRUE	TRUE	FALSE	Sparfloxacin	Sparfloxacine	Esparfloxacina			
+Sparfloxacin	FALSE	TRUE	TRUE	FALSE	Sparfloxacin	Sparfloxacine	Esparfloxacina	Sparfloxacina	Sparfloxacine	Sparfloxacin	Sparfloxacin
-Spectinomycin	FALSE	TRUE	TRUE	FALSE	Spectinomycin	Spectinomycine	Espectinomicina			
+Spectinomycin	FALSE	TRUE	TRUE	FALSE	Spectinomycin	Spectinomycine	Espectinomicina	Spectinomycin	Spectinomycine	Spectinomycin	Spectinomycin
-Spiramycin	FALSE	TRUE	TRUE	FALSE	Spiramycin	Spiramycine	Espiramicina			
+Spiramycin	FALSE	TRUE	TRUE	FALSE	Spiramycin	Spiramycine	Espiramicina	Spiramicina	Spiramycine	Spiramycin	Spiramycin
-Spiramycin/metronidazole	FALSE	TRUE	TRUE	FALSE	Spiramycin/Metronidazol	Spiramycine/metronidazol	Espiramicina/metronidazol			
+Spiramycin/metronidazole	FALSE	TRUE	TRUE	FALSE	Spiramycin/Metronidazol	Spiramycine/metronidazol	Espiramicina/metronidazol	Spiramicina/metronidazolo	Spiramycine/métronidazole	Spiramycin/metronidazol	Spiramycin/metronidazol
-Staphylococcus immunoglobulin	FALSE	TRUE	TRUE	FALSE	Staphylococcus-Immunoglobulin	Stafylokokkenimmunoglobuline	Inmunoglobulina estafilocócica			
+Staphylococcus immunoglobulin	FALSE	TRUE	TRUE	FALSE	Staphylococcus-Immunoglobulin	Stafylokokkenimmunoglobuline	Inmunoglobulina estafilocócica	Immunoglobulina per stafilococco	Immunoglobuline staphylococcique	Imunoglobulina de Staphylococcus	Stafylokok-immunglobulin
-Streptoduocin	FALSE	TRUE	TRUE	FALSE	Streptoduocin	Streptoduocine	Estreptoduocina			
+Streptoduocin	FALSE	TRUE	TRUE	FALSE	Streptoduocin	Streptoduocine	Estreptoduocina	Streptoduocin	Streptoduocine	Estreptoduocina	Streptoduocin
-Streptomycin	FALSE	TRUE	TRUE	FALSE	Streptomycin	Streptomycine	Estreptomicina			
+Streptomycin	FALSE	TRUE	TRUE	FALSE	Streptomycin	Streptomycine	Estreptomicina	Streptomicina	Streptomycine	Streptomycin	Streptomycin
-Streptomycin/isoniazid	FALSE	TRUE	TRUE	FALSE	Streptomycin/Isoniazid	Streptomycine/isoniazide	Estreptomicina/isoniazida			
+Streptomycin/isoniazid	FALSE	TRUE	TRUE	FALSE	Streptomycin/Isoniazid	Streptomycine/isoniazide	Estreptomicina/isoniazida	Streptomicina/isoniazide	Streptomycine/isoniazide	Streptomicina/isoniazida	Streptomycin/isoniazid
-Sulbenicillin	FALSE	TRUE	TRUE	FALSE	Sulbenicillin	Sulbenicilline	Sulbenicilina			
+Sulbenicillin	FALSE	TRUE	TRUE	FALSE	Sulbenicillin	Sulbenicilline	Sulbenicilina	Sulbenicillina	Sulbenicilline	Sulbenicilina	Sulbenicillin
-Sulfadiazine/tetroxoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Tetroxoprim	Sulfadiazine/tetroxoprim	Sulfadiazina/tetroxoprima			
+Sulfadiazine/tetroxoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Tetroxoprim	Sulfadiazine/tetroxoprim	Sulfadiazina/tetroxoprim	Sulfadiazina/tetroxoprim	Sulfadiazine/tetroxoprime	Sulfadiazina/tetroxoprim	Sulfadiazin/tetroxoprim
-Sulfadiazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Trimethoprim	Sulfadiazine/trimethoprim	Sulfadiazina/trimetoprima			
+Sulfadiazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadiazin/Trimethoprim	Sulfadiazine/trimethoprim	Sulfadiazina/trimetoprima	Sulfadiazina/trimetoprim	Sulfadiazine/triméthoprime	Sulfadiazina/trimethoprim	Sulfadiazin/trimethoprim
-Sulfadimidine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadimidin/Trimethoprim	Sulfadimidine/trimethoprim	Sulfadimidina/trimetoprima			
+Sulfadimidine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfadimidin/Trimethoprim	Sulfadimidine/trimethoprim	Sulfadimidina/trimetoprima	Sulfadimidina/trimetoprim	Sulfadimidine/triméthoprime	Sulfadimidina/trimethoprim	Sulfadimidin/trimethoprim
-Sulfafurazole	FALSE	TRUE	TRUE	FALSE	Sulfafurazol	Sulfafurazol	Sulfafurazol			
+Sulfafurazole	FALSE	TRUE	TRUE	FALSE	Sulfafurazol	Sulfafurazol	Sulfafurazol	Sulfafurazolo	Sulfafurazole	Sulfafurazole	Sulfafurazol
-Sulfaisodimidine	FALSE	TRUE	TRUE	FALSE	Sulfaisodimidin	Sulfisomidine	Sulfaisodimidina			
+Sulfaisodimidine	FALSE	TRUE	TRUE	FALSE	Sulfaisodimidin	Sulfisomidine	Sulfaisodimidina	Sulfaisodimidina	Sulfaisodimidine	Sulfaisodimidina	Sulfaisodimidin
-Sulfalene	FALSE	TRUE	TRUE	FALSE	Sulfalene	Sulfaleen	Sulfaleno			
+Sulfalene	FALSE	TRUE	TRUE	FALSE	Sulfalene	Sulfaleen	Sulfaleno	Sulfalene	Sulfalène	Sulfaleno	Sulfalen
-Sulfamazone	FALSE	TRUE	TRUE	FALSE	Sulfamazon	Sulfamazon	Sulfamazona			
+Sulfamazone	FALSE	TRUE	TRUE	FALSE	Sulfamazon	Sulfamazon	Sulfamazona	Sulfamazone	Sulfamazone	Sulfamazona	Sulfamazon
-Sulfamerazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamerazin/Trimethoprim	Sulfamerazine/trimethoprim	Sulfamerazina/trimetoprima			
+Sulfamerazine/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamerazin/Trimethoprim	Sulfamerazine/trimethoprim	Sulfamerazina/trimetoprima	Sulfamerazina/trimetoprim	Sulfamérazine/triméthoprime	Sulfamerazina/trimethoprim	Sulfamerazin/trimethoprim
-Sulfamethizole	FALSE	TRUE	TRUE	FALSE	Sulfamethizol	Sulfamethizol	Sulfametozol			
+Sulfamethizole	FALSE	TRUE	TRUE	FALSE	Sulfamethizol	Sulfamethizol	Sulfametozol	Sulfamethizolo	Sulfaméthizole	Sulfametizole	Sulfamethizol
-Sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol	Sulfamethoxazol	Sulfametoxazol			
+Sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol	Sulfamethoxazol	Sulfametoxazol	Sulfametossazolo	Sulfaméthoxazole	Sulfamethoxazole	Sulfamethoxazol
-Sulfamethoxazole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol/Trimethoprim	Sulfamethoxazol/trimethoprim	Sulfametoxazol/trimetoprima			
+Sulfamethoxazole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamethoxazol/Trimethoprim	Sulfamethoxazol/trimethoprim	Sulfametoxazol/trimetoprima	Sulfametossazolo/trimetoprim	Sulfaméthoxazole/triméthoprime	Sulfametoxazol/trimethoprim	Sulfamethoxazol/trimethoprim
-Sulfametoxydiazine	FALSE	TRUE	TRUE	FALSE	Sulfametoxydiazin	Sulfamethoxydiazine	Sulfametoxidiazina			
+Sulfametoxydiazine	FALSE	TRUE	TRUE	FALSE	Sulfametoxydiazin	Sulfamethoxydiazine	Sulfametoxidiazina	Sulfametoxydiazine	Sulfamétoxydiazine	Sulfametoxidiazina	Sulfametoxydiazin
-Sulfametrole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfametrole/Trimethoprim	Sulfametrol/trimethoprim	Sulfametrole/trimethoprim			
+Sulfametrole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfametrole/Trimethoprim	Sulfametrol/trimethoprim	Sulfametrol/trimetoprima	Sulfametrole/trimetoprim	Sulfamétrole/triméthoprime	Sulfametrole/trimethoprim	Sulfametrol/trimethoprim
-Sulfamoxole	FALSE	TRUE	TRUE	FALSE	Sulfamoxol	Sulfamoxol	Sulfamoxole			
+Sulfamoxole	FALSE	TRUE	TRUE	FALSE	Sulfamoxol	Sulfamoxol	Sulfamoxole	Sulfamoxolo	Sulfamoxole	Sulfamoxole	Sulfamoxol
-Sulfamoxole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamoxol/Trimethoprim	Sulfamoxol/trimethoprim	Sulfamoxol/trimetoprima			
+Sulfamoxole/trimethoprim	FALSE	TRUE	TRUE	FALSE	Sulfamoxol/Trimethoprim	Sulfamoxol/trimethoprim	Sulfamoxol/trimetoprima	Sulfamoxolo/trimetoprim	Sulfamoxole/triméthoprime	Sulfamoxole/trimethoprim	Sulfamoxol/trimethoprim
-Sulfaperin	FALSE	TRUE	TRUE	FALSE	Sulfaperin	Sulfaperine	Sulfaproxeno			
+Sulfaperin	FALSE	TRUE	TRUE	FALSE	Sulfaperin	Sulfaperine	Sulfametoxazol	Sulfaperin	Sulfapérine	Sulfaperin	Sulfaperin
-Sulfaphenazole	FALSE	TRUE	TRUE	FALSE	Sulfaphenazol	Sulfafenazol	Sulfafenazol			
+Sulfaphenazole	FALSE	TRUE	TRUE	FALSE	Sulfaphenazol	Sulfafenazol	Sulfafenazol	Sulfafenazolo	Sulfaphénazole	Sulfafenazol	Sulfaphenazol
-Sulfathiazole	FALSE	TRUE	TRUE	FALSE	Sulfathiazol	Sulfathiazol	Sulfatiazol			
+Sulfathiazole	FALSE	TRUE	TRUE	FALSE	Sulfathiazol	Sulfathiazol	Sulfatiazol	Sulfathiazole	Sulfathiazole	Sulfatazol	Sulfathiazol
-Sulfathiourea	FALSE	TRUE	TRUE	FALSE	Sulfathioharnstoff	Sulfathioureum	Sulfathiourea			
+Sulfathiourea	FALSE	TRUE	TRUE	FALSE	Sulfathioharnstoff	Sulfathioureum	Sulfathiourea	Sulfathiourea	Sulfathiourée	Sulfathiourea	Sulfathiourea
-Sultamicillin	FALSE	TRUE	TRUE	FALSE	Sultamicillin	Sultamicilline	Sultamicilina			
+Sultamicillin	FALSE	TRUE	TRUE	FALSE	Sultamicillin	Sultamicilline	Sultamicilina	Sultamicillina	Sultamicilline	Sultamicillin	Sultamicillin
-Talampicillin	FALSE	TRUE	TRUE	FALSE	Talampicillin	Talampicilline	Talampicilina			
+Talampicillin	FALSE	TRUE	TRUE	FALSE	Talampicillin	Talampicilline	Talampicilina	Talampicillina	Talampicilline	Talampicilina	Talampicillin
-Teicoplanin	FALSE	TRUE	TRUE	FALSE	Teicoplanin	Teicoplanine	Teicoplanina			
+Teicoplanin	FALSE	TRUE	TRUE	FALSE	Teicoplanin	Teicoplanine	Teicoplanina	Teicoplanina	Teicoplanine	Teicoplanin	Teicoplanin
-Telithromycin	FALSE	TRUE	TRUE	FALSE	Telithromycin	Telitromycine	Telitromicina			
+Telithromycin	FALSE	TRUE	TRUE	FALSE	Telithromycin	Telitromycine	Telitromicina	Telitromicina	Télithromycine	Telitromicina	Telithromycin
-Temafloxacin	FALSE	TRUE	TRUE	FALSE	Temafloxacin	Temafloxacine	Temafloxacina			
+Temafloxacin	FALSE	TRUE	TRUE	FALSE	Temafloxacin	Temafloxacine	Temafloxacina	Temafloxacina	Temafloxacine	Temafloxacin	Temafloxacin
-Temocillin	FALSE	TRUE	TRUE	FALSE	Temocillin	Temocilline	Temocilina			
+Temocillin	FALSE	TRUE	TRUE	FALSE	Temocillin	Temocilline	Temocilina	Temocillina	Temocillin	Temocillin	Temocillin
-Tenofovir disoproxil	FALSE	TRUE	TRUE	FALSE	Tenofovir Disoproxil	Tenofovir	Tenofovir disoproxil			
+Tenofovir disoproxil	FALSE	TRUE	TRUE	FALSE	Tenofovir Disoproxil	Tenofovir	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil	Tenofovir disoproxil
-Terizidone	FALSE	TRUE	TRUE	FALSE	Terizidon	Terizidon	Terizidona			
+Terizidone	FALSE	TRUE	TRUE	FALSE	Terizidon	Terizidon	Terizidona	Terizidone	Terizidone	Terizidone	Terizidon
-Thiamphenicol	FALSE	TRUE	TRUE	FALSE	Thiamphenicol	Thiamfenicol	Tiamfenicol			
+Thiamphenicol	FALSE	TRUE	TRUE	FALSE	Thiamphenicol	Thiamfenicol	Tiamfenicol	Tiamfenicolo	Thiamphénicol	Tiamfenicol	Thiamphenicol
-Thioacetazone/isoniazid	FALSE	TRUE	TRUE	FALSE	Thioacetazon/Isoniazid	Thioacetazon/isoniazide	Tioacetazona/isoniazida			
+Thioacetazone/isoniazid	FALSE	TRUE	TRUE	FALSE	Thioacetazon/Isoniazid	Thioacetazon/isoniazide	Tioacetazona/isoniazida	Tioacetazone/isoniazide	Thioacétazone/isoniazide	Thioacetazone/isoniazid	Thioacetazon/isoniazid
-Ticarcillin	FALSE	TRUE	TRUE	FALSE	Ticarcillin	Ticarcilline	Ticarcilina			
+Ticarcillin	FALSE	TRUE	TRUE	FALSE	Ticarcillin	Ticarcilline	Ticarcilina	Ticarcillina	Ticarcilline	Ticarcilina	Ticarcillin
-Ticarcillin/beta-lactamase inhibitor	FALSE	TRUE	TRUE	FALSE	Ticarcillin/Beta-Lactamase-Hemmer	Ticarcilline/enzymremmer	Ticarcilina/inhib. de la betalactamasa			
+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/clavulanic acid	FALSE	TRUE	TRUE	FALSE	Ticarcillin/Clavulansäure	Ticarcilline/clavulaanzuur	Ticarcilina/ácido clavulánico			
+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
-Tinidazole	FALSE	TRUE	TRUE	FALSE	Tinidazol	Tinidazol	Tinidazol			
+Tinidazole	FALSE	TRUE	TRUE	FALSE	Tinidazol	Tinidazol	Tinidazol	Tinidazolo	Tinidazole	Tinidazole	Tinidazol
-Tobramycin	FALSE	TRUE	TRUE	FALSE	Tobramycin	Tobramycine	Tobramicina			
+Tobramycin	FALSE	TRUE	TRUE	FALSE	Tobramycin	Tobramycine	Tobramicina	Tobramicina	Tobramycine	Tobramycin	Tobramycin
-Trimethoprim/sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Trimethoprim/Sulfamethoxazol	Cotrimoxazol	Trimetoprima/sulfametoxazol			
+Trimethoprim/sulfamethoxazole	FALSE	TRUE	TRUE	FALSE	Trimethoprim/Sulfamethoxazol	Cotrimoxazol	Trimetoprima/sulfametoxazol	Trimetoprim/sulfametossazolo	Triméthoprime/sulfaméthoxazole	Trimethoprim/sulfametoxazol	Trimethoprim/sulfamethoxazol
-Troleandomycin	FALSE	TRUE	TRUE	FALSE	Troleandomycin	Troleandomycine	Troleandomicina			
+Troleandomycin	FALSE	TRUE	TRUE	FALSE	Troleandomycin	Troleandomycine	Troleandomicina	Troleandomicina	Troleandomycine	Troleandomicina	Troleandomycin
-Trovafloxacin	FALSE	TRUE	TRUE	FALSE	Trovafloxacin	Trovafloxacine	Trovafloxacina			
+Trovafloxacin	FALSE	TRUE	TRUE	FALSE	Trovafloxacin	Trovafloxacine	Trovafloxacina	Trovafloxacin	Trovafloxacine	Trovafloxacin	Trovafloxacin
-Vancomycin	FALSE	TRUE	TRUE	FALSE	Vancomycin	Vancomycine	Vancomicina			
+Vancomycin	FALSE	TRUE	TRUE	FALSE	Vancomycin	Vancomycine	Vancomicina	Vancomicina	Vancomycine	Vancomycin	Vancomycin
-Voriconazole	FALSE	TRUE	TRUE	FALSE	Voriconazol	Voriconazol	Voriconazol			
+Voriconazole	FALSE	TRUE	TRUE	FALSE	Voriconazol	Voriconazol	Voriconazol	Voriconazolo	Voriconazole	Voriconazol	Voriconazol
-Aminoglycosides	FALSE	TRUE	TRUE	FALSE	Aminoglykoside	Aminoglycosiden	Aminoglucósidos			
+Aminoglycosides	FALSE	TRUE	TRUE	FALSE	Aminoglykoside	Aminoglycosiden	Aminoglucósidos	Aminoglicosidi	Aminoglycosides	Aminoglycosides	Aminoglykosider
-Amphenicols	FALSE	TRUE	TRUE	FALSE	Amphenicole	Amfenicolen	Anfenicoles			
+Amphenicols	FALSE	TRUE	TRUE	FALSE	Amphenicole	Amfenicolen	Anfenicoles	Amphenicols	Amphénicols	Anfenicóis	Amphenicoler
-Antifungals/antimycotics	FALSE	TRUE	TRUE	FALSE	Antimykotika/Antimykotika	Antifungica/antimycotica	Antifúngicos/antimicóticos			
+Antifungals/antimycotics	FALSE	TRUE	TRUE	FALSE	Antimykotika/Antimykotika	Antifungica/antimycotica	Antifúngicos/antimicóticos	Antifungini/antimicotici	Antifongiques/antimycotiques	Antifúngicos/antimicóticos	Antimykotika/antimykotika
-Antimycobacterials	FALSE	TRUE	TRUE	FALSE	Antimykobakterielle Mittel	Antimycobacteriele middelen	Antimicrobianos			
+Antimycobacterials	FALSE	TRUE	TRUE	FALSE	Antimykobakterielle Mittel	Antimycobacteriele middelen	Antimicrobianos	Antimicobatterici	Antimycobactériens	Antimycobacterials	Antimycobakterier
-Beta-lactams/penicillins	FALSE	TRUE	TRUE	FALSE	Beta-Lactame/Penicilline	Beta-lactams/penicillines	Beta-lactámicos/penicilinas			
+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
-Cephalosporins (1st gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (1. Gen.)	Cefalosporines (1e gen.)	Cefalosporinas (1er gen.)			
+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.)
-Cephalosporins (2nd gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (2. Gen.)	Cefalosporines (2e gen.)	Cefalosporinas (2do gen.)			
+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.)
-Cephalosporins (3rd gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (3. Gen.)	Cefalosporines (3e gen.)	Cefalosporinas (3er gen.)			
+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.)
-Cephalosporins (4th gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (4. Gen.)	Cefalosporines (4e gen.)	Cefalosporinas (4º gen.)			
+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.)
-Cephalosporins (5th gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (5. Gen.)	Cefalosporines (5e gen.)	Cefalosporinas (5º gen.)			
+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.)
-Cephalosporins (unclassified gen.)	FALSE	TRUE	TRUE	FALSE	Cephalosporine (unklassifiziert)	Cefalosporines (ongeclassificeerd)	Cefalosporinas (no clasificado)			
+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.)
-Cephalosporins	FALSE	TRUE	TRUE	FALSE	Cephalosporine	Cefalosporines	Cefalosporinas			
+Cephalosporins	FALSE	TRUE	TRUE	FALSE	Cephalosporine	Cefalosporines	Cefalosporinas	Cefalosporine	Céphalosporines	Cefalosporinas	Cefalosporiner
-Glycopeptides	FALSE	TRUE	TRUE	FALSE	Glykopeptide	Glycopeptiden	Glicopéptidos			
+Glycopeptides	FALSE	TRUE	TRUE	FALSE	Glykopeptide	Glycopeptiden	Glicopéptidos	Glicopeptidi	Glycopeptides	Glycopeptides	Glykopeptider
-Macrolides/lincosamides	FALSE	TRUE	TRUE	FALSE	Makrolide/Linkosamide	Macroliden/lincosamiden	Macrólidos/lincosamidas			
+Macrolides/lincosamides	FALSE	TRUE	TRUE	FALSE	Makrolide/Linkosamide	Macroliden/lincosamiden	Macrólidos/lincosamidas	Macrolidi/lincosamidi	Macrolides/lincosamides	Macrolides/lincosamidas	Makrolider/lincosamider
-Other antibacterials	FALSE	TRUE	TRUE	FALSE	Andere Antibiotika	Overige antibiotica	Otros antibacterianos			
+Other antibacterials	FALSE	TRUE	TRUE	FALSE	Andere Antibiotika	Overige antibiotica	Otros antibacterianos	Altri antibatterici	Autres antibactériens	Outros antibacterianos	Andre antibakterielle stoffer
-Polymyxins	FALSE	TRUE	TRUE	FALSE	Polymyxine	Polymyxines	Polimixinas			
+Polymyxins	FALSE	TRUE	TRUE	FALSE	Polymyxine	Polymyxines	Polimixinas	Polimixine	Polymyxines	Polimixinas	Polymyxiner
-Quinolones	FALSE	TRUE	TRUE	FALSE	Quinolone	Quinolonen	Quinolonas			
+Quinolones	FALSE	TRUE	TRUE	FALSE	Quinolone	Quinolonen	Quinolonas	Chinoloni	Quinolones	Quinolones	Kinoloner

docs/404.html

@@ -1,76 +1,38 @@
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 <!DOCTYPE html>
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   <div class="container">
     <div class="navbar-header">
       <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
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       <span class="navbar-brand">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
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+<li>
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+      <a href="https://msberends.github.io/AMR/articles/resistance_predict.html">
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         Predict antimicrobial resistance
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+      <a href="https://msberends.github.io/AMR/articles/datasets.html">
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+      <a href="https://msberends.github.io/AMR/articles/PCA.html">
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+        <span class="fa fa-compress"></span>
          
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-      <a href="articles/MDR.html">
+      <a href="https://msberends.github.io/AMR/articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
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-      <a href="articles/WHONET.html">
+      <a href="https://msberends.github.io/AMR/articles/WHONET.html">
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+        <span class="fa fa-globe-americas"></span>
          
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+      <a href="https://msberends.github.io/AMR/articles/SPSS.html">
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+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
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-      <a href="articles/EUCAST.html">
+      <a href="https://msberends.github.io/AMR/articles/EUCAST.html">
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+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
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-      <a href="reference/mo_property.html">
+      <a href="https://msberends.github.io/AMR/reference/mo_property.html">
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+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
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-      <a href="reference/ab_property.html">
+      <a href="https://msberends.github.io/AMR/reference/ab_property.html">
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+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
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+      <a href="https://msberends.github.io/AMR/articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
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       </a>
@@ -183,53 +145,46 @@
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 </li>
 <li>
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+  <a href="https://msberends.github.io/AMR/reference/index.html">
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+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
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+  <a href="https://msberends.github.io/AMR/authors.html">
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+    <span class="fa fa-users"></span>
      
     Authors
   </a>
 </li>
 <li>
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+  <a href="https://msberends.github.io/AMR/news/index.html">
     <span class="far fa-newspaper"></span>
      
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   </a>
 </li>
       </ul>
-      <ul class="nav navbar-nav navbar-right">
+<ul class="nav navbar-nav navbar-right">
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-     
-    Survey
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 </li>
       </ul>
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+</div>
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+<!--/.nav-collapse -->
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+  </div>
-</div><!--/.navbar -->
+<!--/.container -->
+</div>
+<!--/.navbar -->
 
       
 
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+      </header><div class="row">
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   <div class="contents col-md-9">
     <div class="page-header">
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@@ -240,31 +195,31 @@ Content not found. Please use links in the navbar.
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@@ -1,4 +0,0 @@
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-.hasAnchor:hover a.anchor-section {visibility: visible;}

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@@ -1,33 +0,0 @@
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docs/articles/EUCAST.html

@@ -21,12 +21,17 @@
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@@ -47,14 +52,14 @@
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@@ -63,77 +68,77 @@
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@@ -142,14 +147,14 @@
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@@ -164,18 +169,11 @@
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+  <a href="https://github.com/msberends/AMR" class="external-link">
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 </div>
@@ -187,13 +185,13 @@
 
       
 
-      </header><script src="EUCAST_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
+      </header><script src="EUCAST_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to apply EUCAST rules</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd"><code>vignettes/EUCAST.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/EUCAST.Rmd" class="external-link"><code>vignettes/EUCAST.Rmd</code></a></small>
       <div class="hidden name"><code>EUCAST.Rmd</code></div>
 
     </div>
@@ -202,21 +200,21 @@
     
 <div id="introduction" class="section level2">
 <h2 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h2>
+<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h2>
-<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">on their website</a>:</p>
+<p>What are EUCAST rules? The European Committee on Antimicrobial Susceptibility Testing (EUCAST) states <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">on their website</a>:</p>
 <blockquote>
 <p><em>EUCAST expert rules are a tabulated collection of expert knowledge on intrinsic resistances, exceptional resistance phenotypes and interpretive rules that may be applied to antimicrobial susceptibility testing in order to reduce errors and make appropriate recommendations for reporting particular resistances.</em></p>
 </blockquote>
-<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
+<p>In Europe, a lot of medical microbiological laboratories already apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown <em>et al.</em>, 2015</a>). Our package features their latest insights on intrinsic resistance and unusual phenotypes (v3.2, 2020).</p>
 <p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this purpose can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R in isolates when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
 </div>
 <div id="examples" class="section level2">
 <h2 class="hasAnchor">
-<a href="#examples" class="anchor"></a>Examples</h2>
+<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h2>
 <p>These rules can be used to discard impossible bug-drug combinations in your data. For example, <em>Klebsiella</em> produces beta-lactamase that prevents ampicillin (or amoxicillin) from working against it. In other words, practically every strain of <em>Klebsiella</em> is resistant to ampicillin.</p>
 <p>Sometimes, laboratory data can still contain such strains with ampicillin being susceptible to ampicillin. This could be because an antibiogram is available before an identification is available, and the antibiogram is then not re-interpreted based on the identification (namely, <em>Klebsiella</em>). EUCAST expert rules solve this, that can be applied using <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, 
+<code class="sourceCode R"><span class="va">oops</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, 
                           <span class="st">"Escherichia"</span><span class="op">)</span>,
                    ampicillin <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
 <span class="va">oops</span>
@@ -230,16 +228,16 @@
 <span class="co"># 2 Escherichia          S</span></code></pre></div>
 <p>A more convenient function is <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> that uses the same guideline, but allows to check for one or more specific microorganisms or antibiotics:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
+<code class="sourceCode R"><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,
                           <span class="st">"ampicillin"</span><span class="op">)</span>
 <span class="co"># [1]  TRUE FALSE</span>
 
 <span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"Klebsiella"</span>,
-                          <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
+                          <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span><span class="op">)</span>
 <span class="co"># [1]  TRUE FALSE</span></code></pre></div>
 <p>EUCAST rules can not only be used for correction, they can also be used for filling in known resistance and susceptibility based on results of other antimicrobials drugs. This process is called <em>interpretive reading</em>, is basically a form of imputation, and is part of the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function as well:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
+<code class="sourceCode R"><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Staphylococcus aureus"</span>,
                           <span class="st">"Enterococcus faecalis"</span>,
                           <span class="st">"Escherichia coli"</span>,
                           <span class="st">"Klebsiella pneumoniae"</span>,
@@ -398,11 +396,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p></p>
+<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
 </div>
 
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
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@@ -411,5 +411,7 @@
   
 
 
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docs/articles/EUCAST_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -1,15 +0,0 @@
-// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
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-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});

docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.css

@@ -1,4 +0,0 @@
-/* Styles for section anchors */
-a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
-a.anchor-section::before {content: '#';}
-.hasAnchor:hover a.anchor-section {visibility: visible;}

docs/articles/EUCAST_files/anchor-sections-1.0/anchor-sections.js

@@ -1,33 +0,0 @@
-// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
-document.addEventListener('DOMContentLoaded', function() {
-  // Do nothing if AnchorJS is used
-  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
-    return;
-  }
-
-  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
-
-  // Do nothing if sections are already anchored
-  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
-    return null;
-  }
-
-  // Use section id when pandoc runs with --section-divs
-  const section_id = function(x) {
-    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
-            ? x.id : '');
-  };
-
-  // Add anchors
-  h.forEach(function(x) {
-    const id = x.id || section_id(x.parentElement);
-    if (id === '') {
-      return null;
-    }
-    let anchor = document.createElement('a');
-    anchor.href = '#' + id;
-    anchor.classList = ['anchor-section'];
-    x.classList.add('hasAnchor');
-    x.appendChild(anchor);
-  });
-});

docs/articles/MDR.html

@@ -21,12 +21,17 @@
 <script src="../extra.js"></script><meta property="og:title" content="How to determine multi-drug resistance (MDR)">
 <meta property="og:description" content="AMR">
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
+<meta name="twitter:card" content="summary_large_image">
+<meta name="twitter:creator" content="@msberends">
+<meta name="twitter:site" content="@univgroningen">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -39,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
       </span>
     </div>
 
@@ -47,14 +52,14 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
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 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -63,77 +68,77 @@
   <ul class="dropdown-menu" role="menu">
 <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
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       </a>
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     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
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     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
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     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -142,14 +147,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -164,18 +169,11 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/msberends/AMR">
+  <a href="https://github.com/msberends/AMR" class="external-link">
     <span class="fab fa-github"></span>
      
     Source Code
   </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
       </ul>
 </div>
@@ -187,13 +185,13 @@
 
       
 
-      </header><script src="MDR_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
+      </header><script src="MDR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd" class="external-link"><code>vignettes/MDR.Rmd</code></a></small>
       <div class="hidden name"><code>MDR.Rmd</code></div>
 
     </div>
@@ -203,50 +201,50 @@
 <p>With the function <code><a href="../reference/mdro.html">mdro()</a></code>, you can determine which micro-organisms are multi-drug resistant organisms (MDRO).</p>
 <div id="type-of-input" class="section level3">
 <h3 class="hasAnchor">
-<a href="#type-of-input" class="anchor"></a>Type of input</h3>
+<a href="#type-of-input" class="anchor" aria-hidden="true"></a>Type of input</h3>
-<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, like the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function takes a data set as input, such as a regular <code>data.frame</code>. It tries to automatically determine the right columns for info about your isolates, such as the name of the species and all columns with results of antimicrobial agents. See the help page for more info about how to set the right settings for your data with the command <code><a href="../reference/mdro.html">?mdro</a></code>.</p>
 <p>For WHONET data (and most other data), all settings are automatically set correctly.</p>
 </div>
 <div id="guidelines" class="section level3">
 <h3 class="hasAnchor">
-<a href="#guidelines" class="anchor"></a>Guidelines</h3>
+<a href="#guidelines" class="anchor" aria-hidden="true"></a>Guidelines</h3>
-<p>The function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function support multiple guidelines. You can select a guideline with the <code>guideline</code> parameter. Currently supported guidelines are (case-insensitive):</p>
 <ul>
 <li>
 <p><code>guideline = "CMI2012"</code> (default)</p>
-<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext">link</a>)</p>
+<p>Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012) (<a href="https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "EUCAST3.2"</code> (or simply <code>guideline = "EUCAST"</code>)</p>
-<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf">link</a>)</p>
+<p>The European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance and Unusual Phenotypes” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "EUCAST3.1"</code></p>
-<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
+<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "TB"</code></p>
-<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/">link</a>)</p>
+<p>The international guideline for multi-drug resistant tuberculosis - World Health Organization “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis” (<a href="https://www.who.int/tb/publications/pmdt_companionhandbook/en/" class="external-link">link</a>)</p>
 </li>
 <li>
 <p><code>guideline = "MRGN"</code></p>
-<p>The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
+<p>The German national guideline - Mueller <em>et al.</em> (2015) Antimicrobial Resistance and Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6</p>
 </li>
 <li>
 <p><code>guideline = "BRMO"</code></p>
-<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh">link</a>)</p>
+<p>The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (<a href="https://www.rivm.nl/wip-richtlijn-brmo-bijzonder-resistente-micro-organismen-zkh" class="external-link">link</a>)</p>
 </li>
 </ul>
-<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="uri">https://github.com/msberends/AMR/issues/new</a>.</p>
+<p>Please suggest your own (country-specific) guidelines by letting us know: <a href="https://github.com/msberends/AMR/issues/new" class="external-link uri">https://github.com/msberends/AMR/issues/new</a>.</p>
 <div id="custom-guidelines" class="section level4">
 <h4 class="hasAnchor">
-<a href="#custom-guidelines" class="anchor"></a>Custom Guidelines</h4>
+<a href="#custom-guidelines" class="anchor" aria-hidden="true"></a>Custom Guidelines</h4>
 <p>You can also use your own custom guideline. Custom guidelines can be set with the <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function. This is of great importance if you have custom rules to determine MDROs in your hospital, e.g., rules that are dependent on ward, state of contact isolation or other variables in your data.</p>
-<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html">case_when()</a></code> of the <code>dplyr</code> package, you will recognise the input method to set your own rules. Rules must be set using what considers to be the ‘formula notation’:</p>
+<p>If you are familiar with <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code> of the <code>dplyr</code> 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’:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">custom</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">custom_mdro_guideline</a></span><span class="op">(</span><span class="va">CIP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type A"</span>,
                                 <span class="va">ERY</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">age</span> <span class="op">&gt;</span> <span class="fl">60</span> <span class="op">~</span> <span class="st">"Elderly Type B"</span><span class="op">)</span></code></pre></div>
-<p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The number of rules is unlimited.</p>
+<p>If a row/an isolate matches the first rule, the value after the first <code><a href="https://rdrr.io/r/base/tilde.html" class="external-link">~</a></code> (in this case <em>‘Elderly Type A’</em>) will be set as MDRO value. Otherwise, the second rule will be tried and so on. The maximum number of rules is unlimited.</p>
 <p>You can print the rules set in the console for an overview. Colours will help reading it if your console supports colours.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">custom</span>
@@ -257,30 +255,50 @@
 <span class="co"># </span>
 <span class="co"># Unmatched rows will return NA.</span>
 <span class="co"># Results will be of class &lt;factor&gt;, with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span></code></pre></div>
-<p>The outcome of the function can be used for the <code>guideline</code> argument in the [mdro()] function:</p>
+<p>The outcome of the function can be used for the <code>guideline</code> argument in the <code><a href="../reference/mdro.html">mdro()</a></code> function:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">custom</span><span class="op">)</span>
-<span class="fu"><a href="https://rdrr.io/r/base/table.html">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
+<span class="co"># Determining MDROs based on custom rules, resulting in factor levels:</span>
+<span class="co"># Negative &lt; Elderly Type A &lt; Elderly Type B.</span>
+<span class="co"># - Custom MDRO rule 1: `CIP == "R" &amp; age &gt; 60` (198 rows matched)</span>
+<span class="co"># - Custom MDRO rule 2: `ERY == "R" &amp; age &gt; 60` (732 rows matched)</span>
+<span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>
 <span class="co"># x</span>
 <span class="co">#       Negative Elderly Type A Elderly Type B </span>
 <span class="co">#           1070            198            732</span></code></pre></div>
-<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html">readRDS()</a></code>.</p>
+<p>The rules set (the <code>custom</code> object in this case) could be exported to a shared file location using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> if you collaborate with multiple users. The custom rules set could then be imported using <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>.</p>
 </div>
 </div>
 <div id="examples" class="section level3">
 <h3 class="hasAnchor">
-<a href="#examples" class="anchor"></a>Examples</h3>
+<a href="#examples" class="anchor" aria-hidden="true"></a>Examples</h3>
-<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code>. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
+<p>The <code><a href="../reference/mdro.html">mdro()</a></code> function always returns an ordered <code>factor</code> for predefined guidelines. For example, the output of the default guideline by Magiorakos <em>et al.</em> returns a <code>factor</code> with levels ‘Negative’, ‘MDR’, ‘XDR’ or ‘PDR’ in that order.</p>
-<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practice AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
+<p>The next example uses the <code>example_isolates</code> data set. This is a data set included with this package and contains full antibiograms of 2,000 microbial isolates. It reflects reality and can be used to practise AMR data analysis. If we test the MDR/XDR/PDR guideline on this data set, we get:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>   <span class="co"># to support pipes: %&gt;%</span>
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>   <span class="co"># to support pipes: %&gt;%</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/cleaner" class="external-link">cleaner</a></span><span class="op">)</span> <span class="co"># to create frequency tables</span></code></pre></div>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
   <span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
+  <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
+<span class="co"># ℹ Using column 'mo' as input for `col_mo`.</span>
+<span class="co"># Auto-guessing columns suitable for analysis... OK.</span>
+<span class="co"># ℹ Reliability would be improved if these antimicrobial results would be</span>
+<span class="co">#   available too: ampicillin/sulbactam (SAM), aztreonam (ATM), cefotetan</span>
+<span class="co">#   (CTT), ceftaroline (CPT), daptomycin (DAP), doripenem (DOR), ertapenem</span>
+<span class="co">#   (ETP), fusidic acid (FUS), gentamicin-high (GEH), levofloxacin (LVX),</span>
+<span class="co">#   minocycline (MNO), netilmicin (NET), polymyxin B (PLB),</span>
+<span class="co">#   quinupristin/dalfopristin (QDA), streptomycin-high (STH), telavancin (TLV)</span>
+<span class="co">#   and ticarcillin/clavulanic acid (TCC)</span>
+<span class="co"># Table 1 - Staphylococcus aureus... OK.</span>
+<span class="co"># Table 2 - Enterococcus spp.... OK.</span>
+<span class="co"># Table 3 - Enterobacteriaceae... OK.</span>
+<span class="co"># Table 4 - Pseudomonas aeruginosa... OK.</span>
+<span class="co"># Table 5 - Acinetobacter spp.... OK.</span>
 <span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
 <span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
+<p>Only results with ‘R’ are considered as resistance. Use <code>combine_SI = FALSE</code> to also consider ‘I’ as resistance.</p>
+<p>Determining multidrug-resistant organisms (MDRO), according to: Guideline: Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Author(s): Magiorakos AP, Srinivasan A, Carey RB, …, Vatopoulos A, Weber JT, Monnet DL Source: Clinical Microbiology and Infection 18:3, 2012; doi: 10.1111/j.1469-0691.2011.03570.x</p>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 2,000<br>
@@ -319,16 +337,16 @@ Unique: 2</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
 <span class="co"># a random vector with values S, I and R</span>
-<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
+<span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
-<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
+<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
+<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
                          ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
@@ -337,20 +355,20 @@ Unique: 2</p>
                          KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
 <p>The data set now looks like this:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
-<span class="co"># 1          S         I            R          R            R            S</span>
+<span class="co"># 1          S         S            R          R            I            I</span>
-<span class="co"># 2          I         R            R          R            R            R</span>
+<span class="co"># 2          S         R            R          S            I            S</span>
-<span class="co"># 3          S         S            S          R            I            R</span>
+<span class="co"># 3          S         I            I          S            R            I</span>
-<span class="co"># 4          R         I            R          R            S            S</span>
+<span class="co"># 4          I         I            R          I            S            I</span>
-<span class="co"># 5          I         R            S          S            R            I</span>
+<span class="co"># 5          R         I            R          R            S            S</span>
-<span class="co"># 6          I         S            S          R            R            R</span>
+<span class="co"># 6          I         R            S          I            I            R</span>
 <span class="co">#   kanamycin</span>
 <span class="co"># 1         I</span>
-<span class="co"># 2         R</span>
+<span class="co"># 2         S</span>
-<span class="co"># 3         R</span>
+<span class="co"># 3         S</span>
-<span class="co"># 4         R</span>
+<span class="co"># 4         I</span>
-<span class="co"># 5         S</span>
+<span class="co"># 5         R</span>
 <span class="co"># 6         S</span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -359,10 +377,22 @@ Unique: 2</p>
 <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
 <span class="co"># ℹ No column found as input for `col_mo`, assuming all rows contain</span>
-<span class="co">#   Mycobacterium tuberculosis.</span></code></pre></div>
+<span class="co">#   Mycobacterium tuberculosis.</span>
+<span class="co"># Auto-guessing columns suitable for analysis... OK.</span>
+<span class="co"># ℹ Reliability would be improved if these antimicrobial results would be</span>
+<span class="co">#   available too: capreomycin (CAP), rifabutin (RIB) and rifapentine (RFP)</span>
+<span class="co"># </span>
+<span class="co"># Only results with 'R' are considered as resistance. Use `combine_SI = FALSE` to also consider 'I' as resistance.</span>
+<span class="co"># </span>
+<span class="co"># Determining multidrug-resistant organisms (MDRO), according to:</span>
+<span class="co"># Guideline: Companion handbook to the WHO guidelines for the programmatic</span>
+<span class="co">#            management of drug-resistant tuberculosis</span>
+<span class="co"># Author(s): WHO (World Health Organization)</span>
+<span class="co"># Version:   WHO/HTM/TB/2014.11, 2014</span>
+<span class="co"># Source:    https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></code></pre></div>
 <p>Create a frequency table of the results:</p>
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span><span class="op">)</span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered (numeric)<br>
 Length: 5,000<br>
@@ -382,40 +412,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3187</td>
+<td align="right">3194</td>
-<td align="right">63.74%</td>
+<td align="right">63.88%</td>
-<td align="right">3187</td>
+<td align="right">3194</td>
-<td align="right">63.74%</td>
+<td align="right">63.88%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">1027</td>
+<td align="right">964</td>
-<td align="right">20.54%</td>
+<td align="right">19.28%</td>
-<td align="right">4214</td>
+<td align="right">4158</td>
-<td align="right">84.28%</td>
+<td align="right">83.16%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">430</td>
+<td align="right">451</td>
-<td align="right">8.60%</td>
+<td align="right">9.02%</td>
-<td align="right">4644</td>
+<td align="right">4609</td>
-<td align="right">92.88%</td>
+<td align="right">92.18%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">245</td>
+<td align="right">253</td>
-<td align="right">4.90%</td>
+<td align="right">5.06%</td>
-<td align="right">4889</td>
+<td align="right">4862</td>
-<td align="right">97.78%</td>
+<td align="right">97.24%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">111</td>
+<td align="right">138</td>
-<td align="right">2.22%</td>
+<td align="right">2.76%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -433,11 +463,13 @@ Unique: 5</p>
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p></p>
+<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
 </div>
 
       </footer>
@@ -446,5 +478,7 @@ Unique: 5</p>
   
 
 
+  
+
   </body>
 </html>

docs/articles/MDR_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -1,15 +0,0 @@
-// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});

docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.css

@@ -1,4 +0,0 @@
-/* Styles for section anchors */
-a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
-a.anchor-section::before {content: '#';}
-.hasAnchor:hover a.anchor-section {visibility: visible;}

docs/articles/MDR_files/anchor-sections-1.0/anchor-sections.js

@@ -1,33 +0,0 @@
-// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
-document.addEventListener('DOMContentLoaded', function() {
-  // Do nothing if AnchorJS is used
-  if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
-    return;
-  }
-
-  const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
-
-  // Do nothing if sections are already anchored
-  if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
-    return null;
-  }
-
-  // Use section id when pandoc runs with --section-divs
-  const section_id = function(x) {
-    return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
-            ? x.id : '');
-  };
-
-  // Add anchors
-  h.forEach(function(x) {
-    const id = x.id || section_id(x.parentElement);
-    if (id === '') {
-      return null;
-    }
-    let anchor = document.createElement('a');
-    anchor.href = '#' + id;
-    anchor.classList = ['anchor-section'];
-    x.classList.add('hasAnchor');
-    x.appendChild(anchor);
-  });
-});

docs/articles/PCA.html

@@ -21,12 +21,17 @@
 <script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
 <meta property="og:description" content="AMR">
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
+<meta name="twitter:card" content="summary_large_image">
+<meta name="twitter:creator" content="@msberends">
+<meta name="twitter:site" content="@univgroningen">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -39,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
       </span>
     </div>
 
@@ -47,14 +52,14 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fas fa-home"></span>
+    <span class="fa fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fas fa-question-circle"></span>
+    <span class="fa fa-question-circle"></span>
      
     How to
      
@@ -63,77 +68,77 @@
   <ul class="dropdown-menu" role="menu">
 <li>
       <a href="../articles/AMR.html">
-        <span class="fas fa-directions"></span>
+        <span class="fa fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fas fa-dice"></span>
+        <span class="fa fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fas fa-database"></span>
+        <span class="fa fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fas fa-compress"></span>
+        <span class="fa fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fas fa-skull-crossbones"></span>
+        <span class="fa fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fas fa-globe-americas"></span>
+        <span class="fa fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fas fa-file-upload"></span>
+        <span class="fa fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fas fa-exchange-alt"></span>
+        <span class="fa fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fas fa-bug"></span>
+        <span class="fa fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fas fa-capsules"></span>
+        <span class="fa fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fas fa-shipping-fast"></span>
+        <span class="fa fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -142,14 +147,14 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fas fa-book-open"></span>
+    <span class="fa fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fas fa-users"></span>
+    <span class="fa fa-users"></span>
      
     Authors
   </a>
@@ -164,18 +169,11 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/msberends/AMR">
+  <a href="https://github.com/msberends/AMR" class="external-link">
     <span class="fab fa-github"></span>
      
     Source Code
   </a>
-</li>
-<li>
-  <a href="../survey.html">
-    <span class="fas fa-clipboard-list"></span>
-     
-    Survey
-  </a>
 </li>
       </ul>
 </div>
@@ -187,13 +185,13 @@
 
       
 
-      </header><script src="PCA_files/header-attrs-2.8/header-attrs.js"></script><div class="row">
+      </header><script src="PCA_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>How to conduct principal component analysis (PCA) for AMR</h1>
             
       
-      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd"><code>vignettes/PCA.Rmd</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/PCA.Rmd" class="external-link"><code>vignettes/PCA.Rmd</code></a></small>
       <div class="hidden name"><code>PCA.Rmd</code></div>
 
     </div>
@@ -203,16 +201,16 @@
 <p><strong>NOTE: This page will be updated soon, as the pca() function is currently being developed.</strong></p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h1>
+<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
 </div>
 <div id="transforming" class="section level1">
 <h1 class="hasAnchor">
-<a href="#transforming" class="anchor"></a>Transforming</h1>
+<a href="#transforming" class="anchor" aria-hidden="true"></a>Transforming</h1>
 <p>For PCA, we need to transform our AMR data first. This is what the <code>example_isolates</code> data set in this package looks like:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
+<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/msberends/AMR" class="external-link">AMR</a></span><span class="op">)</span>
-<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
+<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
-<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
+<span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span>
 <span class="co"># Rows: 2,000</span>
 <span class="co"># Columns: 49</span>
 <span class="co"># $ date            &lt;date&gt; 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-…</span>
@@ -267,13 +265,13 @@
 <p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">resistance_data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op">%&gt;%</span> 
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>,       <span class="co"># group on anything, like order</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span>order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>,       <span class="co"># group on anything, like order</span>
            genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span>   <span class="co">#  and genus as we do here</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op">%&gt;%</span> <span class="co"># then get resistance of all drugs</span>
-  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, 
+  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>, 
          <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span><span class="op">)</span>      <span class="co"># and select only relevant columns</span>
 
-<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
+<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
 <span class="co"># # A tibble: 6 x 10</span>
 <span class="co"># # Groups:   order [5]</span>
 <span class="co">#   order            genus           AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT</span>
@@ -287,15 +285,15 @@
 </div>
 <div id="perform-principal-component-analysis" class="section level1">
 <h1 class="hasAnchor">
-<a href="#perform-principal-component-analysis" class="anchor"></a>Perform principal component analysis</h1>
+<a href="#perform-principal-component-analysis" class="anchor" aria-hidden="true"></a>Perform principal component analysis</h1>
 <p>The new <code><a href="../reference/pca.html">pca()</a></code> function will automatically filter on rows that contain numeric values in all selected variables, so we now only need to do:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">pca_result</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/pca.html">pca</a></span><span class="op">(</span><span class="va">resistance_data</span><span class="op">)</span>
 <span class="co"># ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
 <span class="co">#   and "TOB". Total observations available: 7.</span></code></pre></div>
-<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> function:</p>
+<p>The result can be reviewed with the good old <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span>
 <span class="co"># Groups (n=4, named as 'order'):</span>
 <span class="co"># [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span>
 <span class="co"># Importance of components:</span>
@@ -305,13 +303,13 @@
 <span class="co"># Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></code></pre></div>
 <pre><code># Groups (n=4, named as 'order'):
 # [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</code></pre>
-<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
+<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
 </div>
 <div id="plotting-the-results" class="section level1">
 <h1 class="hasAnchor">
-<a href="#plotting-the-results" class="anchor"></a>Plotting the results</h1>
+<a href="#plotting-the-results" class="anchor" aria-hidden="true"></a>Plotting the results</h1>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/stats/biplot.html" class="external-link">biplot</a></span><span class="op">(</span><span class="va">pca_result</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-5-1.png" width="750"></p>
 <p>But we can’t see the explanation of the points. Perhaps this works better with our new <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function, that automatically adds the right labels and even groups:</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
@@ -320,7 +318,7 @@
 <p>You can also print an ellipse per group, and edit the appearance:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="fu"><a href="../reference/ggplot_pca.html">ggplot_pca</a></span><span class="op">(</span><span class="va">pca_result</span>, ellipse <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">+</span>
-  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></code></pre></div>
+  <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"An AMR/PCA biplot!"</span><span class="op">)</span></code></pre></div>
 <p><img src="PCA_files/figure-html/unnamed-chunk-7-1.png" width="750"></p>
 </div>
   </div>
@@ -336,11 +334,13 @@
 
 
       <footer><div class="copyright">
-  <p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
+  <p></p>
+<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link external-link">pkgdown</a> 1.6.1.9001.</p>
 </div>
 
       </footer>
@@ -349,5 +349,7 @@
   
 
 
+  
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docs/articles/PCA_files/accessible-code-block-0.0.1/empty-anchor.js

@@ -1,15 +0,0 @@
-// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) -->
-// v0.0.1
-// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020.
-
-document.addEventListener('DOMContentLoaded', function() {
-  const codeList = document.getElementsByClassName("sourceCode");
-  for (var i = 0; i < codeList.length; i++) {
-    var linkList = codeList[i].getElementsByTagName('a');
-    for (var j = 0; j < linkList.length; j++) {
-      if (linkList[j].innerHTML === "") {
-        linkList[j].setAttribute('aria-hidden', 'true');
-      }
-    }
-  }
-});

docs/articles/PCA_files/anchor-sections-1.0/anchor-sections.css

@@ -1,4 +0,0 @@
-/* Styles for section anchors */
-a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
-a.anchor-section::before {content: '#';}
-.hasAnchor:hover a.anchor-section {visibility: visible;}