v1.8.0 as accepted by CRAN

.Rbuildignore

@@ -32,3 +32,4 @@
 ^vignettes/resistance_predict.Rmd$
 ^vignettes/SPSS.Rmd$
 ^vignettes/WHONET.Rmd$
+^logo.svg$

.github/workflows/check.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -23,16 +23,14 @@
 # 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
+      - development
+      - main
   pull_request:
     branches:
-      - master
+      - main
   schedule:
     # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
@@ -52,40 +50,37 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # these are the developmental version of R - we allow those tests to fail
-          - {os: macOS-latest,   r: 'devel',   allowfail: false}
-          - {os: windows-latest, r: 'devel',   allowfail: false}
-          - {os: ubuntu-20.04,   r: 'devel',   allowfail: false,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          
           # 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: windows-latest, r: '4.1',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '4.0',     allowfail: false}
-          - {os: windows-latest, r: '4.0',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '3.6',     allowfail: false}
-          - {os: windows-latest, r: '3.6',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '3.5',     allowfail: false}
-          - {os: windows-latest, r: '3.5',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '3.4',     allowfail: false}
-          - {os: windows-latest, r: '3.4',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '3.3',     allowfail: false}
-          - {os: windows-latest, r: '3.3',     allowfail: false}
-          - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: macOS-latest,   r: '3.2',     allowfail: false}
-          - {os: windows-latest, r: '3.2',     allowfail: false}
+          # - {os: macOS-latest,   r: '3.1',     allowfail: true}
+          # - {os: macOS-latest,   r: '3.0',     allowfail: true}
+          - {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: macOS-latest,   r: '3.1',     allowfail: false}
-          # - {os: windows-latest, r: '3.1',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          # - {os: macOS-latest,   r: '3.0',     allowfail: false}
-          # - {os: windows-latest, r: '3.0',     allowfail: false}
           - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-
+          - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: '4.1',     allowfail: false}
+          - {os: windows-latest, r: '4.0',     allowfail: false}
+          - {os: windows-latest, r: '3.6',     allowfail: false}
+          - {os: windows-latest, r: '3.5',     allowfail: false}
+          - {os: windows-latest, r: '3.4',     allowfail: false}
+          - {os: windows-latest, r: '3.3',     allowfail: false}
+          # - {os: windows-latest, r: '3.2',     allowfail: true}
+          # - {os: windows-latest, r: '3.1',     allowfail: true}
+          # - {os: windows-latest, r: '3.0',     allowfail: true}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -94,9 +89,11 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+      
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
@@ -104,20 +101,14 @@ jobs:
         # 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}
-        
+          sudo apt install -y libssl-dev libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
+      
       - 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
+          key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
 
       - name: Unpack AMR and install R dependencies
         if: always()
@@ -134,10 +125,8 @@ jobs:
           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
         shell: Rscript {0}
         
-      # - name: Only keep vignettes on release version
-      - name: Remove vignettes
-        # if: matrix.config.r != 'release'
-        if: always()
+      - name: Remove vignettes on R without knitr support
+        if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
         # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
         run: |
           rm -rf AMR/vignettes
@@ -171,5 +160,5 @@ jobs:
         if: always()
         uses: actions/upload-artifact@v2
         with:
-          name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
+          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
           path: AMR.Rcheck

.github/workflows/codecovr.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
-      - master
+      - development
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: code-coverage
 
@@ -42,11 +42,13 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: release
-          
-      - uses: r-lib/actions/setup-pandoc@master
+      
+      - uses: r-lib/actions/setup-pandoc@v2
+        # with:
+        #   pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
 
       - name: Query dependencies
         # this will change once a week, so it will cache dependency updates

.github/workflows/lintr.yaml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
-      - master
+      - development
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: lintr
 
@@ -42,7 +42,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
       - name: Query dependencies
         run: |

.gitignore

@@ -25,3 +25,5 @@ data-raw/taxon.tab
 data-raw/DSMZ_bactnames.xlsx
 data-raw/country_analysis_url_token.R
 data-raw/country_analysis2.R
+data-raw/taxonomy.csv
+data-raw/WHONET

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9030
-Date: 2021-08-29
+Version: 1.8.0
+Date: 2022-01-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by
@@ -10,34 +10,34 @@ Authors@R: c(
   person(given = c("Matthijs", "S."),
          family = "Berends", 
          email = "m.s.berends@umcg.nl",
-         role = c("aut", "cre"), 
+         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 = c("aut", "ths"),
-         comment = c(ORCID = "0000-0003-4881-038X")),
-  person(given = c("Bhanu", "N.", "M."),
-         family = "Sinha", 
-         role = c("aut", "ths"),
-         comment = c(ORCID = "0000-0003-1634-0010")),
+  person(given = "Dennis",
+         family = "Souverein", 
+         role = c("aut", "ctb"),
+         comment = c(ORCID = "0000-0003-0455-0336")),
+  person(given = c("Erwin", "E.", "A."),
+         family = "Hassing", 
+         role = c("aut", "ctb")),
   person(given = c("Casper", "J."),
          family = "Albers", 
-         role = c("aut", "ths"),
+         role = "ths",
          comment = c(ORCID = "0000-0002-9213-6743")),
-  person(given = "Corinna",
-         family = "Glasner", 
-         role = c("aut", "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("Alex", "W."),
+         family = "Friedrich", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-4881-038X")),
+  person(given = "Corinna",
+         family = "Glasner", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-1241-1328")),
   person(given = c("Eric", "H.", "L.", "C.", "M."),
          family = "Hazenberg", 
          role = "ctb"),
@@ -59,14 +59,14 @@ Authors@R: c(
   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 = c("Bhanu", "N.", "M."),
+         family = "Sinha", 
+         role = "ths",
+         comment = c(ORCID = "0000-0003-1634-0010")),
   person(given = "Anthony", 
          family = "Underwood", 
          role = "ctb",
-         comment = c(ORCID = "0000-0002-8547-427")))
+         comment = c(ORCID = "0000-0002-8547-4277")))
 Depends: R (>= 3.0.0)
 Enhances:
   cleaner,
@@ -77,16 +77,17 @@ Suggests:
   dplyr,
   ggtext,
   knitr,
+  progress,
   readxl,
   rmarkdown,
   rvest,
   tinytest,
   xml2
 VignetteBuilder: knitr,rmarkdown
-URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
+URL: https://msberends.github.io/AMR/, https://github.com/msberends/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

@@ -75,6 +75,7 @@ S3method(c,mic)
 S3method(c,mo)
 S3method(c,rsi)
 S3method(ceiling,mic)
+S3method(close,progress_bar)
 S3method(cos,mic)
 S3method(cosh,mic)
 S3method(cospi,mic)
@@ -157,6 +158,9 @@ export("%like%")
 export("%like_case%")
 export("%unlike%")
 export("%unlike_case%")
+export(NA_disk_)
+export(NA_mic_)
+export(NA_rsi_)
 export(ab_atc)
 export(ab_atc_group1)
 export(ab_atc_group2)
@@ -227,8 +231,8 @@ export(fluoroquinolones)
 export(full_join_microorganisms)
 export(g.test)
 export(geom_rsi)
+export(get_AMR_locale)
 export(get_episode)
-export(get_locale)
 export(get_mo_source)
 export(ggplot_pca)
 export(ggplot_rsi)
@@ -270,6 +274,7 @@ export(mo_is_gram_positive)
 export(mo_is_intrinsic_resistant)
 export(mo_is_yeast)
 export(mo_kingdom)
+export(mo_lpsn)
 export(mo_matching_score)
 export(mo_name)
 export(mo_order)
@@ -290,6 +295,7 @@ export(mo_url)
 export(mo_year)
 export(mrgn)
 export(n_rsi)
+export(not_intrinsic_resistant)
 export(oxazolidinones)
 export(pca)
 export(penicillins)

NEWS.md

@@ -1,15 +1,28 @@
-# `AMR` 1.7.1.9030
-## <small>Last updated: 29 August 2021</small>
+# `AMR` 1.8.0
+
+
+All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.
 
 ### 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.
+* Renamed function `get_locale()` to `get_AMR_locale()` to prevent conflicts with other packages
 
 ### 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 the CLSI 2021 guideline for interpreting MIC/disk diffusion values, which are incorporated in the `rsi_translation` data set. This data set now more strictly follows the WHONET software as well.
+* Support for EUCAST Intrinsic Resistance and Unusual Phenotypes v3.3 (October 2021). This is now the default EUCAST guideline in the package (all older guidelines are still available) for `eucast_rules()`, `mo_is_intrinsic_resistant()` and `mdro()`. The `intrinsic_resistant` data set was also updated accordingly.
+* Support for all antimicrobial drug (group) names and colloquial microorganism names in Danish, Dutch, English, French, German, Italian, Portuguese, Russian, Spanish and Swedish
+* 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. Its second argument can be a tidyverse way of selecting:
+  ```r
+  example_isolates %>% set_ab_names(where(is.rsi))
+  example_isolates %>% set_ab_names(AMC:GEN, property = "atc")
+  ```
+* Function `mo_lpsn()` to retrieve the [LPSN](https://lpsn.dsmz.de) record ID
+* Function `ab_ddd_units()` to get units of DDDs (daily defined doses), deprecating the use of `ab_ddd(..., units = TRUE)` to be more consistent in data types of function output
 
 ### Changed
+* Updated the bacterial taxonomy to 5 October 2021 (according to [LPSN](https://lpsn.dsmz.de)), including all 11 new staphylococcal species named since 1 January last year
 * 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
@@ -29,22 +42,39 @@
     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 the selector `not_intrinsic_resistant()`, which only keeps antibiotic columns that are not intrinsic resistant for all microorganisms in a data set, based on the latest EUCAST guideline on intrinsic resistance. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function.
   * 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)
+  * Fix for using selectors multiple times in one call (e.g., using them in `dplyr::filter()` and immediately after in `dplyr::select()`)
+  * Fix for using having multiple columns that are coerced to the same antibiotic agent
+  * Fixed for using `all()` or `any()` on antibiotic selectors in an R Markdown file
+* Added the following antimicrobial agents that are now covered by the WHO: aztreonam/nacubactam (ANC), cefepime/nacubactam (FNC), exebacase (EXE), ozenoxacin (OZN), zoliflodacin (ZFD), manogepix (MGX), ibrexafungerp (IBX), and rezafungin (RZF). None of these agents have an ATC code yet.
 * 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*.
+* Dramatic speed improvement for `first_isolate()`
 * 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
+* `as.rsi()` has an improved algorithm and can now also correct for textual input (such as "Susceptible", "Resistant") in all supported languages
+* `as.mic()` has an improved algorithm
 * 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 of `as.mo()`
 * 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
+* Added `fortify()` extensions for plotting methods
+* `NA` values of the classes `<mic>`, `<disk>` and `<rsi>` are now exported objects of this package, e.g. `NA_mic_` is an `NA` of class `mic` (just like the base R `NA_character_` is an `NA` of class `character`)
+* The `proportion_df()`, `count_df()` and `rsi_df()` functions now return with the additional S3 class 'rsi_df' so they can be extended by other packages
+* The `mdro()` function now returns `NA` for all rows that have no test results
+* The `species_id` column in the `microorganisms` data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and `mo_url()` has been updated to reflect this change.
+* Fixed a small bug in the functions `get_episode()` and `is_new_episode()`
+* `get_episode()` and `is_new_episode()` can now cope with `NA`s
+
+### Other
+* This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations.
 
 
 # AMR 1.7.1
@@ -499,7 +529,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
 
 ### New
 * Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](https://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
-* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
+* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/main/data-raw/read_EUCAST.R).
 * Support for LOINC and SNOMED codes
   * Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
     ```r
@@ -702,7 +732,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
   * Added support for *Blastocystis*
   * Added support for 5,000 new fungi
   * Added support for unknown yeasts and fungi
-  * Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
+  * Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character ae is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
     **IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
 * More intelligent guessing for `as.ab()`, including bidirectional language support
 * Added support for the German national guideline (3MRGN/4MRGN) in the `mdro()` function, to determine multi-drug resistant organisms
@@ -760,7 +790,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
   * EIEC (Entero-Invasive *E. coli*) 
   * EPEC (Entero-Pathogenic *E. coli*) 
   * ETEC (Entero-Toxigenic *E. coli*) 
-  * NMEC (Neonatal Meningitis‐causing *E. coli*) 
+  * NMEC (Neonatal Meningitis-causing *E. coli*) 
   * STEC (Shiga-toxin producing *E. coli*) 
   * UPEC (Uropathogenic *E. coli*)
   
@@ -816,7 +846,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
   * All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
   * Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
   * All `atc_*` functions are superseded by `ab_*` functions
-  * All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
+  * All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv)
 * Improvements to plotting AMR results with `ggplot_rsi()`:
   * New argument `colours` to set the bar colours
   * New arguments `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
@@ -840,7 +870,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
       freq(age) %>%
       boxplot()
     ```
-* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
+* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv)
 * Added ceftazidim intrinsic resistance to *Streptococci*
 * Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+
 * Fix for `freq()` for when all values are `NA`
@@ -986,13 +1016,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
     Using `as.mo(..., allow_uncertain = 3)` could lead to very unreliable results.
   * Implemented the latest publication of Becker *et al.* (2019), for categorising coagulase-negative *Staphylococci*
   * All microbial IDs that found are now saved to a local file `~/.Rhistory_mo`. Use the new function `clean_mo_history()` to delete this file, which resets the algorithms.
-  * Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
-    ```r
-    mo_genus("qwerty", language = "es")
-    # Warning: 
-    # one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
-    #> [1] "(género desconocido)"
-    ```
+  * Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese.
   * Fix for vector containing only empty values
   * Finds better results when input is in other languages
   * Better handling for subspecies
@@ -1268,7 +1292,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
   * New Becker classification for *Staphylococcus* to categorise them into Coagulase Negative *Staphylococci* (CoNS) and Coagulase Positve *Staphylococci* (CoPS)
   * New Lancefield classification for *Streptococcus* to categorise them into Lancefield groups
 * For convience, new descriptive statistical functions `kurtosis` and `skewness` that are lacking in base R - they are generic functions and have support for vectors, data.frames and matrices
-* Function `g.test` to perform the Χ<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
+* Function `g.test` to perform the X<sup>2</sup> distributed [*G*-test](https://en.wikipedia.org/wiki/G-test), which use is the same as `chisq.test`
 * ~~Function `ratio` to transform a vector of values to a preset ratio~~
   * ~~For example: `ratio(c(10, 500, 10), ratio = "1:2:1")` would return `130, 260, 130`~~
 * Support for Addins menu in RStudio to quickly insert `%in%` or `%like%` (and give them keyboard shortcuts), or to view the datasets that come with this package
@@ -1351,7 +1375,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
 * Added [ORCID](https://orcid.org) of authors to DESCRIPTION file
 * Added unit testing with the `testthat` package
 * 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)
+* Added line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/main/R)
 
 # AMR 0.1.1
 

R/aa_globals.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -40,6 +40,10 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
                                     "3.2" = list(version_txt = "v3.2",
                                                  year = 2020, 
                                                  title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
+                                                 url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"),
+                                    "3.3" = list(version_txt = "v3.3",
+                                                 year = 2021, 
+                                                 title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
                                                  url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
 
 SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
@@ -52,9 +56,9 @@ SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Acc
 CATALOGUE_OF_LIFE <- list(
   year = 2019,
   version = "Catalogue of Life: {year} Annual Checklist",
-  url_CoL = "http://www.catalogueoflife.org/col/",
+  url_CoL = "http://www.catalogueoflife.org",
   url_LPSN = "https://lpsn.dsmz.de",
-  yearmonth_LPSN = "March 2021"
+  yearmonth_LPSN = "5 October 2021"
 )
 
 globalVariables(c(".rowid",
@@ -105,6 +109,7 @@ globalVariables(c(".rowid",
                   "old_name",
                   "pattern",
                   "R",
+                  "rank_index",
                   "reference.rule",
                   "reference.rule_group",
                   "reference.version",

R/aa_helper_functions.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -53,15 +53,87 @@ pm_left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
   merged
 }
 
-quick_case_when <- function(...) {
-  vectors <- list(...)
-  split <- lapply(vectors, function(x) unlist(strsplit(paste(deparse(x), collapse = ""), "~", fixed = TRUE)))
-  for (i in seq_len(length(vectors))) {
-    if (eval(parse(text = split[[i]][1]), envir = parent.frame())) {
-      return(eval(parse(text = split[[i]][2]), envir = parent.frame()))
+# support where() like tidyverse:
+# adapted from https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
+where <- function(fn) {
+  if (!is.function(fn)) {
+    stop(pm_deparse_var(fn), " is not a valid predicate function.")
+  }
+  preds <- unlist(lapply(
+    pm_select_env$.data,
+    function(x, fn) {
+      do.call("fn", list(x))
+    },
+    fn
+  ))
+  if (!is.logical(preds)) stop("`where()` must be used with functions that return `TRUE` or `FALSE`.")
+  data_cols <- pm_select_env$get_colnames()
+  cols <- data_cols[preds]
+  which(data_cols %in% cols)
+}
+
+# copied and slightly rewritten from poorman under same license (2021-10-15)
+quick_case_when <- function (...) {
+  fs <- list(...)
+  lapply(fs, function(x) if (class(x) != "formula") 
+    stop("`case_when()` requires formula inputs."))
+  n <- length(fs)
+  if (n == 0L) 
+    stop("No cases provided.")
+  
+  validate_case_when_length <- function (query, value, fs) {
+    lhs_lengths <- lengths(query)
+    rhs_lengths <- lengths(value)
+    all_lengths <- unique(c(lhs_lengths, rhs_lengths))
+    if (length(all_lengths) <= 1L) 
+      return(all_lengths[[1L]])
+    non_atomic_lengths <- all_lengths[all_lengths != 1L]
+    len <- non_atomic_lengths[[1L]]
+    if (length(non_atomic_lengths) == 1L) 
+      return(len)
+    inconsistent_lengths <- non_atomic_lengths[-1L]
+    lhs_problems <- lhs_lengths %in% inconsistent_lengths
+    rhs_problems <- rhs_lengths %in% inconsistent_lengths
+    problems <- lhs_problems | rhs_problems
+    if (any(problems)) {
+      stop("The following formulas must be length ", len, " or 1, not ", 
+           paste(inconsistent_lengths, collapse = ", "), ".\n    ", 
+           paste(fs[problems], collapse = "\n    "),
+           call. = FALSE)
     }
   }
-  return(NA)
+  
+  replace_with <- function (x, i, val, arg_name) {
+    if (is.null(val)) 
+      return(x)
+    i[is.na(i)] <- FALSE
+    if (length(val) == 1L) {
+      x[i] <- val
+    }
+    else {
+      x[i] <- val[i]
+    }
+    x
+  }
+  
+  query <- vector("list", n)
+  value <- vector("list", n)
+  default_env <- parent.frame()
+  for (i in seq_len(n)) {
+    query[[i]] <- eval(fs[[i]][[2]], envir = default_env)
+    value[[i]] <- eval(fs[[i]][[3]], envir = default_env)
+    if (!is.logical(query[[i]])) 
+      stop(fs[[i]][[2]], " does not return a `logical` vector.")
+  }
+  m <- validate_case_when_length(query, value, fs)
+  out <- value[[1]][rep(NA_integer_, m)]
+  replaced <- rep(FALSE, m)
+  for (i in seq_len(n)) {
+    out <- replace_with(out, query[[i]] & !replaced, value[[i]], 
+                        NULL)
+    replaced <- replaced | (query[[i]] & !is.na(query[[i]]))
+  }
+  out
 }
 
 # No export, no Rd
@@ -122,14 +194,14 @@ check_dataset_integrity <- function() {
   data_in_globalenv <- ls(envir = globalenv())
   overwritten <- data_in_pkg[data_in_pkg %in% data_in_globalenv]
   # exception for example_isolates
-  overwritten <- overwritten[overwritten != "example_isolates"]
+  overwritten <- overwritten[overwritten %unlike% "example_isolates"]
   if (length(overwritten) > 0) {
     if (length(overwritten) > 1) {
       plural <- c("s are", "", "s")
     } else {
       plural <- c(" is", "s", "")
     }
-    if (message_not_thrown_before("dataset_overwritten")) {
+    if (message_not_thrown_before("check_dataset_integrity", overwritten)) {
       warning_("The following data set", plural[1],
                " overwritten by your global environment and prevent", plural[2], 
                " the AMR package from working correctly: ",
@@ -251,7 +323,7 @@ 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))) {
+    if (message_not_thrown_before("search_in_type", type)) {
       msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
       if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
         msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
@@ -296,12 +368,15 @@ stop_ifnot_installed <- function(package) {
   return(invisible())
 }
 
-pkg_is_available <- function(pkg, also_load = TRUE) {
+pkg_is_available <- function(pkg, also_load = TRUE, min_version = NULL) {
   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)
   }
+  if (!is.null(min_version)) {
+    out <- out && utils::packageVersion(pkg) >= min_version
+  }
   isTRUE(out)
 }
 
@@ -729,14 +804,17 @@ meet_criteria <- function(object,
 }
 
 get_current_data <- function(arg_name, call) {
+  valid_df <- function(x) {
+    !is.null(x) && is.data.frame(x)
+  }
   # 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
   cur_data_all <- import_fn("cur_data_all", "dplyr", error_on_fail = FALSE)
   if (!is.null(cur_data_all)) {
     out <- tryCatch(cur_data_all(), error = function(e) NULL)
-    if (is.data.frame(out)) {
-      return(structure(out, type = "dplyr_cur_data_all"))
+    if (valid_df(out)) {
+      return(out)
     }
   }
   
@@ -745,18 +823,18 @@ get_current_data <- function(arg_name, call) {
     if (!is.null(env$`.Generic`)) {
       # don't check `".Generic" %in% names(env)`, because in R < 3.2, `names(env)` is always NULL
       
-      if (!is.null(env$`.data`) && is.data.frame(env$`.data`)) {
+      if (valid_df(env$`.data`)) {
         # an element `.data` will be in the environment when using `dplyr::select()`
         # (but not when using `dplyr::filter()`, `dplyr::mutate()` or `dplyr::summarise()`)
-        return(structure(env$`.data`, type = "dplyr_selector"))
+        return(env$`.data`)
         
-      } else if (!is.null(env$xx) && is.data.frame(env$xx)) {
+      } else if (valid_df(env$xx)) {
         # an element `xx` will be in the environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
-        return(structure(env$xx, type = "base_R"))
+        return(env$xx)
         
-      } else if (!is.null(env$x) && is.data.frame(env$x)) {
+      } else if (valid_df(env$x)) {
         # an element `x` will be in the environment for only cols, e.g. `example_isolates[, carbapenems()]`
-        return(structure(env$x, type = "base_R"))
+        return(env$x)
       }
     }
   }
@@ -826,32 +904,44 @@ is_null_or_grouped_tbl <- function(x) {
   is.null(x) || inherits(x, "grouped_df")
 }
 
-unique_call_id <- function(entire_session = FALSE) {
+unique_call_id <- function(entire_session = FALSE, match_fn = NULL) {
   if (entire_session == TRUE) {
-    c(envir = "session",
-      call = "session")
-  } else {
-    # 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") {
-      # unit tests will keep the same call and environment - give them a unique ID
-      call <- paste0(sample(c(c(0:9), letters[1:6]), size = 64, replace = TRUE), collapse = "")
-    }
-    c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
-      call = call)
+    return(c(envir = "session", call = "session"))
   }
+  
+  # combination of environment ID (such as "0x7fed4ee8c848")
+  # and relevant system call (where 'match_fn' is being called in)
+  calls <- sys.calls()
+  if (!identical(Sys.getenv("R_RUN_TINYTEST"), "true") &&
+      !any(as.character(calls[[1]]) %like_case% "run_test_dir|run_test_file|test_all|tinytest|test_package|testthat")) {
+    for (i in seq_len(length(calls))) {
+      call_clean <- gsub("[^a-zA-Z0-9_().-]", "", as.character(calls[[i]]), perl = TRUE)
+      if (any(call_clean %like% paste0(match_fn, "\\("), na.rm = TRUE)) {
+        return(c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]]), perl = TRUE),
+                 call = paste0(deparse(calls[[i]]), collapse = "")))
+      }
+    }
+  }
+  c(envir = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = ""),
+    call = paste0(sample(c(c(0:9), letters[1:6]), size = 32, replace = TRUE), collapse = ""))
 }
 
-message_not_thrown_before <- function(fn, entire_session = FALSE) {
+#' @noRd
+#' @param fn name of the function as a character
+#' @param ... character elements to be pasted together as a 'salt'
+#' @param entire_session show message once per session
+message_not_thrown_before <- function(fn, ..., entire_session = FALSE) {
   # 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))
+  salt <- gsub("[^a-zA-Z0-9|_-]", "?", paste(c(...), sep = "|", collapse = "|"), perl = TRUE)
+  not_thrown_before <- is.null(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]]) ||
+    !identical(pkg_env[[paste0("thrown_msg.", fn, ".", salt)]],
+               unique_call_id(entire_session = entire_session,
+                              match_fn = fn))
   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),
+    assign(x = paste0("thrown_msg.", fn, ".", salt),
+           value = unique_call_id(entire_session = entire_session, match_fn = fn),
            envir = pkg_env)
   }
   not_thrown_before
@@ -1006,14 +1096,30 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, ...) {
     }
     set_clean_class(pb, new_class = "txtProgressBar")
   } else if (n >= n_min) {
-    pb <- utils::txtProgressBar(max = n, style = 3)
-    pb$tick <- function() {
-      pb$up(pb$getVal() + 1)
+    # rely on the progress package if it is available - it has a more verbose output
+    progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
+    if (!is.null(progress_bar)) {
+      # so we use progress::progress_bar
+      # a close() method was also added, see below this function
+      pb <- progress_bar$new(format = "[:bar] :percent (:current/:total)",
+                             total = n)
+    } else {
+      pb <- utils::txtProgressBar(max = n, style = 3)
+      pb$tick <- function() {
+        pb$up(pb$getVal() + 1)
+      }
     }
     pb
   }
 }
 
+#' @method close progress_bar
+#' @export
+#' @noRd
+close.progress_bar <- function(con, ...) {
+  con$terminate()
+}
+
 set_clean_class <- function(x, new_class) {
   # return the object with only the new class and no additional attributes where possible
   if (is.null(x)) {

R/aa_helper_pm_functions.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ab.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -48,8 +48,6 @@
 #' @section Source:
 #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
 #'
-#' WHONET 2019 software: \url{http://www.whonet.org/software.html}
-#'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
 #' @return A [character] [vector] with additional class [`ab`]
@@ -118,7 +116,9 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   # 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)
+  # penicillin is a special case: we call it so, but then mean benzylpenicillin
+  x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
   x_bak_clean <- x
   if (already_regex == FALSE) {
     x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
@@ -131,8 +131,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   note_if_more_than_one_found <- function(found, index, from_text) {
     if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
       abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
-      if (ab_name(found[1L], language = NULL) %like% "clavulanic acid") {
-        abnames <- abnames[!abnames == "clavulanic acid"]
+      if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|avibactam)") {
+        abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam")]
       }
       if (length(abnames) > 1) {
         message_("More than one result was found for item ", index, ": ",
@@ -153,7 +153,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
                                                 x[known_codes_atc],
                                                 function(x_) which(vapply(FUN.VALUE = logical(1),
                                                                           AB_lookup$atc,
-                                                                          function(atc) x_ %in% atc)),
+                                                                          function(atc) x_ %in% atc))[1L],
                                                 USE.NAMES = FALSE)]
   x_new[known_codes_cid] <- AB_lookup$ab[match(x[known_codes_cid], AB_lookup$cid)]
   already_known <- known_names | known_codes_ab | known_codes_atc | known_codes_cid
@@ -220,6 +220,16 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       next
     }
     
+    # length of input is quite long, and Levenshtein distance is only max 2
+    if (nchar(x[i]) >= 10) {
+      levenshtein <- as.double(utils::adist(x[i], AB_lookup$generalised_name))
+      if (any(levenshtein <= 2)) {
+        found <- AB_lookup$ab[which(levenshtein <= 2)]
+        x_new[i] <- note_if_more_than_one_found(found, i, from_text)
+        next
+      }
+    }
+    
     # allow characters that resemble others, but only continue when having more than 3 characters
     if (nchar(x[i]) <= 3) {
       x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
@@ -227,6 +237,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     }
     x_spelling <- x[i]
     if (already_regex == FALSE) {
+      
       x_spelling <- gsub("[IY]+", "[IY]+", x_spelling, perl = TRUE)
       x_spelling <- gsub("(C|K|Q|QU|S|Z|X|KS)+", "(C|K|Q|QU|S|Z|X|KS)+", x_spelling, perl = TRUE)
       x_spelling <- gsub("(PH|F|V)+", "(PH|F|V)+", x_spelling, perl = TRUE)
@@ -235,7 +246,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       x_spelling <- gsub("E+", "E+", x_spelling, perl = TRUE)
       x_spelling <- gsub("O+", "O+", x_spelling, perl = TRUE)
       # allow any ending of -in/-ine and -im/-ime
-      x_spelling <- gsub("(\\[IY\\]\\+(N|M)|\\[IY\\]\\+(N|M)E\\+)$", "[IY]+(N|M)E*", x_spelling, perl = TRUE)
+      x_spelling <- gsub("(\\[IY\\]\\+(N|M)|\\[IY\\]\\+(N|M)E\\+?)$", "[IY]+(N|M)E*", x_spelling, perl = TRUE)
       # allow any ending of -ol/-ole
       x_spelling <- gsub("(O\\+L|O\\+LE\\+)$", "O+LE*", x_spelling, perl = TRUE)
       # allow any ending of -on/-one
@@ -443,7 +454,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   # 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)

R/ab_from_text.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ab_property.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -30,11 +30,11 @@
 #' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
 #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
 #' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
-#' @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 language language of the returned text, defaults to system language (see [get_AMR_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 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
+#' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: variables to select (supports tidy selection such as `column1:column4`), otherwise 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.
@@ -97,16 +97,30 @@
 #' # use set_ab_names() for renaming columns
 #' colnames(example_isolates)
 #' colnames(set_ab_names(example_isolates))
+#' colnames(set_ab_names(example_isolates, NIT:VAN))
 #' \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")
+#'     set_ab_names(property = "atc")
+#'     
+#'  example_isolates %>%
+#'    set_ab_names(where(is.rsi)) %>%
+#'    colnames()
+#'    
+#'  example_isolates %>%
+#'    set_ab_names(NIT:VAN) %>%
+#'    colnames()
 #' }
 #' }
-ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
+ab_name <- function(x, language = get_AMR_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)
   meet_criteria(tolower, allow_class = "logical", has_length = 1)
@@ -120,68 +134,6 @@ ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
   x
 }
 
-#' @rdname ab_property
-#' @aliases ATC
-#' @export
-set_ab_names <- function(data, property = "name", language = get_locale(), snake_case = property == "name") {
-  meet_criteria(data, allow_class = "data.frame")
-  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)
-  
-  x_deparsed <- deparse(substitute(data))
-  if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) {
-    x_deparsed <- "your_data"
-  }
-  
-  property <- tolower(property)
-  
-  columns <- get_column_abx(data, info = FALSE, only_rsi_columns = FALSE, sort = FALSE)
-  if (length(columns) == 0) {
-    message_("No columns with antibiotic results found for `set_ab_names()`, leaving names unchanged.")
-    return(data)
-  }
-  x <- vapply(FUN.VALUE = character(1),
-              ab_property(columns, 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])
-                }
-              })
-  if (any(x %in% c("", NA))) {
-    warning_("No ", property, " found for column(s): ", vector_and(columns[x %in% c("", NA)], sort = FALSE), call = FALSE)
-    x[x %in% c("", NA)] <- columns[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)))
-                       }
-                     }))
-  }
-  colnames(data)[colnames(data) %in% columns] <- x
-  data
-}
-
 #' @rdname ab_property
 #' @export
 ab_cid <- function(x, ...) {
@@ -211,7 +163,7 @@ ab_tradenames <- function(x, ...) {
 
 #' @rdname ab_property
 #' @export
-ab_group <- function(x, language = get_locale(), ...) {
+ab_group <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   translate_AMR(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
@@ -249,7 +201,7 @@ ab_atc <- function(x, only_first = FALSE, ...) {
 
 #' @rdname ab_property
 #' @export
-ab_atc_group1 <- function(x, language = get_locale(), ...) {
+ab_atc_group1 <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language, only_affect_ab_names = TRUE)
@@ -257,7 +209,7 @@ ab_atc_group1 <- function(x, language = get_locale(), ...) {
 
 #' @rdname ab_property
 #' @export
-ab_atc_group2 <- function(x, language = get_locale(), ...) {
+ab_atc_group2 <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language, only_affect_ab_names = TRUE)
@@ -324,7 +276,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
 
 #' @rdname ab_property
 #' @export
-ab_info <- function(x, language = get_locale(), ...) {
+ab_info <- function(x, language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
@@ -375,13 +327,95 @@ ab_url <- function(x, open = FALSE, ...) {
 
 #' @rdname ab_property
 #' @export
-ab_property <- function(x, property = "name", language = get_locale(), ...) {
+ab_property <- function(x, property = "name", language = get_AMR_locale(), ...) {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(property, is_in = colnames(antibiotics), has_length = 1)
   meet_criteria(language, is_in = c(LANGUAGES_SUPPORTED, ""), has_length = 1, allow_NULL = TRUE, allow_NA = TRUE)
   translate_AMR(ab_validate(x = x, property = property, ...), language = language)
 }
 
+#' @rdname ab_property
+#' @aliases ATC
+#' @export
+set_ab_names <- function(data, ..., property = "name", language = get_AMR_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)) {
+    if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
+      df <- pm_select(data, ...)
+    } else {
+      df <- data
+    }
+    vars <- get_column_abx(df, info = FALSE, only_rsi_columns = FALSE, sort = FALSE, fn = "set_ab_names")
+    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()

R/ab_selectors.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -38,11 +38,6 @@
 #' 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. 
 #' 
 #' 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`.
-#' 
-#' 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 [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 = "")`
@@ -105,6 +100,12 @@
 #'   # You can combine selectors with '&' to be more specific:
 #'   example_isolates %>%
 #'     select(penicillins() & administrable_per_os())
+#'   
+#'   # get AMR for only drugs that matter - no intrinsic resistance:
+#'   example_isolates %>%
+#'     filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>% 
+#'     group_by(hospital_id) %>% 
+#'     summarise(across(not_intrinsic_resistant(), resistance))
 #'     
 #'   # get susceptibility for antibiotics whose name contains "trim":
 #'   example_isolates %>%
@@ -167,6 +168,7 @@ ab_class <- function(ab_class,
 }
 
 #' @rdname antibiotic_class_selectors
+#' @details 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.
 #' @export
 ab_selector <- function(filter, 
                         only_rsi_columns = FALSE,
@@ -179,7 +181,8 @@ ab_selector <- function(filter,
   # 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)
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
+                               sort = FALSE, fn = "ab_selector")
   call <- substitute(filter)
   agents <- tryCatch(AMR::antibiotics[which(eval(call, envir = AMR::antibiotics)), "ab", drop = TRUE],
                      error = function(e) stop_(e$message, call = -5))
@@ -193,90 +196,6 @@ ab_selector <- function(filter,
             class = c("ab_selector", "character"))
 }
 
-#' @rdname antibiotic_class_selectors
-#' @export
-administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
-  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$oral_ddd)), "ab", drop = TRUE]
-  agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
-  agents <- ab_in_data[ab_in_data %in% agents]
-  message_agent_names(function_name = "administrable_per_os", 
-                      agents = agents,
-                      ab_group = "administrable_per_os",
-                      examples = paste0(" (such as ", 
-                                        vector_or(ab_name(sample(agents_all,
-                                                                 size = min(5, length(agents_all)),
-                                                                 replace = FALSE),
-                                                          tolower = TRUE,
-                                                          language = NULL),
-                                                  quotes = FALSE), 
-                                        ")"))
-  structure(unname(agents),
-            class = c("ab_selector", "character"))
-}
-
-#' @rdname antibiotic_class_selectors
-#' @export
-administrable_iv <- function(only_rsi_columns = FALSE, ...) {
-  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
-  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
-  # but it only takes a couple of milliseconds
-  vars_df <- get_current_data(arg_name = NA, call = -2)
-  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
-  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
-  agents_all <- antibiotics[which(!is.na(antibiotics$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, ...) {
@@ -456,6 +375,97 @@ ureidopenicillins <- function(only_rsi_columns = FALSE, ...) {
   ab_select_exec("ureidopenicillins", only_rsi_columns = only_rsi_columns)
 }
 
+#' @rdname antibiotic_class_selectors
+#' @details 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.
+#' @export
+administrable_per_os <- function(only_rsi_columns = FALSE, ...) {
+  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, fn = "administrable_per_os")
+  agents_all <- antibiotics[which(!is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
+  agents <- antibiotics[which(antibiotics$ab %in% ab_in_data & !is.na(antibiotics$oral_ddd)), "ab", drop = TRUE]
+  agents <- ab_in_data[ab_in_data %in% agents]
+  message_agent_names(function_name = "administrable_per_os", 
+                      agents = agents,
+                      ab_group = "administrable_per_os",
+                      examples = paste0(" (such as ", 
+                                        vector_or(ab_name(sample(agents_all,
+                                                                 size = min(5, length(agents_all)),
+                                                                 replace = FALSE),
+                                                          tolower = TRUE,
+                                                          language = NULL),
+                                                  quotes = FALSE), 
+                                        ")"))
+  structure(unname(agents),
+            class = c("ab_selector", "character"))
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+administrable_iv <- function(only_rsi_columns = FALSE, ...) {
+  meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1)
+  # get_current_data() has to run each time, for cases where e.g., filter() and select() are used in same call
+  # but it only takes a couple of milliseconds
+  vars_df <- get_current_data(arg_name = NA, call = -2)
+  # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
+                               sort = FALSE, fn = "administrable_iv")
+  agents_all <- antibiotics[which(!is.na(antibiotics$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"))
+}
+
+#' @rdname antibiotic_class_selectors
+#' @inheritParams eucast_rules
+#' @details The [not_intrinsic_resistant()] function can be used to only select antibiotic columns that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPERT_RULES[length(EUCAST_VERSION_EXPERT_RULES)]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
+#' @export
+not_intrinsic_resistant <- function(only_rsi_columns = FALSE, col_mo = NULL, version_expertrules = 3.3, ...) {
+  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, fn = "not_intrinsic_resistant")
+  # intrinsic vars
+  vars_df_R <- tryCatch(sapply(eucast_rules(vars_df,
+                                            col_mo = col_mo,
+                                            version_expertrules = version_expertrules,
+                                            rules = "expert",
+                                            info = FALSE),
+                               function(col) tryCatch(!any(is.na(col)) && all(col == "R"),
+                                                      error = function(e) FALSE)),
+                        error = function(e) stop_("in not_intrinsic_resistant(): ", e$message, call = FALSE))
+  
+  agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]
+  if (length(agents) > 0 &&
+      message_not_thrown_before("not_intrinsic_resistant", sort(agents))) {
+    agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")
+    agents_names <- ab_name(names(agents), tolower = TRUE, language = NULL)
+    need_name <- generalise_antibiotic_name(agents) != generalise_antibiotic_name(agents_names)
+    agents_formatted[need_name] <- paste0(agents_formatted[need_name], " (", agents_names[need_name], ")")
+    message_("For `not_intrinsic_resistant()` removing ",
+             ifelse(length(agents) == 1, "column ", "columns "),
+             vector_and(agents_formatted, quotes = FALSE, sort = FALSE))
+  }
+  
+  vars_df_R <- names(vars_df_R)[which(!vars_df_R)]
+  # find columns that are abx, but also intrinsic R
+  out <- unname(intersect(ab_in_data, vars_df_R))
+  structure(out,
+            class = c("ab_selector", "character"))
+}
+
 ab_select_exec <- function(function_name,
                            only_rsi_columns = FALSE,
                            only_treatable = FALSE,
@@ -464,22 +474,24 @@ ab_select_exec <- function(function_name,
   # but it only takes a couple of milliseconds
   vars_df <- get_current_data(arg_name = NA, call = -3)
   # to improve speed, get_column_abx() will only run once when e.g. in a select or group call
-  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns, sort = FALSE)
-  
+  ab_in_data <- get_column_abx(vars_df, info = FALSE, only_rsi_columns = only_rsi_columns,
+                               sort = FALSE, fn = function_name)
   # untreatable drugs
-  untreatable <- antibiotics[which(antibiotics$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)
+  if (only_treatable == TRUE) {
+    untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
+    if (any(untreatable %in% names(ab_in_data))) {
+      if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
+        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]
     }
-    ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
   }
   
   if (length(ab_in_data) == 0) {
@@ -661,14 +673,14 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
 }
 
 is_any <- function(el1) {
-  syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
+  syscalls <- paste0(trimws(deparse(sys.calls())), collapse = " ")
   el1 <- gsub("(.*),.*", "\\1", el1)
-  syscall %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
+  syscalls %like% paste0("[^_a-zA-Z0-9]any\\(", "(c\\()?", el1)
 }
 is_all <- function(el1) {
-  syscall <- paste0(trimws(deparse(sys.calls()[[1]])), collapse = " ")
+  syscalls <- paste0(trimws(deparse(sys.calls())), collapse = " ")
   el1 <- gsub("(.*),.*", "\\1", el1)
-  syscall %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
+  syscalls %like% paste0("[^_a-zA-Z0-9]all\\(", "(c\\()?", el1)
 }
 
 find_ab_group <- function(ab_class_args) {
@@ -709,7 +721,7 @@ find_ab_names <- function(ab_group, n = 3) {
 }
 
 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 (message_not_thrown_before(function_name, sort(agents))) {
     if (length(agents) == 0) {
       if (is.null(ab_group)) {
         message_("For `", function_name, "()` no antimicrobial agents found", examples, ".")

R/age.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/amr.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/atc_online.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -138,15 +138,21 @@ atc_online_property <- function(atc_code,
     atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE)
     
     if (property == "groups") {
-      tbl <- read_html(atc_url) %pm>%
-        html_node("#content") %pm>%
-        html_children() %pm>%
-        html_node("a")
+      out <- tryCatch(
+        read_html(atc_url) %pm>%
+          html_node("#content") %pm>%
+          html_children() %pm>%
+          html_node("a"), 
+        error = function(e) NULL)
+      if (is.null(out)) {
+        message_("Connection to ", atc_url, " failed.")
+        return(rep(NA, length(atc_code)))
+      }
       
       # get URLS of items
-      hrefs <- tbl %pm>% html_attr("href")
+      hrefs <- out %pm>% html_attr("href")
       # get text of items
-      texts <- tbl %pm>% html_text()
+      texts <- out %pm>% html_text()
       # select only text items where URL like "code="
       texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
       # last one is antibiotics, skip it
@@ -154,15 +160,21 @@ atc_online_property <- function(atc_code,
       returnvalue <- c(list(texts), returnvalue)
       
     } else {
-      tbl <- read_html(atc_url) %pm>%
-        html_nodes("table") %pm>%
-        html_table(header = TRUE) %pm>%
-        as.data.frame(stringsAsFactors = FALSE)
+      out <- tryCatch(
+        read_html(atc_url) %pm>%
+          html_nodes("table") %pm>%
+          html_table(header = TRUE) %pm>%
+          as.data.frame(stringsAsFactors = FALSE), 
+        error = function(e) NULL)
+      if (is.null(out)) {
+        message_("Connection to ", atc_url, " failed.")
+        return(rep(NA, length(atc_code)))
+      }
       
       # case insensitive column names
-      colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
+      colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
       
-      if (length(tbl) == 0) {
+      if (length(out) == 0) {
         warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
         returnvalue[i] <- NA
         next
@@ -170,15 +182,15 @@ atc_online_property <- function(atc_code,
       
       if (property %in% c("atc", "name")) {
         # ATC and name are only in first row
-        returnvalue[i] <- tbl[1, property]
+        returnvalue[i] <- out[1, property]
       } else {
-        if (!"adm.r" %in% colnames(tbl) | is.na(tbl[1, "adm.r"])) {
+        if (!"adm.r" %in% colnames(out) | is.na(out[1, "adm.r"])) {
           returnvalue[i] <- NA
           next
         } else {
-          for (j in seq_len(nrow(tbl))) {
-            if (tbl[j, "adm.r"] == administration) {
-              returnvalue[i] <- tbl[j, property]
+          for (j in seq_len(nrow(out))) {
+            if (out[j, "adm.r"] == administration) {
+              returnvalue[i] <- out[j, property]
             }
           }
         }

R/availability.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/bug_drug_combinations.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -162,7 +162,7 @@ bug_drug_combinations <- function(x,
 #' @rdname bug_drug_combinations
 format.bug_drug_combinations <- function(x,
                                          translate_ab = "name (ab, atc)",
-                                         language = get_locale(),
+                                         language = get_AMR_locale(),
                                          minimum = 30,
                                          combine_SI = TRUE,
                                          combine_IR = FALSE,

R/catalogue_of_life.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -41,7 +41,7 @@ format_included_data_number <- function(data) {
 
 #' The Catalogue of Life
 #'
-#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
+#' This package contains the complete taxonomic tree (last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`) of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (CoL), supplemented with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN).
 #' @section Catalogue of Life:
 #' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
 #' This package contains the complete taxonomic tree of almost all microorganisms (`r format_included_data_number(microorganisms)` species) from the authoritative and comprehensive Catalogue of Life (CoL, <http://www.catalogueoflife.org>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, [lpsn.dsmz.de](https://lpsn.dsmz.de)). This supplementation is needed until the [CoL+ project](https://github.com/CatalogueOfLife/general) is finished, which we await.
@@ -58,7 +58,7 @@ format_included_data_number <- function(data) {
 #'
 #' The Catalogue of Life (<http://www.catalogueoflife.org>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
 #'
-#' The syntax used to transform the original data to a cleansed \R format, can be found here: <https://github.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R>.
+#' The syntax used to transform the original data to a cleansed \R format, can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R>.
 #' @inheritSection AMR Read more on Our Website!
 #' @name catalogue_of_life
 #' @rdname catalogue_of_life
@@ -141,5 +141,5 @@ print.catalogue_of_life_version <- function(x, ...) {
              "  Number of included bacterial species: ", format(x$LPSN$n, big.mark = ","), "\n\n",
              "=> Total number of species included:  ", format(x$total_included$n_total_species, big.mark = ","), "\n",
              "=> Total number of synonyms included: ", format(x$total_included$n_total_synonyms, big.mark = ","), "\n\n",
-             "See for more info ?microorganisms and ?catalogue_of_life.\n"))
+             "See for more info ", font_grey_bg("`?microorganisms`"), " and ", font_grey_bg("`?catalogue_of_life`"), ".\n"))
 }

R/count.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -213,7 +213,7 @@ n_rsi <- count_all
 #' @export
 count_df <- function(data,
                      translate_ab = "name",
-                     language = get_locale(),
+                     language = get_AMR_locale(),
                      combine_SI = TRUE,
                      combine_IR = FALSE) {
   tryCatch(

R/custom_eucast_rules.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -26,7 +26,7 @@
 #' Define Custom EUCAST Rules
 #' 
 #' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
-#' @inheritSection lifecycle Maturing Lifecycle
+#' @inheritSection lifecycle Stable Lifecycle
 #' @param ... rules in formula notation, see *Examples*
 #' @details
 #' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.

R/data.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -60,17 +60,15 @@
 #' ## Direct download
 #' These data sets are available as 'flat files' for use even without \R - you can find the files here:
 #' 
-#' * <https://github.com/msberends/AMR/raw/master/data-raw/antibiotics.txt>
-#' * <https://github.com/msberends/AMR/raw/master/data-raw/antivirals.txt>
+#' * <https://github.com/msberends/AMR/raw/main/data-raw/antibiotics.txt>
+#' * <https://github.com/msberends/AMR/raw/main/data-raw/antivirals.txt>
 #' 
 #' Files in \R format (with preserved data structure) can be found here:
 #' 
-#' * <https://github.com/msberends/AMR/raw/master/data/antibiotics.rda>
-#' * <https://github.com/msberends/AMR/raw/master/data/antivirals.rda>
+#' * <https://github.com/msberends/AMR/raw/main/data/antibiotics.rda>
+#' * <https://github.com/msberends/AMR/raw/main/data/antivirals.rda>
 #' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
 #'
-#' WHONET 2019 software: <http://www.whonet.org/software.html>
-#'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection WHOCC WHOCC
@@ -83,7 +81,7 @@
 
 #' Data Set with `r format(nrow(microorganisms), big.mark = ",")` Microorganisms
 #'
-#' A data set containing the microbial taxonomy, last updated in `r CATALOGUE_OF_LIFE$yearmonth_LPSN`, of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using [as.mo()].
+#' A data set containing the full microbial taxonomy (**last updated: `r CATALOGUE_OF_LIFE$yearmonth_LPSN`**) of `r nr2char(length(unique(microorganisms$kingdom[!microorganisms$kingdom %like% "unknown"])))` kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using [as.mo()].
 #' @inheritSection catalogue_of_life Catalogue of Life
 #' @format A [data.frame] with `r format(nrow(microorganisms), big.mark = ",")` observations and `r ncol(microorganisms)` variables:
 #' - `mo`\cr ID of microorganism as used by this package
@@ -105,20 +103,21 @@
 #' 
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
-#' - 3 entries of *Trichomonas* (*Trichomonas vaginalis*, and its family and genus)
-#' - 1 entry of *Candida* (*Candida krusei*), that is not (yet) in the Catalogue of Life
-#' - 1 entry of *Blastocystis* (*Blastocystis hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
+#' - 3 entries of *Trichomonas* (*T. vaginalis*, and its family and genus)
+#' - 1 entry of *Candida* (*C.  krusei*), that is not (yet) in the Catalogue of Life
+#' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
+#' - 1 entry of *Moraxella* (*M. catarrhalis*), which was formally named *Branhamella catarrhalis* (Catlin, 1970) though this change was never accepted within the field of clinical microbiology
 #' - 5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)
 #' - 6 families under the Enterobacterales order, according to Adeolu *et al.* (2016, PMID 27620848), that are not (yet) in the Catalogue of Life
 #' 
 #' ## Direct download
 #' This data set is available as 'flat file' for use even without \R - you can find the file here:
 #' 
-#' * <https://github.com/msberends/AMR/raw/master/data-raw/microorganisms.txt>
+#' * <https://github.com/msberends/AMR/raw/main/data-raw/microorganisms.txt>
 #' 
 #' The file in \R format (with preserved data structure) can be found here:
 #' 
-#' * <https://github.com/msberends/AMR/raw/master/data/microorganisms.rda>
+#' * <https://github.com/msberends/AMR/raw/main/data/microorganisms.rda>
 #' @section About the Records from LPSN (see *Source*):
 #' The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. LPSN is a free to use service founded by Jean P. Euzeby in 1997 and later on maintained by Aidan C. Parte.
 #' 
@@ -131,8 +130,8 @@
 #' List of Prokaryotic names with Standing in Nomenclature (`r CATALOGUE_OF_LIFE$yearmonth_LPSN`) as currently implemented in this `AMR` package:
 #' 
 #' * Parte, A.C., Sarda Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Goker, M. (2020). List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \doi{10.1099/ijsem.0.004332}
-#' * Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
-#' * Parte, A.C. (2014). LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613–D616; \doi{10.1093/nar/gkt1111}
+#' * Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
+#' * Parte, A.C. (2014). LPSN - List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Research, 42, Issue D1, D613-D616; \doi{10.1093/nar/gkt1111}
 #' * Euzeby, J.P. (1997). List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet. International Journal of Systematic Bacteriology, 47, 590-592; \doi{10.1099/00207713-47-2-590}
 #' 
 #' `r SNOMED_VERSION$current_source` as currently implemented in this `AMR` package:
@@ -154,7 +153,7 @@
 #' - `prevalence`\cr Prevalence of the microorganism, see [as.mo()]
 #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
 #' 
-#' Parte, A.C. (2018). LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
+#' Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; \doi{10.1099/ijsem.0.002786}
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @seealso [as.mo()] [mo_property()] [microorganisms]
@@ -245,13 +244,14 @@
 #' - `method`\cr Either `r vector_or(rsi_translation$method)`
 #' - `site`\cr Body site, e.g. "Oral" or "Respiratory"
 #' - `mo`\cr Microbial ID, see [as.mo()]
+#' - `rank_index`\cr Taxonomic rank index of `mo` from 1 (subspecies/infraspecies) to 5 (unknown microorganism)
 #' - `ab`\cr Antibiotic ID, see [as.ab()]
 #' - `ref_tbl`\cr Info about where the guideline rule can be found
 #' - `disk_dose`\cr Dose of the used disk diffusion method
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
 #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
 #' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.
+#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt>. This file **allows for machine reading EUCAST and CLSI guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the `mo` and `ab` columns have been transformed to contain the full official names instead of codes.
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @seealso [intrinsic_resistant]
@@ -261,20 +261,22 @@
 #'
 #' Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.
 #' @format A [data.frame] with `r format(nrow(intrinsic_resistant), big.mark = ",")` observations and `r ncol(intrinsic_resistant)` variables:
-#' - `microorganism`\cr Name of the microorganism
-#' - `antibiotic`\cr Name of the antibiotic drug
-#' @details The repository of this `AMR` package contains a file comprising this exact data set: <https://github.com/msberends/AMR/blob/master/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
+#' - `mo`\cr Microorganism ID
+#' - `ab`\cr Antibiotic ID
+#' @details The repository of this `AMR` package contains a file comprising this data set with full taxonomic and antibiotic names: <https://github.com/msberends/AMR/blob/main/data-raw/intrinsic_resistant.txt>. This file **allows for machine reading EUCAST guidelines about intrinsic resistance**, which is almost impossible with the Excel and PDF files distributed by EUCAST. The file is updated automatically.
 #' 
-#' This data set is based on `r format_eucast_version_nr(3.2)`.
+#' This data set is based on `r format_eucast_version_nr(3.3)`.
 #' @inheritSection AMR Reference Data Publicly Available
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' \donttest{
 #' if (require("dplyr")) {
 #'   intrinsic_resistant %>%
-#'     filter(antibiotic == "Vancomycin", microorganism %like% "Enterococcus") %>% 
-#'     pull(microorganism)
-#'   # [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
+#'     mutate(mo = mo_name(mo),
+#'            ab = ab_name(mo))
+#'     filter(ab == "Vancomycin" & mo %like% "Enterococcus") %>% 
+#'     pull(mo)
+#'   #> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"
 #' }
 #' }
 "intrinsic_resistant"

R/deprecated.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/disk.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -119,6 +119,12 @@ all_valid_disks <- function(x) {
   !any(is.na(x_disk)) && !all(is.na(x))
 }
 
+#' @rdname as.disk
+#' @details `NA_disk_` is a missing value of the new `<disk>` class.
+#' @export
+NA_disk_ <- set_clean_class(as.integer(NA_real_),
+                            new_class = c("disk", "integer"))
+
 #' @rdname as.disk
 #' @export
 is.disk <- function(x) {

R/episode.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #' 
 #' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
 #' @inheritSection lifecycle Stable Lifecycle
-#' @param x vector of dates (class `Date` or `POSIXt`)
+#' @param x vector of dates (class `Date` or `POSIXt`), will be sorted internally to determine episodes
 #' @param episode_days required episode length in days, can also be less than a day or `Inf`, see *Details*
 #' @param ... ignored, only in place to allow future extensions
 #' @details 
@@ -105,11 +105,11 @@
 #' }
 #' }
 get_episode <- function(x, episode_days, ...) {
-  meet_criteria(x, allow_class = c("Date", "POSIXt"))
+  meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
   meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
   
-  exec_episode(type = "sequential",
-               x = x, 
+  exec_episode(x = x, 
+               type = "sequential",
                episode_days = episode_days,
                ... = ...)
 }
@@ -117,27 +117,27 @@ get_episode <- function(x, episode_days, ...) {
 #' @rdname get_episode
 #' @export
 is_new_episode <- function(x, episode_days, ...) {
-  meet_criteria(x, allow_class = c("Date", "POSIXt"))
+  meet_criteria(x, allow_class = c("Date", "POSIXt"), allow_NA = TRUE)
   meet_criteria(episode_days, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = FALSE)
   
-  exec_episode(type = "logical",
-               x = x, 
+  exec_episode(x = x, 
+               type = "logical",
                episode_days = episode_days,
                ... = ...)
 }
 
-exec_episode <- function(type, x, episode_days, ...) {
+exec_episode <- function(x, type, episode_days, ...) {
   x <- as.double(as.POSIXct(x)) # as.POSIXct() required for Date classes
   # since x is now in seconds, get seconds from episode_days as well
   episode_seconds <- episode_days * 60 * 60 * 24
   
-  if (length(x) == 1) {
+  if (length(x) == 1) { # this will also match 1 NA, which is fine
     if (type == "logical") {
       return(TRUE)
     } else if (type == "sequential") {
       return(1)
     }
-  } else if (length(x) == 2) {
+  } else if (length(x) == 2 && !all(is.na(x))) {
     if (max(x) - min(x) >= episode_seconds) {
       if (type == "logical") {
         return(c(TRUE, TRUE))
@@ -155,7 +155,7 @@ exec_episode <- function(type, x, episode_days, ...) {
   
   # I asked on StackOverflow:
   # https://stackoverflow.com/questions/42122245/filter-one-row-every-year
-  exec <- function(x, episode_seconds) {
+  run_episodes <- function(x, episode_seconds) {
     indices <- integer()
     start <- x[1]
     ind <- 1
@@ -181,11 +181,8 @@ exec_episode <- function(type, x, episode_days, ...) {
     }
   }
   
-  df <- data.frame(x = x,
-                   y = seq_len(length(x))) %pm>%
-    pm_arrange(x)
-  df$new <- exec(df$x, episode_seconds)
-  df %pm>%
-    pm_arrange(y) %pm>%
-    pm_pull(new)
+  ord <- order(x)
+  out <- run_episodes(x[ord], episode_seconds)[order(ord)]
+  out[is.na(x) & ord != 1] <- NA # every NA but the first must remain NA
+  out
 }

R/eucast_rules.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -23,6 +23,10 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# ====================================================== #
+# || Change the EUCAST version numbers in R/globals.R || #
+# ====================================================== #
+
 format_eucast_version_nr <- function(version, markdown = TRUE) {
   # for documentation - adds title, version number, year and url in markdown language
   lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
@@ -55,7 +59,7 @@ 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_DF[which(EUCAST_RULES_DF$reference.version == 3.2 & EUCAST_RULES_DF$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` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state 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$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$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$administration)`
@@ -66,7 +70,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
 #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
 #'
-#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.  **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
+#' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>.  **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()].
 #' 
 #' ## Custom Rules
 #' 
@@ -105,6 +109,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #'   Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
 #' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
 #' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
+#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
 #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
@@ -159,7 +164,7 @@ eucast_rules <- function(x,
                          rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
                          verbose = FALSE,
                          version_breakpoints = 11.0,
-                         version_expertrules = 3.2,
+                         version_expertrules = 3.3,
                          ampc_cephalosporin_resistance = NA,
                          only_rsi_columns = FALSE,
                          custom_rules = NULL,
@@ -300,6 +305,7 @@ eucast_rules <- function(x,
                             verbose = verbose,
                             info = info,
                             only_rsi_columns = only_rsi_columns,
+                            fn = "eucast_rules",
                             ...)
   
   if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
@@ -316,25 +322,6 @@ eucast_rules <- function(x,
   }
   
   # Some helper functions ---------------------------------------------------
-  get_antibiotic_columns <- function(x, cols_ab) {
-    x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
-    x_new <- character()
-    for (val in x) {
-      if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-        # antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
-        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)
-      } else {
-        stop_("unknown antimicrobial agent (group) in EUCAST rules file: ", val, call = FALSE)
-      }
-      x_new <- c(x_new, val)
-    }
-    x_new <- unique(x_new)
-    out <- cols_ab[match(x_new, names(cols_ab))]
-    out[!is.na(out)]
-  }
   get_antibiotic_names <- function(x) {
     x <- x %pm>%
       strsplit(",") %pm>%
@@ -580,6 +567,7 @@ eucast_rules <- function(x,
                                 (reference.rule_group %like% "expert" & reference.version == version_expertrules))
   }
   # filter out AmpC de-repressed cephalosporin-resistant mutants ----
+  # no need to filter on version number here - the rules contain these version number, so are inherently filtered
   # cefotaxime, ceftriaxone, ceftazidime
   if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) {
     eucast_rules_df <- subset(eucast_rules_df,
@@ -720,7 +708,7 @@ eucast_rules <- function(x,
       rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% mo_value),
                        error = function(e) integer(0))
     } else {
-      source_antibiotics <- get_antibiotic_columns(source_antibiotics, cols_ab)
+      source_antibiotics <- get_ab_from_namespace(source_antibiotics, cols_ab)
       if (length(source_value) == 1 & length(source_antibiotics) > 1) {
         source_value <- rep(source_value, length(source_antibiotics))
       }
@@ -748,7 +736,7 @@ eucast_rules <- function(x,
       }
     }
     
-    cols <- get_antibiotic_columns(target_antibiotics, cols_ab)
+    cols <- get_ab_from_namespace(target_antibiotics, cols_ab)
     
     # Apply rule on data ------------------------------------------------------
     # this will return the unique number of changes
@@ -1068,7 +1056,7 @@ eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0)
   meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))
   
   # show used version_breakpoints number once per session (pkg_env will reload every session)
-  if (message_not_thrown_before(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)) {
+  if (message_not_thrown_before("eucast_dosage",  "v", gsub("[^0-9]", "", version_breakpoints), entire_session = TRUE)) {
     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."))

R/first_isolate.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -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.
 #' 
@@ -125,7 +125,7 @@
 #' 
 #' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition**, 2014, *Clinical and Laboratory Standards Institute (CLSI)*. <https://clsi.org/standards/products/microbiology/documents/m39/>.
 #' 
-#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867–873. \doi{10.1086/511864}
+#' - Hindler JF and Stelling J (2007). **Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.** Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
 #' @inheritSection AMR Read more on Our Website!
 #' @examples
 #' # `example_isolates` is a data set available in the AMR package.
@@ -218,7 +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))
@@ -238,7 +238,7 @@ first_isolate <- function(x = NULL,
   meet_criteria(testcodes_exclude, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(icu_exclude, allow_class = "logical", has_length = 1)
   meet_criteria(specimen_group, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-  meet_criteria(type, allow_class = "character", has_length = 1)
+  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("points", "keyantimicrobials"))
   meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
   meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
   meet_criteria(info, allow_class = "logical", has_length = 1)
@@ -250,17 +250,18 @@ first_isolate <- function(x = NULL,
   
   any_col_contains_rsi <- any(vapply(FUN.VALUE = logical(1), 
                                      X = x, 
-                                     FUN = function(x) any(as.character(x) %in% c("R", "S", "I"), na.rm = TRUE),
+                                     # check only first 10,000 rows
+                                     FUN = function(x) any(as.character(x[1:10000]) %in% c("R", "S", "I"), na.rm = TRUE),
                                      USE.NAMES = FALSE))
   if (method == "phenotype-based" & !any_col_contains_rsi) {
     method <- "episode-based"
   }
-  if (info == TRUE & message_not_thrown_before("first_isolate.method")) {
-    message_(paste0("Determining first isolates using the '", font_bold(method), "' method",
+  if (info == TRUE & message_not_thrown_before("first_isolate", "method")) {
+    message_(paste0("Determining first isolates ",
                     ifelse(method %in% c("episode-based", "phenotype-based"),
                            ifelse(is.infinite(episode_days),
-                                  " without a specified episode length",
-                                  paste(" and an episode length of", episode_days, "days")),
+                                  "without a specified episode length",
+                                  paste("using an episode length of", episode_days, "days")),
                            "")),
              as_note = FALSE,
              add_fn = font_black)
@@ -359,8 +360,8 @@ first_isolate <- function(x = NULL,
     testcodes_exclude <- 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, "'")),
+  if (!is.null(testcodes_exclude) & info == TRUE & message_not_thrown_before("first_isolate", "excludingtestcodes")) {
+    message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
              add_fn = font_black,
              as_note = FALSE)
   }
@@ -372,7 +373,7 @@ first_isolate <- function(x = NULL,
   # filter on specimen group and keyantibiotics when they are filled in
   if (!is.null(specimen_group)) {
     check_columns_existance(col_specimen, x)
-    if (info == TRUE & message_not_thrown_before("first_isolate.excludingspecimen")) {
+    if (info == TRUE & message_not_thrown_before("first_isolate", "excludingspecimen")) {
       message_("Excluding other than specimen group '", specimen_group, "'",
                add_fn = font_black,
                as_note = FALSE)
@@ -443,21 +444,8 @@ first_isolate <- function(x = NULL,
                                !is.na(x$newvar_mo)), , drop = FALSE])
   
   # Analysis of first isolate ----
-  x$other_pat_or_mo <- ifelse(x$newvar_patient_id == pm_lag(x$newvar_patient_id) &
-                                x$newvar_genus_species == pm_lag(x$newvar_genus_species),
-                              FALSE,
-                              TRUE)
-  x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
-  x$more_than_episode_ago <- unlist(lapply(split(x$newvar_date,
-                                                 x$episode_group), 
-                                           is_new_episode,
-                                           episode_days = episode_days),
-                                    use.names = FALSE)
-  
-  weighted.notice <- ""
   if (!is.null(col_keyantimicrobials)) {
-    weighted.notice <- "weighted "
-    if (info == TRUE & message_not_thrown_before("first_isolate.type")) {
+    if (info == TRUE & message_not_thrown_before("first_isolate", "type")) {
       if (type == "keyantimicrobials") {
         message_("Basing inclusion on key antimicrobials, ",
                  ifelse(ignore_I == FALSE, "not ", ""),
@@ -472,21 +460,34 @@ first_isolate <- function(x = NULL,
                  as_note = FALSE)
       }
     }
-    type_param <- type
-    
+  }
+  
+  x$other_pat_or_mo <- ifelse(x$newvar_patient_id == pm_lag(x$newvar_patient_id) &
+                                x$newvar_genus_species == pm_lag(x$newvar_genus_species),
+                              FALSE,
+                              TRUE)
+  
+  x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
+  x$more_than_episode_ago <- unlist(lapply(split(x$newvar_date,
+                                                 x$episode_group),
+                                           exec_episode, # this will skip meet_criteria() in is_new_episode(), saving time
+                                           type = "logical",
+                                           episode_days = episode_days),
+                                    use.names = FALSE)
+  
+  if (!is.null(col_keyantimicrobials)) {
+    # with key antibiotics
     x$other_key_ab <- !antimicrobials_equal(y = x$newvar_key_ab,
                                             z = pm_lag(x$newvar_key_ab),
-                                            type = type_param,
+                                            type = type,
                                             ignore_I = ignore_I,
                                             points_threshold = points_threshold)
-    # with key antibiotics
     x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
                                            x$newvar_row_index_sorted <= row.end &
                                            x$newvar_genus_species != "" & 
                                            (x$other_pat_or_mo | x$more_than_episode_ago | x$other_key_ab),
                                          TRUE,
                                          FALSE)
-    
   } else {
     # no key antibiotics
     x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
@@ -568,7 +569,7 @@ first_isolate <- function(x = NULL,
   }
   
   # arrange back according to original sorting again
-  x <- x[order(x$newvar_row_index), ]
+  x <- x[order(x$newvar_row_index), , drop = FALSE]
   rownames(x) <- NULL
   
   if (info == TRUE) {
@@ -583,16 +584,16 @@ 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) {
-      msg_txt <- paste0("=> Found ",
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
-                        " (", method, ", ", p_found_scope, " within scope and ", p_found_total, " of total where a microbial ID was available)")
-    } else {
-      msg_txt <- paste0("=> Found ",
-                        font_bold(paste0(n_found, " first ", weighted.notice, "isolates")),
-                        " (", method, ", ", p_found_total, " of total where a microbial ID was available)")
-    }
-    message_(msg_txt, add_fn = font_black, as_note = FALSE)
+    message_(paste0("=> Found ",
+                    font_bold(paste0(n_found,
+                                     ifelse(method == "isolate-based", "", paste0(" '", method, "'")),
+                                     " first isolates")),
+                    " (",
+                    ifelse(p_found_total != p_found_scope,
+                           paste0(p_found_scope, " within scope and "),
+                           ""),
+                    p_found_total, " of total where a microbial ID was available)"),
+             add_fn = font_black, as_note = FALSE)
   }
   
   x$newvar_first_isolate
@@ -619,7 +620,7 @@ 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,
@@ -637,7 +638,7 @@ 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/g.test.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ggplot_pca.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/ggplot_rsi.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -158,7 +158,7 @@ ggplot_rsi <- function(data,
                        combine_SI = TRUE,
                        combine_IR = FALSE,
                        minimum = 30,
-                       language = get_locale(),
+                       language = get_AMR_locale(),
                        nrow = NULL,
                        colours = c(S = "#3CAEA3",
                                    SI = "#3CAEA3",
@@ -269,7 +269,7 @@ geom_rsi <- function(position = NULL,
                      fill = "interpretation",
                      translate_ab = "name",
                      minimum = 30,
-                     language = get_locale(),
+                     language = get_AMR_locale(),
                      combine_SI = TRUE,
                      combine_IR = FALSE,
                      ...)  {
@@ -438,7 +438,7 @@ labels_rsi_count <- function(position = NULL,
                              x = "antibiotic",
                              translate_ab = "name",
                              minimum = 30,
-                             language = get_locale(),
+                             language = get_AMR_locale(),
                              combine_SI = TRUE,
                              combine_IR = FALSE,
                              datalabels.size = 3,

R/guess_ab_col.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -75,7 +75,8 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_r
     meet_criteria(search_string, allow_class = "character", has_length = 1, allow_NULL = FALSE)
   }
   
-  all_found <- get_column_abx(x, info = verbose, only_rsi_columns = only_rsi_columns, verbose = verbose)
+  all_found <- get_column_abx(x, info = verbose, only_rsi_columns = only_rsi_columns,
+                              verbose = verbose, fn = "guess_ab_col")
   search_string.ab <- suppressWarnings(as.ab(search_string))
   ab_result <- unname(all_found[names(all_found) == search_string.ab])
   
@@ -104,10 +105,12 @@ get_column_abx <- function(x,
                            info = TRUE,
                            only_rsi_columns = FALSE,
                            sort = TRUE,
-                           reuse_previous_result = TRUE) {
-  
+                           reuse_previous_result = TRUE,
+                           fn = NULL) {
   # check if retrieved before, then get it from package environment
-  if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE), pkg_env$get_column_abx.call)) {
+  if (isTRUE(reuse_previous_result) && identical(unique_call_id(entire_session = FALSE,
+                                                                match_fn = fn),
+                                                 pkg_env$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
     
@@ -179,7 +182,7 @@ 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
@@ -192,13 +195,29 @@ get_column_abx <- function(x,
   
   # add from self-defined dots (...):
   # such as get_column_abx(example_isolates %>% rename(thisone = AMX), amox = "thisone")
+  all_okay <- TRUE
   dots <- list(...)
+  # remove data.frames, since this is also used running `eucast_rules(eucast_rules_df = df)`
+  dots <- dots[!vapply(FUN.VALUE = logical(1), dots, is.data.frame)]
   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(dot) if (is.null(dot)) NA else dot))
@@ -211,10 +230,10 @@ get_column_abx <- function(x,
   }
   
   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.call <- unique_call_id(entire_session = FALSE, match_fn = fn)
     pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
     pkg_env$get_column_abx.out <- out
     return(out)
@@ -224,33 +243,42 @@ get_column_abx <- function(x,
   if (sort == TRUE) {
     out <- out[order(names(out), out)]
   }
-  duplicates <- c(out[duplicated(out)], out[duplicated(names(out))]) 
-  duplicates <- duplicates[unique(names(duplicates))]
-  out <- c(out[!names(out) %in% names(duplicates)], duplicates)
+  # only keep the first hits, no duplicates
+  duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
+  if (length(duplicates) > 0) {
+    all_okay <- FALSE
+  }
+  
+  if (info == TRUE) {
+    if (all_okay == TRUE) {
+      message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+    } else {
+      message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+    }
+    for (i in seq_len(length(out))) {
+      if (verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
+        message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
+                 " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
+      }
+      if (names(out[i]) %in% names(duplicates)) {
+        already_set_as <- out[unname(out) == unname(out[i])][1L]
+        warning_(paste0("Column '", font_bold(out[i]), "' will not be used for ", 
+                        names(out)[i], " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")",
+                        ", as it is already set for ", 
+                        names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"),
+                 add_fn = font_red,
+                 call = FALSE, 
+                 immediate = verbose)
+      }
+    }
+  }
+  
+  out <- out[!duplicated(names(out))]
+  out <- out[!duplicated(unname(out))]
   if (sort == TRUE) {
     out <- out[order(names(out), out)]
   }
   
-  # succeeded with auto-guessing
-  if (info == TRUE) {
-    message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
-  }
-  
-  for (i in seq_len(length(out))) {
-    if (info == TRUE & verbose == TRUE & !names(out[i]) %in% names(duplicates)) {
-      message_("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
-               " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ").")
-    }
-    if (info == TRUE & names(out[i]) %in% names(duplicates)) {
-      warning_(paste0("Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
-                      " (", ab_name(names(out)[i], tolower = TRUE, language = NULL),
-                      "), although it was matched for multiple antibiotics or columns."),
-               add_fn = font_red,
-               call = FALSE, 
-               immediate = verbose)
-    }
-  }
-  
   if (!is.null(hard_dependencies)) {
     hard_dependencies <- unique(hard_dependencies)
     if (!all(hard_dependencies %in% names(out))) {
@@ -273,12 +301,34 @@ get_column_abx <- function(x,
     }
   }
   
-  pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE)
+  pkg_env$get_column_abx.call <- unique_call_id(entire_session = FALSE, match_fn = fn)
   pkg_env$get_column_abx.checked_cols <- colnames(x.bak)
   pkg_env$get_column_abx.out <- out
   out
 }
 
+get_ab_from_namespace <- function(x, cols_ab) {
+  # cols_ab comes from get_column_abx()
+  
+  x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
+  x_new <- character()
+  for (val in x) {
+    if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
+      # antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
+      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)
+    } else {
+      stop_("unknown antimicrobial agent (group): ", val, call = FALSE)
+    }
+    x_new <- c(x_new, val)
+  }
+  x_new <- unique(x_new)
+  out <- cols_ab[match(x_new, names(cols_ab))]
+  out[!is.na(out)]
+}
+
 generate_warning_abs_missing <- function(missing, any = FALSE) {
   missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE, language = NULL), ")")
   if (any == TRUE) {

R/italicise_taxonomy.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -26,7 +26,7 @@
 #' Italicise Taxonomic Families, Genera, Species, Subspecies
 #' 
 #' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italic. This function finds taxonomic names within strings and makes them italic.
-#' @inheritSection lifecycle Maturing Lifecycle
+#' @inheritSection lifecycle Stable Lifecycle
 #' @param string a [character] (vector)
 #' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
 #' @details 

R/join_microorganisms.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/key_antimicrobials.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -142,7 +142,7 @@ key_antimicrobials <- function(x = NULL,
   
   # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
-  cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
+  cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns, fn = "key_antimicrobials")
   
   # try to find columns based on type
   # -- mo
@@ -171,7 +171,7 @@ key_antimicrobials <- function(x = NULL,
     
     if (values_new_length < values_old_length &
         any(filter, na.rm = TRUE) &
-        message_not_thrown_before(paste0("key_antimicrobials.", name))) {
+        message_not_thrown_before("key_antimicrobials", name)) {
       warning_(ifelse(values_new_length == 0,
                       "No columns available ",
                       paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
@@ -238,7 +238,8 @@ all_antimicrobials <- function(x = NULL,
   
   # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)
-  cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE)
+  cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE,
+                         sort = FALSE, fn = "all_antimicrobials")
   
   generate_antimcrobials_string(x[ , cols, drop = FALSE])
 }
@@ -250,16 +251,16 @@ generate_antimcrobials_string <- function(df) {
   if (NROW(df) == 0) {
     return(character(0))
   }
-  out <- tryCatch(
+  tryCatch({
     do.call(paste0,
             lapply(as.list(df),
                    function(x) {
                      x <- toupper(as.character(x))
                      x[!x %in% c("R", "S", "I")] <- "."
                      paste(x)
-                   })),
-    error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
-  out
+                   }))
+  },
+  error = function(e) rep(strrep(".", NCOL(df)), NROW(df)))
 }
 
 #' @rdname key_antimicrobials
@@ -279,10 +280,20 @@ antimicrobials_equal <- function(y,
   stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
 
   key2rsi <- function(val) {
-    as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
+    val <- strsplit(val, "")[[1L]]
+    val.int <- rep(NA_real_, length(val))
+    val.int[val == "S"] <- 1
+    val.int[val == "I"] <- 2
+    val.int[val == "R"] <- 3
+    val.int
   }
-  y <- lapply(y, key2rsi)
-  z <- lapply(z, key2rsi)
+  # only run on uniques
+  uniq <- unique(c(y, z))
+  uniq_list <- lapply(uniq, key2rsi)
+  names(uniq_list) <- uniq
+  
+  y <- uniq_list[match(y, names(uniq_list))]
+  z <- uniq_list[match(z, names(uniq_list))]
   
   determine_equality <- function(a, b, type, points_threshold, ignore_I) {
     if (length(a) != length(b)) {

R/kurtosis.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/lifecycle.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -44,7 +44,7 @@
 #' \if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **stable**. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
 #' 
-#' If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
+#' If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
 #' @section Retired Lifecycle:
 #' \if{html}{\figure{lifecycle_retired.svg}{options: style=margin-bottom:5px} \cr}
 #' The [lifecycle][AMR::lifecycle] of this function is **retired**. A retired function is no longer under active development, and (if appropiate) a better alternative is available. No new arguments will be added, and only the most critical bugs will be fixed. In a future version, this function will be removed.

R/like.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -69,7 +69,7 @@
 #' # get isolates whose name start with 'Ent' or 'ent'
 #' example_isolates[which(mo_name(example_isolates$mo) %like% "^ent"), ]
 #' \donttest{
-#' # faster way, only works in R 3.2 and later:
+#' # faster way, since mo_name() is context-aware:
 #' example_isolates[which(mo_name() %like% "^ent"), ]
 #' 
 #' if (require("dplyr")) {
@@ -124,31 +124,23 @@ like <- function(x, pattern, ignore.case = TRUE) {
 #' @rdname like
 #' @export
 "%like%" <- function(x, pattern) {
-  meet_criteria(x, allow_NA = TRUE)
-  meet_criteria(pattern, allow_NA = FALSE)
   like(x, pattern, ignore.case = TRUE)
 }
 
 #' @rdname like
 #' @export
 "%unlike%" <- function(x, pattern) {
-  meet_criteria(x, allow_NA = TRUE)
-  meet_criteria(pattern, allow_NA = FALSE)
   !like(x, pattern, ignore.case = TRUE)
 }
 
 #' @rdname like
 #' @export
 "%like_case%" <- function(x, pattern) {
-  meet_criteria(x, allow_NA = TRUE)
-  meet_criteria(pattern, allow_NA = FALSE)
   like(x, pattern, ignore.case = FALSE)
 }
 
 #' @rdname like
 #' @export
 "%unlike_case%" <- function(x, pattern) {
-  meet_criteria(x, allow_NA = TRUE)
-  meet_criteria(pattern, allow_NA = FALSE)
   !like(x, pattern, ignore.case = FALSE)
 }

R/mdro.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -51,7 +51,11 @@
 #'
 #'   Magiorakos AP, Srinivasan A *et al.* "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) ([link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext))
 #' 
-#' * `guideline = "EUCAST3.2"` (or simply `guideline = "EUCAST"`)
+#' * `guideline = "EUCAST3.3"` (or simply `guideline = "EUCAST"`)
+#'
+#'   The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf))
+#'   
+#' * `guideline = "EUCAST3.2"`
 #'
 #'   The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf))
 #' 
@@ -73,7 +77,6 @@
 #' 
 #' Please suggest your own (country-specific) guidelines by letting us know: <https://github.com/msberends/AMR/issues/new>.
 #' 
-#' 
 #' @section Using Custom Guidelines:
 #' 
 #' Custom guidelines can be set with the [custom_mdro_guideline()] 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.
@@ -283,7 +286,7 @@ mdro <- function(x = NULL,
   }
   if (guideline == "eucast") {
     # turn into latest EUCAST guideline
-    guideline <- "eucast3.2"
+    guideline <- "eucast3.3"
   }
   if (guideline == "nl") {
     guideline <- "brmo"
@@ -291,7 +294,7 @@ mdro <- function(x = NULL,
   if (guideline == "de") {
     guideline <- "mrgn"
   }
-  stop_ifnot(guideline %in% c("brmo", "mrgn", "eucast3.1", "eucast3.2", "tb", "cmi2012"),
+  stop_ifnot(guideline %in% c("brmo", "mrgn", "eucast3.1", "eucast3.2", "eucast3.3", "tb", "cmi2012"),
              "invalid guideline: ", guideline.bak)
   guideline <- list(code = guideline)
   
@@ -325,10 +328,17 @@ mdro <- function(x = NULL,
   } else if (guideline$code == "eucast3.2") {
     guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
     guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
-    guideline$version <- "3.2, 2020"
+    guideline$version <- "3.2, February 2020"
     guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
     guideline$type <- "EUCAST Unusual Phenotypes"
     
+  } else if (guideline$code == "eucast3.3") {
+    guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
+    guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
+    guideline$version <- "3.3, October 2021"
+    guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf"
+    guideline$type <- "EUCAST Unusual Phenotypes"
+    
   } else if (guideline$code == "tb") {
     guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
     guideline$author <- "WHO (World Health Organization)"
@@ -474,6 +484,7 @@ mdro <- function(x = NULL,
                               verbose = verbose,
                               info = info,
                               only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
                               ...)
   } else if (guideline$code == "eucast3.2") {
     cols_ab <- get_column_abx(x = x,
@@ -502,6 +513,36 @@ mdro <- function(x = NULL,
                               verbose = verbose,
                               info = info,
                               only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
+                              ...)
+  } else if (guideline$code == "eucast3.3") {
+    cols_ab <- get_column_abx(x = x,
+                              soft_dependencies = c("AMP",
+                                                    "AMX",
+                                                    "CIP",
+                                                    "DAL",
+                                                    "DAP",
+                                                    "ERV",
+                                                    "FDX",
+                                                    "GEN",
+                                                    "LNZ",
+                                                    "MEM",
+                                                    "MTR",
+                                                    "OMC",
+                                                    "ORI",
+                                                    "PEN",
+                                                    "QDA",
+                                                    "RIF",
+                                                    "TEC",
+                                                    "TGC",
+                                                    "TLV",
+                                                    "TOB",
+                                                    "TZD",
+                                                    "VAN"),
+                              verbose = verbose,
+                              info = info,
+                              only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
                               ...)
   } else if (guideline$code == "tb") {
     cols_ab <- get_column_abx(x = x,
@@ -516,6 +557,7 @@ mdro <- function(x = NULL,
                               verbose = verbose,
                               info = info,
                               only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
                               ...)
   } else if (guideline$code == "mrgn") {
     cols_ab <- get_column_abx(x = x,
@@ -528,14 +570,23 @@ mdro <- function(x = NULL,
                               verbose = verbose,
                               info = info,
                               only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
                               ...)
   } else {
     cols_ab <- get_column_abx(x = x,
                               verbose = verbose,
                               info = info,
                               only_rsi_columns = only_rsi_columns,
+                              fn = "mdro",
                               ...)
   }
+  if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) {
+    # ampicillin column is missing, but amoxicillin is available
+    if (info == TRUE) {
+      message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.")
+    }
+    cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
+  }
 
   # nolint start
   AMC <- cols_ab["AMC"]
@@ -738,7 +789,8 @@ mdro <- function(x = NULL,
       x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
                                                    rows, 
                                                    function(row, group_vct = cols) {
-                                                     cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE], 
+                                                     cols_nonsus <- vapply(FUN.VALUE = logical(1),
+                                                                           x[row, group_vct, drop = FALSE], 
                                                                            function(y) y %in% search_result)
                                                      paste(sort(c(unlist(strsplit(x[row, "columns_nonsusceptible", drop = TRUE], ", ")),
                                                                   names(cols_nonsus)[cols_nonsus])), 
@@ -752,17 +804,20 @@ mdro <- function(x = NULL,
       }
       x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE]),
                                             stringsAsFactors = FALSE))
-      row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
-      row_filter <- x[which(row_filter), "row_number", drop = TRUE]
-      rows <- rows[rows %in% row_filter]
-      x[rows, "MDRO"] <<- to
-      x[rows, "reason"] <<- paste0(any_all, 
-                                   " of the required antibiotics ",
-                                   ifelse(any_all == "any", "is", "are"),
-                                   " R",
-                                   ifelse(!isTRUE(combine_SI), " or I", ""))
+      rows_affected <- vapply(FUN.VALUE = logical(1),
+                              x_transposed,
+                              function(y) search_function(y %in% search_result, na.rm = TRUE))
+      rows_affected <- x[which(rows_affected), "row_number", drop = TRUE]
+      rows_to_change <- rows[rows %in% rows_affected]
+      x[rows_to_change, "MDRO"] <<- to
+      x[rows_to_change, "reason"] <<- paste0(any_all, 
+                                             " of the required antibiotics ",
+                                             ifelse(any_all == "any", "is", "are"),
+                                             " R",
+                                             ifelse(!isTRUE(combine_SI), " or I", ""))
     }
   }
+  
   trans_tbl2 <- function(txt, rows, lst) {
     if (info == TRUE) {
       message_(txt, "...", appendLF = FALSE, as_note = FALSE)
@@ -1160,10 +1215,80 @@ mdro <- function(x = NULL,
               which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
               c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
               "any")
-    streps <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE]
-    streps_ABCG <- streps[as.mo(streps, Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")]
     trans_tbl(3, # Sr. groups A/B/C/G
-              which(x$mo %in% streps_ABCG),
+              which(x$mo %in% MO_STREP_ABCG),
+              c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Enterococcus"),
+              c(DAP, LNZ, TGC, ERV, OMC, TEC),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Enterococcus" & x$species == "faecalis"),
+              c(AMP, AMX),
+              "any")
+    # Table 8
+    trans_tbl(3,
+              which(x$genus == "Bacteroides"),
+              MTR,
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Clostridium" & x$species == "difficile"),
+              c(MTR, VAN, FDX),
+              "any")
+  }
+  
+  if (guideline$code == "eucast3.3") {
+    # EUCAST 3.3 --------------------------------------------------------------
+    # note: this guideline is equal to EUCAST 3.2 - no MDRO insights changed
+    # Table 6
+    trans_tbl(3,
+              which((x$order == "Enterobacterales" &
+                       !x$family == "Morganellaceae" & 
+                       !(x$genus == "Serratia" & x$species == "marcescens"))
+                    | (x$genus == "Pseudomonas" & x$species == "aeruginosa")
+                    | x$genus == "Acinetobacter"),
+              COL,
+              "all")
+    trans_tbl(3,
+              which(x$genus == "Salmonella" & x$species == "Typhi"),
+              c(carbapenems),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Haemophilus" & x$species == "influenzae"),
+              c(cephalosporins_3rd, carbapenems, fluoroquinolones),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Moraxella" & x$species == "catarrhalis"),
+              c(cephalosporins_3rd, fluoroquinolones),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Neisseria" & x$species == "meningitidis"),
+              c(cephalosporins_3rd, fluoroquinolones),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Neisseria" & x$species == "gonorrhoeae"),
+              SPT,
+              "any")
+    # Table 7
+    trans_tbl(3,
+              which(x$genus == "Staphylococcus" & x$species == "aureus"),
+              c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
+              "any")
+    trans_tbl(3,
+              which(x$mo %in% MO_CONS), # coagulase-negative Staphylococcus
+              c(VAN, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Corynebacterium"),
+              c(VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC),
+              "any")
+    trans_tbl(3,
+              which(x$genus == "Streptococcus" & x$species == "pneumoniae"),
+              c(carbapenems, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC, RIF),
+              "any")
+    trans_tbl(3, # Sr. groups A/B/C/G
+              which(x$mo %in% MO_STREP_ABCG),
               c(PEN, cephalosporins, VAN, TEC, TLV, DAL, ORI, DAP, LNZ, TZD, QDA, TGC, ERV, OMC),
               "any")
     trans_tbl(3,
@@ -1382,16 +1507,6 @@ mdro <- function(x = NULL,
     x$reason <- "PDR/MDR/XDR criteria were met"
   }
   
-  if (info.bak == TRUE) {
-    cat(group_msg)
-    if (sum(!is.na(x$MDRO)) == 0) {
-      cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the guideline")))
-    } else {
-      cat(font_bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " ", guideline$type, " out of ", sum(!is.na(x$MDRO)), 
-                           " isolates (", trimws(percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")\n")))
-    }
-  }
-  
   # some more info on negative results
   if (verbose == TRUE) {
     if (guideline$code == "cmi2012") {
@@ -1406,10 +1521,35 @@ mdro <- function(x = NULL,
     }
   }
   
+  if (info.bak == TRUE) {
+    cat(group_msg)
+    if (sum(!is.na(x$MDRO)) == 0) {
+      cat(font_bold(paste0("=> Found 0 MDROs since no isolates are covered by the guideline")))
+    } else {
+      cat(font_bold(paste0("=> Found ", sum(x$MDRO %in% c(2:5), na.rm = TRUE), " ", guideline$type, " out of ", sum(!is.na(x$MDRO)), 
+                           " isolates (", trimws(percentage(sum(x$MDRO %in% c(2:5), na.rm = TRUE) / sum(!is.na(x$MDRO)))), ")")))
+    }
+  }
+  
+  # Fill in blanks ----
+  # for rows that have no results
+  x_transposed <- as.list(as.data.frame(t(x[, cols_ab, drop = FALSE]),
+                                        stringsAsFactors = FALSE))
+  rows_empty <- which(vapply(FUN.VALUE = logical(1),
+                             x_transposed,
+                             function(y) all(is.na(y))))
+  if (length(rows_empty) > 0) {
+    cat(font_italic(paste0(" (", length(rows_empty), " isolates had no test results)\n")))
+    x[rows_empty, "MDRO"] <- NA
+    x[rows_empty, "reason"] <- "none of the antibiotics have test results"
+  } else {
+    cat("\n")
+  }
+  
   # Results ----
   if (guideline$code == "cmi2012") {
     if (any(x$MDRO == -1, na.rm = TRUE)) {
-      if (message_not_thrown_before("mdro.availability")) {
+      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)
       }

R/mic.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -23,9 +23,26 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# these are allowed MIC values and will become [factor] levels
+ops <- c("<", "<=", "", ">=", ">")
+valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
+                                 function(x) paste0(x, "0.00", 1:9)))),
+                      unique(c(t(vapply(FUN.VALUE = character(104), ops,
+                                        function(x) paste0(x, sort(as.double(paste0("0.0", 
+                                                                                    sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
+                      unique(c(t(vapply(FUN.VALUE = character(103), ops,
+                                        function(x) paste0(x, sort(as.double(paste0("0.", 
+                                                                                    c(1:99, 125, 128, 256, 512))))))))),
+                      c(t(vapply(FUN.VALUE = character(10), ops,
+                                 function(x) paste0(x, sort(c(1:9, 1.5)))))),
+                      c(t(vapply(FUN.VALUE = character(45), ops,
+                                 function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
+                      c(t(vapply(FUN.VALUE = character(16), ops,
+                                 function(x) paste0(x, sort(c(2 ^ c(7:11), 80 * c(2:12))))))))
+
 #' Transform Input to Minimum Inhibitory Concentrations (MIC)
 #'
-#' This ransforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
+#' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
 #' @inheritSection lifecycle Stable Lifecycle
 #' @rdname as.mic
 #' @param x a [character] or [numeric] vector
@@ -117,6 +134,8 @@ as.mic <- function(x, na.rm = FALSE) {
     # transform Unicode for >= and <=
     x <- gsub("\u2264", "<=", x, fixed = TRUE)
     x <- gsub("\u2265", ">=", x, fixed = TRUE)
+    # remove other invalid characters
+    x <- gsub("[^a-zA-Z0-9.><= ]+", "", x, perl = TRUE)
     # remove space between operator and number ("<= 0.002" -> "<=0.002")
     x <- gsub("(<|=|>) +", "\\1", x, perl = TRUE)
     # transform => to >= and =< to <=
@@ -141,27 +160,14 @@ as.mic <- function(x, na.rm = FALSE) {
     x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
     # never end with dot
     x <- gsub("[.]$", "", x, perl = TRUE)
-    # force to be character
-    x <- as.character(x)
     # trim it
     x <- trimws(x)
     
     ## previously unempty values now empty - should return a warning later on
     x[x.bak != "" & x == ""] <- "invalid"
     
-    # these are allowed MIC values and will become [factor] levels
-    ops <- c("<", "<=", "", ">=", ">")
-    lvls <- c(c(t(vapply(FUN.VALUE = character(9), ops, function(x) paste0(x, "0.00", 1:9)))),
-              unique(c(t(vapply(FUN.VALUE = character(104), ops, function(x) paste0(x, sort(as.double(paste0("0.0", 
-                                                                                 sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
-              unique(c(t(vapply(FUN.VALUE = character(103), ops, function(x) paste0(x, sort(as.double(paste0("0.", 
-                                                                                 c(1:99, 125, 128, 256, 512))))))))),
-              c(t(vapply(FUN.VALUE = character(10), ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
-              c(t(vapply(FUN.VALUE = character(45), ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
-              c(t(vapply(FUN.VALUE = character(15), ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
-    
     na_before <- x[is.na(x) | x == ""] %pm>% length()
-    x[!x %in% lvls] <- NA
+    x[!x %in% valid_mic_levels] <- NA
     na_after <- x[is.na(x) | x == ""] %pm>% length()
     
     if (na_before != na_after) {
@@ -175,7 +181,7 @@ as.mic <- function(x, na.rm = FALSE) {
                list_missing, call = FALSE)
     }
     
-    set_clean_class(factor(x, levels = lvls, ordered = TRUE),
+    set_clean_class(factor(x, levels = valid_mic_levels, ordered = TRUE),
                     new_class =  c("mic", "ordered", "factor"))
   }
 }
@@ -189,6 +195,12 @@ all_valid_mics <- function(x) {
   !any(is.na(x_mic)) && !all(is.na(x))
 }
 
+#' @rdname as.mic
+#' @details `NA_mic_` is a missing value of the new `<mic>` class.
+#' @export
+NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
+                           new_class =  c("mic", "ordered", "factor"))
+
 #' @rdname as.mic
 #' @export
 is.mic <- function(x) {
@@ -616,6 +628,12 @@ cummin.mic <- function(x) {
 
 # Ops (see ?groupGeneric) -----------------------------------------------
 
+is_greater <- function(el) {
+  el %like_case% ">[0-9]"
+}
+is_lower <- function(el) {
+  el %like_case% "<[0-9]"
+}
 
 #' @method + mic
 #' @export
@@ -727,6 +745,12 @@ cummin.mic <- function(x) {
 #' @noRd
 `>.mic` <- function(e1, e2) {
   as.double(e1) > as.double(e2)
+  # doesn't work...
+  # nolint start
+  # as.double(e1) > as.double(e2) |
+  #   (as.double(e1) == as.double(e2) & is_lower(e2) & !is_lower(e1)) |
+  #   (as.double(e1) == as.double(e2) & is_greater(e1) & !is_greater(e2))
+  # nolint end
 }
 
 # Summary (see ?groupGeneric) -------------------------------------------

R/mo.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -37,7 +37,7 @@
 #' @param allow_uncertain a number between `0` (or `"none"`) and `3` (or `"all"`), or `TRUE` (= `2`) or `FALSE` (= `0`) to indicate whether the input should be checked for less probable results, see *Details*
 #' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
 #' @param ignore_pattern a regular expression (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
-#' @param language language to translate text like "no growth", which defaults to the system language (see [get_locale()])
+#' @param language language to translate text like "no growth", which defaults to the system language (see [get_AMR_locale()])
 #' @param info a [logical] to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to `TRUE` only in interactive mode
 #' @param ... other arguments passed on to functions
 #' @rdname as.mo
@@ -103,10 +103,10 @@
 #' @inheritSection catalogue_of_life Catalogue of Life
 #  (source as a section here, so it can be inherited by other man pages:)
 #' @section Source:
-#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870–926; \doi{10.1128/CMR.00109-13}
+#' 1. Becker K *et al.* **Coagulase-Negative Staphylococci**. 2014. Clin Microbiol Rev. 27(4): 870-926; \doi{10.1128/CMR.00109-13}
 #' 2. Becker K *et al.* **Implications of identifying the recently defined members of the *S. aureus* complex, *S. argenteus* and *S. schweitzeri*: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).** 2019. Clin Microbiol Infect; \doi{10.1016/j.cmi.2019.02.028}
 #' 3. Becker K *et al.* **Emergence of coagulase-negative staphylococci** 2020. Expert Rev Anti Infect Ther. 18(4):349-366; \doi{10.1080/14787210.2020.1730813}
-#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571–95; \doi{10.1084/jem.57.4.571}
+#' 4. Lancefield RC **A serological differentiation of human and other groups of hemolytic streptococci**. 1933. J Exp Med. 57(4): 571-95; \doi{10.1084/jem.57.4.571}
 #' 5. `r gsub("{year}", CATALOGUE_OF_LIFE$year, CATALOGUE_OF_LIFE$version, fixed = TRUE)`, <http://www.catalogueoflife.org>
 #' 6. List of Prokaryotic names with Standing in Nomenclature (`r CATALOGUE_OF_LIFE$yearmonth_LPSN`), \doi{10.1099/ijsem.0.004332}
 #' 7. `r SNOMED_VERSION$current_source`, retrieved from the `r SNOMED_VERSION$title`, OID `r SNOMED_VERSION$current_oid`, version `r SNOMED_VERSION$current_version`; url: <`r SNOMED_VERSION$url`>
@@ -161,7 +161,7 @@ as.mo <- function(x,
                   allow_uncertain = TRUE,
                   reference_df = get_mo_source(),
                   ignore_pattern = getOption("AMR_ignore_pattern"),
-                  language = get_locale(),
+                  language = get_AMR_locale(),
                   info = interactive(),
                   ...) {
   meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
@@ -201,7 +201,8 @@ as.mo <- function(x,
                & isFALSE(Becker)
                & isFALSE(Lancefield), error = function(e) FALSE)) {
     # to improve speed, special case for taxonomically correct full names (case-insensitive)
-    return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
+    return(set_clean_class(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE],
+                           new_class = c("mo", "character")))
   }
 
   if (!is.null(reference_df)
@@ -233,7 +234,7 @@ as.mo <- function(x,
                      info = info,
                      ...)
   }
-
+  
   set_clean_class(y,
                   new_class = c("mo", "character"))
 }
@@ -266,7 +267,7 @@ exec_as.mo <- function(x,
                        reference_data_to_use = MO_lookup,
                        actual_uncertainty = 1,
                        actual_input = NULL,
-                       language = get_locale()) {
+                       language = get_AMR_locale()) {
   meet_criteria(x, allow_class = c("mo", "data.frame", "list", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
   meet_criteria(Becker, allow_class = c("logical", "character"), has_length = 1)
   meet_criteria(Lancefield, allow_class = c("logical", "character"), has_length = 1)
@@ -372,7 +373,7 @@ exec_as.mo <- function(x,
   # Laboratory systems: remove (translated) entries like "no growth", etc.
   x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
   x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
-
+  
   if (initial_search == TRUE) {
     # keep track of time - give some hints to improve speed if it takes a long time
     start_time <- Sys.time()
@@ -468,7 +469,7 @@ exec_as.mo <- function(x,
     x_backup_untouched <- 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)) {
+    if (any(tolower(x) %like_case% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
       trns <- subset(TRANSLATIONS, pattern %like% "unknown")
       langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
       for (l in langs) {
@@ -484,6 +485,10 @@ exec_as.mo <- function(x,
       }
     }
     
+    # remove spp and species
+    x <- gsub("(^| )[ .]*(spp|ssp|ss|sp|subsp|subspecies|biovar|biotype|serovar|species)[ .]*( |$)", "", x, ignore.case = TRUE, perl = TRUE)
+    x <- strip_whitespace(x, dyslexia_mode)
+    
     x_backup <- x
     
     # from here on case-insensitive
@@ -495,26 +500,26 @@ exec_as.mo <- function(x,
     # 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$mo
-    x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
-    already_known <- known_names | known_codes
-
+    known_codes_mo <- toupper(x_backup) %in% MO_lookup$mo
+    x[known_codes_mo] <- MO_lookup[match(toupper(x_backup)[known_codes_mo], MO_lookup$mo), property, drop = TRUE]
+    known_codes_lis <- toupper(x_backup) %in% microorganisms.codes$code
+    x[known_codes_lis] <- MO_lookup[match(microorganisms.codes[match(toupper(x_backup)[known_codes_lis],
+                                                                     microorganisms.codes$code), "mo", drop = TRUE],
+                                          MO_lookup$mo), property, drop = TRUE]
+    already_known <- known_names | known_codes_mo | known_codes_lis
+    
     # now only continue where the right taxonomic output is not already known
     if (any(!already_known)) {
       x_known <- x[already_known]
-
-      # remove spp and species
-      x <- gsub(" +(spp.?|ssp.?|sp.? |ss ?.?|subsp.?|subspecies|biovar |serovar |species)", " ", x)
-      x <- gsub("(spp.?|subsp.?|subspecies|biovar|serovar|species)", "", x)
-      x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE) # when ending in SPE instead of SPP and preceded by 2-4 characters
-      x <- strip_whitespace(x, dyslexia_mode)
       
+      # when ending in SPE instead of SPP and preceded by 2-4 characters
+      x <- gsub("^([a-z]{2,4})(spe.?)$", "\\1", x, perl = TRUE)
+
       x_backup_without_spp <- x
-      x_species <- paste(x, "species")
       # translate to English for supported languages of mo_property
       x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, perl = TRUE)
       # no groups and complexes as ending
-      x <- gsub("(complex|group)$", "", x, perl = TRUE)
+      x <- gsub("(complex|group|serotype|serovar|serogroup)[^a-zA-Z]*$", "", x, perl = TRUE)
       x <- gsub("(^|[^a-z])((an)?aero+b)[a-z]*", "", x, perl = TRUE)
       x <- gsub("^atyp[a-z]*", "", x, perl = TRUE)
       x <- gsub("(vergroen)[a-z]*", "viridans", x, perl = TRUE)
@@ -541,12 +546,12 @@ exec_as.mo <- function(x,
       # allow characters that resemble others = dyslexia_mode ----
       if (dyslexia_mode == TRUE) {
         x <- tolower(x)
-        x <- gsub("[iy]+", "[iy]+", x)
-        x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
-        x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x)
-        x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
-        x <- gsub("a+", "a+", x)
-        x <- gsub("u+", "u+", x)
+        x <- gsub("[iy]+", "[iy]+", x, perl = TRUE)
+        x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x, perl = TRUE)
+        x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x, perl = TRUE)
+        x <- gsub("(th|ht|t)+", "(th|ht|t)+", x, perl = TRUE)
+        x <- gsub("a+", "a+", x, perl = TRUE)
+        x <- gsub("u+", "u+", x, perl = TRUE)
         # allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup):
         x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
                   "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
@@ -556,9 +561,9 @@ exec_as.mo <- function(x,
                   "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE)
         x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])",
                   "([iy]*a+|[iy]+a*)", x, perl = TRUE)
-        x <- gsub("e+", "e+", x)
-        x <- gsub("o+", "o+", x)
-        x <- gsub("(.)\\1+", "\\1+", x)
+        x <- gsub("e+", "e+", x, perl = TRUE)
+        x <- gsub("o+", "o+", x, perl = TRUE)
+        x <- gsub("(.)\\1+", "\\1+", x, perl = TRUE)
         # allow multiplication of all other consonants
         x <- gsub("([bdgjlnrw]+)", "\\1+", x, perl = TRUE)
         # allow ending in -en or -us
@@ -570,6 +575,8 @@ exec_as.mo <- function(x,
         # allow au and ou after all above regex implementations
         x <- gsub("a+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
         x <- gsub("o+[bcdfghjklmnpqrstvwxyz]?u+[bcdfghjklmnpqrstvwxyz]?", "(a+u+|o+u+)[bcdfghjklmnpqrstvwxyz]?", x, fixed = TRUE)
+        # correct for a forgotten Latin ae instead of e
+        x <- gsub("e+", "a*e+", x, fixed = TRUE)
       }
       x <- strip_whitespace(x, dyslexia_mode)
       # make sure to remove regex overkill (will lead to errors)
@@ -577,10 +584,9 @@ exec_as.mo <- function(x,
       x <- gsub("?+", "?", x, fixed = TRUE)
       
       x_trimmed <- x
-      x_trimmed_species <- paste(x_trimmed, "species")
       x_trimmed_without_group <- gsub(" gro.u.p$", "", x_trimmed, perl = TRUE)
       # remove last part from "-" or "/"
-      x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
+      x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group, perl = TRUE)
       # replace space and dot by regex sign
       x_withspaces <- gsub("[ .]+", ".* ", x, perl = TRUE)
       x <- gsub("[ .]+", ".*", x, perl = TRUE)
@@ -593,14 +599,12 @@ exec_as.mo <- function(x,
       
       if (isTRUE(debug)) {
         cat(paste0(font_blue("x"), '                       "', x, '"\n'))
-        cat(paste0(font_blue("x_species"), '               "', x_species, '"\n'))
         cat(paste0(font_blue("x_withspaces_start_only"), ' "', x_withspaces_start_only, '"\n'))
         cat(paste0(font_blue("x_withspaces_end_only"), '   "', x_withspaces_end_only, '"\n'))
         cat(paste0(font_blue("x_withspaces_start_end"), '  "', x_withspaces_start_end, '"\n'))
         cat(paste0(font_blue("x_backup"), '                "', x_backup, '"\n'))
         cat(paste0(font_blue("x_backup_without_spp"), '    "', x_backup_without_spp, '"\n'))
         cat(paste0(font_blue("x_trimmed"), '               "', x_trimmed, '"\n'))
-        cat(paste0(font_blue("x_trimmed_species"), '       "', x_trimmed_species, '"\n'))
         cat(paste0(font_blue("x_trimmed_without_group"), ' "', x_trimmed_without_group, '"\n'))
       }
       
@@ -712,7 +716,7 @@ exec_as.mo <- function(x,
           # fewer than 3 chars and not looked for species, add as failure
           x[i] <- lookup(mo == "UNKNOWN")
           if (initial_search == TRUE) {
-            failures <- c(failures, x_backup[i])
+            failures <- c(failures, x_backup_untouched[i])
           }
           next
         }
@@ -749,7 +753,7 @@ exec_as.mo <- function(x,
         # - EIEC (Entero-Invasive E. coli)
         # - EPEC (Entero-Pathogenic E. coli)
         # - ETEC (Entero-Toxigenic E. coli)
-        # - NMEC (Neonatal Meningitis‐causing E. coli)
+        # - NMEC (Neonatal Meningitis-causing E. coli)
         # - STEC (Shiga-toxin producing E. coli)
         # - UPEC (Uropathogenic E. coli)
         if (toupper(x_backup_without_spp[i]) %in% c("AIEC", "ATEC", "DAEC", "EAEC", "EHEC", "EIEC", "EPEC", "ETEC", "NMEC", "STEC", "UPEC")
@@ -799,7 +803,7 @@ exec_as.mo <- function(x,
                                             perl = TRUE)), uncertainty = -1)
           next
         }
-        if (x_backup_without_spp[i] %like_case% "haemoly.*strep") {
+        if (x_backup_without_spp[i] %like_case% "ha?emoly.*strep") {
           # Haemolytic streptococci in different languages
           x[i] <- lookup(mo == "B_STRPT_HAEM", uncertainty = -1)
           next
@@ -895,7 +899,7 @@ exec_as.mo <- function(x,
           # (at this point the latest reference_df has also been checked)
           x[i] <- lookup(mo == "UNKNOWN")
           if (initial_search == TRUE) {
-            failures <- c(failures, x_backup[i])
+            failures <- c(failures, x_backup_untouched[i])
           }
           next
         }
@@ -909,20 +913,12 @@ exec_as.mo <- function(x,
                                          d.x_withspaces_start_end,
                                          e.x_withspaces_start_only,
                                          f.x_withspaces_end_only,
-                                         g.x_backup_without_spp,
-                                         h.x_species,
-                                         i.x_trimmed_species) {
+                                         g.x_backup_without_spp) {
           
           # FIRST TRY FULLNAMES AND CODES ----
           # if only genus is available, return only genus
           
           if (all(c(x[i], b.x_trimmed) %unlike_case% " ")) {
-            found <- lookup(fullname_lower %in% c(h.x_species, i.x_trimmed_species),
-                            haystack = data_to_check)
-            if (!is.na(found)) {
-              x[i] <- found[1L]
-              return(x[i])
-            }
             if (nchar(g.x_backup_without_spp) >= 6) {
               found <- lookup(fullname_lower %like_case% paste0("^", unregex(g.x_backup_without_spp), "[a-z]+"),
                               haystack = data_to_check)
@@ -1420,18 +1416,15 @@ exec_as.mo <- function(x,
                                      d.x_withspaces_start_end = x_withspaces_start_end[i],
                                      e.x_withspaces_start_only = x_withspaces_start_only[i],
                                      f.x_withspaces_end_only = x_withspaces_end_only[i],
-                                     g.x_backup_without_spp = x_backup_without_spp[i],
-                                     h.x_species = x_species[i],
-                                     i.x_trimmed_species = x_trimmed_species[i])
+                                     g.x_backup_without_spp = x_backup_without_spp[i])
         if (!empty_result(x[i])) {
           next
         }
         
-        
         # no results found: make them UNKNOWN ----
         x[i] <- lookup(mo == "UNKNOWN", uncertainty = -1)
         if (initial_search == TRUE) {
-          failures <- c(failures, x_backup[i])
+          failures <- c(failures, x_backup_untouched[i])
         }
       }
       
@@ -1476,14 +1469,22 @@ exec_as.mo <- function(x,
       if (NROW(uncertainties) > 0 & initial_search == TRUE) {
         uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE))
         pkg_env$mo_uncertainties <- uncertainties
-        
-        plural <- c("", "it", "was")
-        if (length(uncertainties$input) > 1) {
-          plural <- c("s", "them", "were")
+        if (message_not_thrown_before("as.mo", "uncertainties", uncertainties$input)) {
+          plural <- c("", "this")
+          if (length(uncertainties$input) > 1) {
+            plural <- c("s", "these uncertainties")
+          }
+          if (length(uncertainties$input) <= 3) {
+            examples <- vector_and(paste0('"', uncertainties$input,
+                                          '" (assuming ', font_italic(uncertainties$fullname, collapse = NULL), ")"),
+                                   quotes = FALSE)
+          } else {
+            examples <- paste0(nr2char(length(uncertainties$input)), " microorganism", plural[1])
+          }
+          msg <- paste0("Function `as.mo()` is uncertain about ", examples,
+                        ". Run `mo_uncertainties()` to review ", plural[2], ".")
+          message_(msg)
         }
-        msg <- paste0("Translation is uncertain of ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
-                      ". Use `mo_uncertainties()` to review ", plural[2], ".")
-        message_(msg)
       }
       x[already_known] <- x_known
     }
@@ -1495,20 +1496,23 @@ exec_as.mo <- function(x,
     # - Becker et al. 2014, PMID 25278577
     # - Becker et al. 2019, PMID 30872103
     # - Becker et al. 2020, PMID 32056452
-    post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers (otherwise uncomment the section below)
+    post_Becker <- c("caledonicus", "canis", "durrellii", "lloydii", "roterodami")
     
     # nolint start
-    # if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
-    #   warning_("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ",
-    #            font_italic(paste("S.",
-    #                              sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
-    #                              collapse = ", ")),
-    #            ".",
-    #            call = FALSE,
-    #            immediate = TRUE)
-    # }
+    # comment below code if all staphylococcal species are categorised as CoNS/CoPS
+    if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
+      if (message_not_thrown_before("as.mo", "becker")) {
+        warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
+                 font_italic(paste("S.",
+                                   sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
+                                   collapse = ", ")),
+                 ". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
+                 call = FALSE,
+                 immediate = TRUE)
+      }
+    }
     # nolint end
-
+    
     # 'MO_CONS' and 'MO_COPS' are <mo> vectors created in R/zzz.R
     CoNS <- MO_lookup[which(MO_lookup$mo %in% MO_CONS), property, drop = TRUE]
     x[x %in% CoNS] <- lookup(mo == "B_STPHY_CONS", uncertainty = -1)
@@ -1912,7 +1916,7 @@ print.mo_uncertainties <- function(x, ...) {
     txt <- paste(txt,
                  paste0(
                    strwrap(
-                     paste0(font_red('"', x[i, ]$input, '"', collapse = ""),
+                     paste0('"', x[i, ]$input, '"',
                             " -> ",
                             paste0(font_bold(font_italic(x[i, ]$fullname)),
                                    ifelse(!is.na(x[i, ]$renamed_to), paste(", renamed to", font_italic(x[i, ]$renamed_to)), ""),
@@ -2043,6 +2047,8 @@ parse_and_convert <- function(x) {
 }
 
 replace_old_mo_codes <- function(x, property) {
+  # this function transform old MO codes to current codes, such as:
+  # B_ESCH_COL (AMR v0.5.0) -> B_ESCHR_COLI
   ind <- x %like_case% "^[A-Z]_[A-Z_]+$" & !x %in% MO_lookup$mo
   if (any(ind)) {
     # get the ones that match
@@ -2062,6 +2068,12 @@ replace_old_mo_codes <- function(x, property) {
                                                                MO_lookup$fullname_lower %like_case% name]
                                      if (length(results) > 1) {
                                        all_direct_matches <<- FALSE
+                                     } else if (length(results) == 0) {
+                                       # not found, so now search in old taxonomic names
+                                       results <- MO.old_lookup$fullname_new[MO.old_lookup$fullname_lower %like% name]
+                                       if (length(results) > 0) {
+                                         results <- MO_lookup$mo[match(results, MO_lookup$fullname)]
+                                       }
                                      }
                                      results[1L]
                                    }), use.names = FALSE)
@@ -2069,6 +2081,8 @@ replace_old_mo_codes <- function(x, property) {
     # assign on places where a match was found
     x[ind] <- solved
     n_matched <- length(affected[!is.na(affected)])
+    n_solved <- length(affected[!is.na(solved)])
+    n_unsolved <- length(affected[is.na(solved)])
     n_unique <- length(affected_unique[!is.na(affected_unique)])
     if (n_unique < n_matched) {
       n_unique <- paste0(n_unique, " unique, ")
@@ -2082,12 +2096,17 @@ replace_old_mo_codes <- function(x, property) {
                       "Please update your MO codes with `as.mo()` to increase speed."),
                call = FALSE)
     } else {
-      warning_(paste0(n_matched, " old MO code", ifelse(n_matched == 1, "", "s"), 
-                      " (", n_unique, "from a previous AMR package version) ", 
-                      ifelse(n_matched == 1, "was", "were"), 
+      warning_(paste0("The input contained ", n_matched,
+                      " old MO code", ifelse(n_matched == 1, "", "s"),
+                      " (", n_unique, "from a previous AMR package version). ",
+                      n_solved, " old MO code", ifelse(n_solved == 1, "", "s"), 
+                      ifelse(n_solved == 1, " was", " were"), 
                       ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
-                      "to ", ifelse(n_matched == 1, "a ", ""), 
-                      "currently used MO code", ifelse(n_matched == 1, "", "s"), "."),
+                      "to ", ifelse(n_solved == 1, "a ", ""), 
+                      "currently used MO code", ifelse(n_solved == 1, "", "s"),
+                      ifelse(n_unsolved > 0,
+                             paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
+                             ".")),
                call = FALSE)
     }
   }

R/mo_matching_score.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #' 
 #' This algorithm is used by [as.mo()] and all the [`mo_*`][mo_property()] functions to determine the most probable match of taxonomic records based on user input. 
 #' @inheritSection lifecycle Stable Lifecycle
-#' @author Matthijs S. Berends
+#' @author Dr. Matthijs Berends
 #' @param x Any user input value(s)
 #' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
 #' @section Matching Score for Microorganisms:

R/mo_property.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       #
@@ -29,7 +29,7 @@
 #' @inheritSection lifecycle Stable Lifecycle
 #' @param x any [character] (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be left blank for auto-guessing the column containing microorganism codes if used in a data set, see *Examples*.
 #' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
-#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
 #' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
 #' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
 #' @param open browse the URL using [`browseURL()`][utils::browseURL()]
@@ -46,7 +46,7 @@
 #' 
 #' 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`).
 #' 
-#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.2)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
+#' Intrinsic resistance - [mo_is_intrinsic_resistant()] - will be determined based on the [intrinsic_resistant] data set, which is based on `r format_eucast_version_nr(3.3)`. The [mo_is_intrinsic_resistant()] functions can be vectorised over arguments `x` (input for microorganisms) and over `ab` (input for antibiotics).
 #'
 #' All output [will be translated][translate] where possible.
 #'
@@ -96,6 +96,7 @@
 #' mo_ref("E. coli")             # "Castellani et al., 1919"
 #' mo_authors("E. coli")         # "Castellani et al."
 #' mo_year("E. coli")            # 1919
+#' mo_lpsn("E. coli")            # 776057 (LPSN record ID)
 #'
 #' # abbreviations known in the field -----------------------------------------
 #' mo_genus("MRSA")              # "Staphylococcus"
@@ -169,7 +170,7 @@
 #' mo_info("E. coli")
 #' }
 #' }
-mo_name <- function(x, language = get_locale(), ...) {
+mo_name <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_name")
@@ -189,7 +190,7 @@ mo_fullname <- mo_name
 
 #' @rdname mo_property
 #' @export
-mo_shortname <- function(x, language = get_locale(), ...) {
+mo_shortname <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_shortname")
@@ -216,9 +217,9 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
   shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
   # exceptions for streptococci: Group A Streptococcus -> GAS
-  shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
+  shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
   # unknown species etc.
-  shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
+  shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
   
   shortnames[is.na(x.mo)] <- NA_character_
   load_mo_failures_uncertainties_renamed(metadata)
@@ -229,7 +230,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_subspecies <- function(x, language = get_locale(), ...) {
+mo_subspecies <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_subspecies")
@@ -242,7 +243,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_species <- function(x, language = get_locale(), ...) {
+mo_species <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_species")
@@ -255,7 +256,7 @@ mo_species <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_genus <- function(x, language = get_locale(), ...) {
+mo_genus <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_genus")
@@ -268,7 +269,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_family <- function(x, language = get_locale(), ...) {
+mo_family <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_family")
@@ -281,7 +282,7 @@ mo_family <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_order <- function(x, language = get_locale(), ...) {
+mo_order <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_order")
@@ -294,7 +295,7 @@ mo_order <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_class <- function(x, language = get_locale(), ...) {
+mo_class <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_class")
@@ -307,7 +308,7 @@ mo_class <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_phylum <- function(x, language = get_locale(), ...) {
+mo_phylum <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_phylum")
@@ -320,7 +321,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_kingdom <- function(x, language = get_locale(), ...) {
+mo_kingdom <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_kingdom")
@@ -337,7 +338,7 @@ mo_domain <- mo_kingdom
 
 #' @rdname mo_property
 #' @export
-mo_type <- function(x, language = get_locale(), ...) {
+mo_type <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_type")
@@ -353,7 +354,7 @@ mo_type <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_gramstain <- function(x, language = get_locale(), ...) {
+mo_gramstain <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_gramstain")
@@ -384,7 +385,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_is_gram_negative <- function(x, language = get_locale(), ...) {
+mo_is_gram_negative <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_is_gram_negative")
@@ -403,7 +404,7 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_is_gram_positive <- function(x, language = get_locale(), ...) {
+mo_is_gram_positive <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_is_gram_positive")
@@ -422,7 +423,7 @@ mo_is_gram_positive <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_is_yeast <- function(x, language = get_locale(), ...) {
+mo_is_yeast <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_is_yeast")
@@ -448,7 +449,7 @@ mo_is_yeast <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
+mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_is_intrinsic_resistant")
@@ -470,9 +471,9 @@ 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.mo", entire_session = TRUE)) {
+  if (message_not_thrown_before("mo_is_intrinsic_resistant", "version.mo", entire_session = TRUE)) {
     message_("Determining intrinsic resistance based on ",
-             format_eucast_version_nr(3.2, markdown = FALSE), ". ",
+             format_eucast_version_nr(3.3, markdown = FALSE), ". ",
              font_red("This note will be shown once per session."))
   }
   
@@ -482,7 +483,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_snomed <- function(x, language = get_locale(), ...) {
+mo_snomed <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_snomed")
@@ -495,7 +496,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_ref <- function(x, language = get_locale(), ...) {
+mo_ref <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_ref")
@@ -508,7 +509,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_authors <- function(x, language = get_locale(), ...) {
+mo_authors <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_authors")
@@ -518,13 +519,13 @@ mo_authors <- function(x, language = get_locale(), ...) {
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
   # remove last 4 digits and presumably the comma and space that preceed them
-  x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
+  x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)], perl = TRUE)
   suppressWarnings(x)
 }
 
 #' @rdname mo_property
 #' @export
-mo_year <- function(x, language = get_locale(), ...) {
+mo_year <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_year")
@@ -534,13 +535,26 @@ mo_year <- function(x, language = get_locale(), ...) {
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
   # get last 4 digits
-  x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
+  x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE)
   suppressWarnings(as.integer(x))
 }
 
 #' @rdname mo_property
 #' @export
-mo_rank <- function(x, language = get_locale(), ...) {
+mo_lpsn <- function(x, language = get_AMR_locale(), ...) {
+  if (missing(x)) {
+    # this tries to find the data and an <mo> column
+    x <- find_mo_col(fn = "mo_rank")
+  }
+  meet_criteria(x, allow_NA = TRUE)
+  meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
+  
+  mo_validate(x = x, property = "species_id", language = language, ...)
+}
+
+#' @rdname mo_property
+#' @export
+mo_rank <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_rank")
@@ -553,7 +567,7 @@ mo_rank <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_taxonomy <- function(x, language = get_locale(),  ...) {
+mo_taxonomy <- function(x, language = get_AMR_locale(),  ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_taxonomy")
@@ -564,22 +578,22 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
   x <- as.mo(x, language = language, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
   
-  result <- list(kingdom = mo_kingdom(x, language = language),
-                 phylum = mo_phylum(x, language = language),
-                 class = mo_class(x, language = language),
-                 order = mo_order(x, language = language),
-                 family = mo_family(x, language = language),
-                 genus = mo_genus(x, language = language),
-                 species = mo_species(x, language = language),
-                 subspecies = mo_subspecies(x, language = language))
+  out <- list(kingdom = mo_kingdom(x, language = language),
+              phylum = mo_phylum(x, language = language),
+              class = mo_class(x, language = language),
+              order = mo_order(x, language = language),
+              family = mo_family(x, language = language),
+              genus = mo_genus(x, language = language),
+              species = mo_species(x, language = language),
+              subspecies = mo_subspecies(x, language = language))
   
   load_mo_failures_uncertainties_renamed(metadata)
-  result
+  out
 }
 
 #' @rdname mo_property
 #' @export
-mo_synonyms <- function(x, language = get_locale(), ...) {
+mo_synonyms <- function(x, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_synonyms")
@@ -612,7 +626,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_info <- function(x, language = get_locale(),  ...) {
+mo_info <- function(x, language = get_AMR_locale(),  ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_info")
@@ -643,7 +657,7 @@ mo_info <- function(x, language = get_locale(),  ...) {
 
 #' @rdname mo_property
 #' @export
-mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
+mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_url")
@@ -652,31 +666,23 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
   meet_criteria(open, allow_class = "logical", has_length = 1)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  mo <- as.mo(x = x, language = language, ... = ...)
-  mo_names <- mo_name(mo)
+  x.mo <- as.mo(x = x, language = language, ... = ...)
   metadata <- get_mo_failures_uncertainties_renamed()
   
-  df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
-    pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
-  df$url <- ifelse(df$source == "CoL",
-                   paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
-                   NA_character_)
+  df <- microorganisms[match(x.mo, microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank")]
+  df$url <- ifelse(df$source == "LPSN",
+                   paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
+                   paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE)))
+  
+  genera <- which(df$kingdom == "Bacteria" & df$rank == "genus")
+  df$url[genera] <- gsub("/species/", "/genus/", df$url[genera], fixed = TRUE)
+  subsp <- which(df$kingdom == "Bacteria" & df$rank %in% c("subsp.", "infraspecies"))
+  df$url[subsp] <- gsub("/species/", "/subspecies/", df$url[subsp], fixed = TRUE)
+  
   u <- df$url
-  u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
-  u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
-                                                                   "/genus/",
-                                                                   u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
-                                                                   fixed = TRUE)
-  u[mo_kingdom(mo) == "Bacteria" &
-      mo_rank(mo) %in% c("subsp.", "infraspecies")] <- gsub("/species/",
-                                                            "/subspecies/",
-                                                            u[mo_kingdom(mo) == "Bacteria" &
-                                                                mo_rank(mo) %in% c("subsp.", "infraspecies")],
-                                                            fixed = TRUE)
+  names(u) <- df$fullname
   
-  names(u) <- mo_names
-  
-  if (open == TRUE) {
+  if (isTRUE(open)) {
     if (length(u) > 1) {
       warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
     }
@@ -690,7 +696,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
 
 #' @rdname mo_property
 #' @export
-mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
+mo_property <- function(x, property = "fullname", language = get_AMR_locale(), ...) {
   if (missing(x)) {
     # this tries to find the data and an <mo> column
     x <- find_mo_col(fn = "mo_property")
@@ -732,6 +738,8 @@ mo_validate <- function(x, property, language, ...) {
   
   if (property == "mo") {
     return(set_clean_class(x, new_class = c("mo", "character")))
+  } else if (property == "species_id") {
+    return(as.double(x))
   } else if (property == "snomed") {
     return(as.double(eval(parse(text = x))))
   } else {

R/mo_source.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/pca.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -90,7 +90,7 @@ pca <- function(x,
           # this is to support quoted variables: df %pm>% pca("mycol1", "mycol2")
           new_list[[i]] <- x[, new_list[[i]]]
         } else {
-          # remove item - it's a argument like `center`
+          # remove item - it's an argument like `center`
           new_list[[i]] <- NULL
         }
       }

R/plot.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -26,16 +26,16 @@
 #' Plotting for Classes `rsi`, `mic` and `disk`
 #' 
 #' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
-#' @inheritSection lifecycle Maturing Lifecycle
+#' @inheritSection lifecycle Stable Lifecycle
 #' @inheritSection AMR Read more on Our Website!
-#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
+#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
 #' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
 #' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
 #' @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 language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. 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.
 #' @details
 #' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
@@ -46,7 +46,9 @@
 #' @name plot
 #' @rdname plot
 #' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
-#' @param ... arguments passed on to [as.rsi()]
+#' 
+#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function.
+#' @param ... arguments passed on to methods
 #' @examples 
 #' some_mic_values <- random_mic(size = 100)
 #' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
@@ -81,7 +83,7 @@ plot.mic <- function(x,
                      ylab = "Frequency",
                      xlab = "Minimum Inhibitory Concentration (mg/L)",
                      colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                     language = get_locale(),
+                     language = get_AMR_locale(),
                      expand = TRUE,
                      ...) {
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
@@ -144,6 +146,7 @@ plot.mic <- function(x,
       legend_txt <- c(legend_txt, "Resistant")
       legend_col <- c(legend_col, colours_RSI[1])
     }
+    
     legend("top",
            x.intersp = 0.5,
            legend = translate_AMR(legend_txt, language = language),
@@ -167,7 +170,7 @@ barplot.mic <- function(height,
                         ylab = "Frequency",
                         xlab = "Minimum Inhibitory Concentration (mg/L)",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                        language = get_locale(),
+                        language = get_AMR_locale(),
                         expand = TRUE,
                         ...) {
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
@@ -212,7 +215,7 @@ autoplot.mic <- function(object,
                          ylab = "Frequency",
                          xlab = "Minimum Inhibitory Concentration (mg/L)",
                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                         language = get_locale(),
+                         language = get_AMR_locale(),
                          expand = TRUE,
                          ...) {
   stop_ifnot_installed("ggplot2")
@@ -283,6 +286,13 @@ autoplot.mic <- function(object,
     ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
 }
 
+#' @method fortify mic
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+fortify.mic <- function(object, ...) {
+  stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
+                  c("x", "y"))
+}
 
 #' @method plot disk
 #' @export
@@ -296,7 +306,7 @@ plot.disk <- function(x,
                       ab = NULL,
                       guideline = "EUCAST",
                       colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                      language = get_locale(),
+                      language = get_AMR_locale(),
                       expand = TRUE,
                       ...) {
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
@@ -383,7 +393,7 @@ barplot.disk <- function(height,
                          ab = NULL,
                          guideline = "EUCAST",
                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                         language = get_locale(),
+                         language = get_AMR_locale(),
                          expand = TRUE,
                          ...) {
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
@@ -428,7 +438,7 @@ autoplot.disk <- function(object,
                           xlab = "Disk diffusion diameter (mm)",
                           guideline = "EUCAST",
                           colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                          language = get_locale(),
+                          language = get_AMR_locale(),
                           expand = TRUE,
                           ...) {
   stop_ifnot_installed("ggplot2")
@@ -500,6 +510,14 @@ autoplot.disk <- function(object,
     ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
 }
 
+#' @method fortify disk
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+fortify.disk <- function(object, ...) {
+  stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
+                  c("x", "y"))
+}
+
 #' @method plot rsi
 #' @export
 #' @importFrom graphics plot text axis
@@ -562,7 +580,7 @@ barplot.rsi <- function(height,
                         xlab = "Antimicrobial Interpretation",
                         ylab = "Frequency",
                         colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                        language = get_locale(),
+                        language = get_AMR_locale(),
                         expand = TRUE,
                         ...) {
   meet_criteria(xlab, allow_class = "character", has_length = 1)
@@ -606,7 +624,7 @@ autoplot.rsi <- function(object,
                          xlab = "Antimicrobial Interpretation",
                          ylab = "Frequency",
                          colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
-                         language = get_locale(),
+                         language = get_AMR_locale(),
                          ...) {
   stop_ifnot_installed("ggplot2")
   meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
@@ -646,6 +664,14 @@ autoplot.rsi <- function(object,
     ggplot2::theme(legend.position = "none")
 }
 
+#' @method fortify rsi
+#' @rdname plot
+# will be exported using s3_register() in R/zzz.R
+fortify.rsi <- function(object, ...) {
+  stats::setNames(as.data.frame(table(object)),
+                  c("x", "y"))
+}
+
 plot_prepare_table <- function(x, expand) {
   x <- x[!is.na(x)]
   stop_if(length(x) == 0, "no observations to plot", call = FALSE)

R/proportion.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -277,7 +277,7 @@ proportion_S <- function(...,
 #' @export
 proportion_df <- function(data,
                           translate_ab = "name",
-                          language = get_locale(),
+                          language = get_AMR_locale(),
                           minimum = 30,
                           as_percent = FALSE,
                           combine_SI = TRUE,

R/random.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/resistance_predict.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/rsi.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -35,10 +35,10 @@
 #' @inheritParams first_isolate
 #' @param guideline defaults to the latest included EUCAST guideline, see *Details* for all options
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
-#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.2)`.
+#' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [rsi_translation] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [rsi_translation] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
 #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
-#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection like `AMX:VAN`). Otherwise: arguments passed on to methods.
+#' @param ... for using on a [data.frame]: names of columns to apply [as.rsi()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
 #' @details 
 #' ## How it Works
 #' 
@@ -61,7 +61,7 @@
 #'      your_data %>% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
 #'      ```
 #' 
-#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(data)`.
+#' 4. For **interpreting a complete data set**, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running `as.rsi(your_data)`.
 #' 
 #' ## Supported Guidelines
 #' 
@@ -75,7 +75,7 @@
 #' 
 #' ## Machine-Readable Interpretation Guidelines
 #' 
-#' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+#' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
 #'
 #' ## Other
 #' 
@@ -188,6 +188,12 @@ as.rsi <- function(x, ...) {
   UseMethod("as.rsi")
 }
 
+#' @rdname as.rsi
+#' @details `NA_rsi_` is a missing value of the new `<rsi>` class.
+#' @export
+NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE),
+                           new_class =  c("rsi", "ordered", "factor"))
+
 #' @rdname as.rsi
 #' @export
 is.rsi <- function(x) {
@@ -257,12 +263,12 @@ as.rsi.default <- function(x, ...) {
     return(x)
   }
   
-  if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
-    x.bak <- x
-    x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
-    
+  x.bak <- x
+  x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
+  
+  if (inherits(x.bak, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
     # support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
-    lbls <- attributes(x)$labels
+    lbls <- attributes(x.bak)$labels
     if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
       x[x.bak == 1] <- names(lbls[lbls == 1])
       x[x.bak == 2] <- names(lbls[lbls == 2])
@@ -278,9 +284,9 @@ as.rsi.default <- function(x, ...) {
     if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
       # check if they are actually MICs or disks
       if (all_valid_mics(x)) {
-        warning_("The input seems to be MIC values. Transform them with `as.mic()` before running `as.rsi()` to interpret them.")
+        warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
       } else if (all_valid_disks(x)) {
-        warning_("The input seems to be disk diffusion values. Transform them with `as.disk()` before running `as.rsi()` to interpret them.")
+        warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
       }
     }
     
@@ -303,24 +309,17 @@ as.rsi.default <- function(x, ...) {
     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
-    x <- gsub("[0-9.,;:<=>]+", "", x)
-    # remove everything between brackets, and 'high' and 'low'
-    x <- gsub("([(].*[)])", "", x)
-    x <- gsub("(high|low)", "", x, ignore.case = TRUE)
-    # disallow more than 3 characters
-    x[nchar(x) > 3] <- NA
+    # remove other invalid characters
+    x <- gsub("[^rsiRSIHi]+", "", x, perl = 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)
     # set to capitals
     x <- toupper(x)
-    # remove all invalid characters
-    x <- gsub("[^RSI]+", "", x)
     # in cases of "S;S" keep S, but in case of "S;I" make it NA
     x <- gsub("^S+$", "S", x)
     x <- gsub("^I+$", "I", x)
     x <- gsub("^R+$", "R", x)
-    x[!x %in% c("S", "I", "R")] <- NA
+    x[!x %in% c("S", "I", "R")] <- NA_character_
     na_after <- length(x[is.na(x) | x == ""])
     
     if (!isFALSE(list(...)$warn)) { # so as.rsi(..., warn = FALSE) will never throw a warning
@@ -551,7 +550,7 @@ as.rsi.data.frame <- function(x,
 
   x.bak <- x
   for (i in seq_len(ncol(x))) {
-    # don't keep factors
+    # don't keep factors, overwriting them is hard
     if (is.factor(x[, i, drop = TRUE])) {
       x[, i] <- as.character(x[, i, drop = TRUE])
     }
@@ -605,7 +604,11 @@ as.rsi.data.frame <- function(x,
   }
 
   i <- 0
-  sel <- colnames(pm_select(x, ...))
+  if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
+    sel <- colnames(pm_select(x, ...))
+  } else {
+    sel <- colnames(x)
+  }
   if (!is.null(col_mo)) {
     sel <- sel[sel != col_mo]
   }
@@ -772,7 +775,7 @@ exec_as.rsi <- function(method,
   
   guideline_coerced <- get_guideline(guideline, reference_data)
   if (guideline_coerced != guideline) {
-    if (message_not_thrown_before("as.rsi")) {
+    if (message_not_thrown_before("as.rsi", "msg1")) {
       message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
     }
   }
@@ -796,7 +799,8 @@ exec_as.rsi <- function(method,
   lookup_lancefield <- paste(mo_lancefield, ab)
   lookup_other <- paste(mo_other, ab)
   
-  if (all(trans$uti == TRUE, na.rm = TRUE) & all(uti == FALSE)) {
+  if (length(unique(paste(trans$mo, trans$ab))) == length(unique(paste(trans$mo, trans$ab, trans$uti))) &&
+      any(trans$uti == TRUE, na.rm = TRUE) && all(uti == FALSE)) {
     message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
     warning_("Introducing NA: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI). Use argument `uti` to set which isolates are from urine. See ?as.rsi.", call = FALSE)
     warned <- TRUE
@@ -810,7 +814,7 @@ exec_as.rsi <- function(method,
     
     if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
       if (guideline_coerced %unlike% "EUCAST") {
-        if (message_not_thrown_before("as.rsi2")) {
+        if (message_not_thrown_before("as.rsi", "msg2")) {
           warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
         }
       } else {
@@ -833,11 +837,11 @@ exec_as.rsi <- function(method,
       get_record <- get_record %pm>% 
         # be as specific as possible (i.e. prefer species over genus):
         # pm_desc(uti) = TRUE on top and FALSE on bottom
-        pm_arrange(pm_desc(uti), pm_desc(nchar(mo))) # 'uti' is a column in data set 'rsi_translation'
+        pm_arrange(pm_desc(uti), rank_index) # 'uti' is a column in data set 'rsi_translation'
     } else {
       get_record <- get_record %pm>% 
         pm_filter(uti == FALSE) %pm>% # 'uti' is a column in rsi_translation
-        pm_arrange(pm_desc(nchar(mo)))
+        pm_arrange(rank_index)
     }
     
     get_record <- get_record[1L, , drop = FALSE]
@@ -848,21 +852,16 @@ exec_as.rsi <- function(method,
       } else if (method == "mic") {
         new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
                                       isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
-                                      # start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= R
+                                      # these basically call `<=.mic()` and `>=.mic()`:
                                       x[i] <= get_record$breakpoint_S ~ "S",
-                                      guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R ~ "R",
-                                      guideline_coerced %like% "CLSI" & x[i] >= get_record$breakpoint_R ~ "R",
+                                      x[i] >= get_record$breakpoint_R ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise
                                       TRUE ~ NA_character_)
       } else if (method == "disk") {
         new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
-                                      # start interpreting: EUCAST uses >= S and < R, CLSI uses >=S and <= R
-                                      guideline_coerced %like% "EUCAST" &
-                                        isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
-                                      guideline_coerced %like% "CLSI" &
-                                        isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
+                                      isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
                                       # return "I" when not match the bottom or top
                                       !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
                                       # and NA otherwise
@@ -874,7 +873,7 @@ exec_as.rsi <- function(method,
   if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
     # found some intrinsic resistance, but was not applied
     message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
-    if (message_not_thrown_before("as.rsi3")) {
+    if (message_not_thrown_before("as.rsi", "msg3")) {
       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)
     }
     warned <- TRUE

R/rsi_calc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -202,7 +202,7 @@ rsi_calc <- function(...,
 rsi_calc_df <- function(type, # "proportion", "count" or "both"
                         data,
                         translate_ab = "name",
-                        language = get_locale(),
+                        language = get_AMR_locale(),
                         minimum = 30,
                         as_percent = FALSE,
                         combine_SI = TRUE,
@@ -344,6 +344,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
   } 
   
   rownames(out) <- NULL
+  class(out) <- c("rsi_df", class(out))
   out
 }
 

R/rsi_df.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,7 +27,7 @@
 #' @export
 rsi_df <- function(data,
                    translate_ab = "name",
-                   language = get_locale(),
+                   language = get_AMR_locale(),
                    minimum = 30,
                    as_percent = FALSE,
                    combine_SI = TRUE,

R/skewness.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/translate.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -27,9 +27,9 @@
 #'
 #' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
 #' @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.). 
+#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv>. This file will be read by all functions where a translated output can be desired, like all [`mo_*`][mo_property()] functions (such as [mo_name()], [mo_gramstain()], [mo_type()], etc.) and [`ab_*`][ab_property()] functions (such as [ab_name()], [ab_group()], etc.). 
 #'
-#' 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(names(LANGUAGES_SUPPORTED), 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).
 #'
@@ -39,7 +39,7 @@
 #'   1. Setting the R option `AMR_locale`, e.g. by running `options(AMR_locale = "de")`
 #'   2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory
 #' 
-#' So if the R option `AMR_locale` is set, the system variables `LANGUAGE` and `LANG` will be ignored.
+#' Thus, if the R option `AMR_locale` is set, the system variables `LANGUAGE` and `LANG` will be ignored.
 #' @inheritSection AMR Read more on Our Website!
 #' @rdname translate
 #' @name translate
@@ -47,23 +47,23 @@
 #' @examples
 #' # The 'language' argument of below functions
 #' # will be set automatically to your system language
-#' # with get_locale()
+#' # with get_AMR_locale()
 #'
 #' # English
 #' mo_name("CoNS", language = "en")
 #' #> "Coagulase-negative Staphylococcus (CoNS)"
 #'
-#' # German
-#' mo_name("CoNS", language = "de")
-#' #> "Koagulase-negative Staphylococcus (KNS)"
-#'
+#' # Danish
+#' mo_name("CoNS", language = "da")
+#' #> "Koagulase-negative stafylokokker (KNS)"
+#' 
 #' # Dutch
 #' mo_name("CoNS", language = "nl")
 #' #> "Coagulase-negatieve Staphylococcus (CNS)"
 #'
-#' # Spanish
-#' mo_name("CoNS", language = "es")
-#' #> "Staphylococcus coagulasa negativo (SCN)"
+#' # German
+#' mo_name("CoNS", language = "de")
+#' #> "Koagulase-negative Staphylococcus (KNS)"
 #'
 #' # Italian
 #' mo_name("CoNS", language = "it")
@@ -72,7 +72,11 @@
 #' # Portuguese
 #' mo_name("CoNS", language = "pt")
 #' #> "Staphylococcus coagulase negativo (CoNS)"
-get_locale <- function() {
+#'
+#' # Spanish
+#' mo_name("CoNS", language = "es")
+#' #> "Staphylococcus coagulasa negativo (SCN)"
+get_AMR_locale <- function() {
   # AMR versions 1.3.0 and prior used the environmental variable:
   if (!identical("", Sys.getenv("AMR_locale"))) {
     options(AMR_locale = Sys.getenv("AMR_locale"))
@@ -84,10 +88,10 @@ get_locale <- function() {
       return(lang)
     } else {
       stop_("unsupported language set as option 'AMR_locale': \"", lang, "\" - use either ",
-            vector_or(LANGUAGES_SUPPORTED, quotes = TRUE))
+            vector_or(paste0('"', LANGUAGES_SUPPORTED, '" (', names(LANGUAGES_SUPPORTED), ")"), quotes = FALSE))
     }
   } else {
-    # we now support the LANGUAGE system variable - return it if set
+    # now check the LANGUAGE system variable - return it if set
     if (!identical("", Sys.getenv("LANGUAGE"))) {
       return(coerce_language_setting(Sys.getenv("LANGUAGE")))
     }
@@ -96,11 +100,22 @@ get_locale <- function() {
     }
   }
   
+  # fallback - automatic determination based on LC_COLLATE
+  if (interactive() && message_not_thrown_before("get_AMR_locale", entire_session = TRUE)) {
+    lang <- coerce_language_setting(Sys.getlocale("LC_COLLATE"))
+    if (lang != "en") {
+      message_("Assuming the ", names(LANGUAGES_SUPPORTED)[LANGUAGES_SUPPORTED == lang], 
+               " language for the AMR package. Change this with `options(AMR_locale = \"...\")` or see `?get_AMR_locale()`. ",
+               "Supported languages are ", vector_and(names(LANGUAGES_SUPPORTED), quotes = FALSE),
+               ". This note will be shown once per session.")
+    }
+    return(lang)
+  }
   coerce_language_setting(Sys.getlocale("LC_COLLATE"))
 }
 
 coerce_language_setting <- function(lang) {
-  # grepl() with ignore.case = FALSE is faster than %like%
+  # grepl() with ignore.case = FALSE is 8x faster than %like_case%
   if (grepl("^(English|en_|EN_)", lang, ignore.case = FALSE, perl = TRUE)) {
     # as first option to optimise speed
     "en"
@@ -108,6 +123,8 @@ 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)) {
@@ -116,6 +133,10 @@ coerce_language_setting <- function(lang) {
     "fr"
   } else if (grepl("^(Portuguese|Portugu.+s|pt_|PT_)", lang, ignore.case = FALSE, perl = TRUE)) {
     "pt"
+  } else if (grepl("^(Russian|pycc|ru_|RU_)", lang, ignore.case = FALSE, perl = TRUE)) {
+    "ru"
+  } else if (grepl("^(Swedish|Svenskt|sv_|SV_)", lang, ignore.case = FALSE, perl = TRUE)) {
+    "sv"
   } else {
     # other language -> set to English
     "en"
@@ -124,7 +145,7 @@ coerce_language_setting <- function(lang) {
 
 # translate strings based on inst/translations.tsv
 translate_AMR <- function(from,
-                          language = get_locale(), 
+                          language = get_AMR_locale(), 
                           only_unknown = FALSE,
                           only_affect_ab_names = FALSE,
                           only_affect_mo_names = FALSE) {

R/vctrs.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -28,6 +28,18 @@
 # They are to convert AMR-specific classes to bare characters and integers.
 # All of them will be exported using s3_register() in R/zzz.R when loading the package.
 
+# S3: ab_selector
+# see https://github.com/tidyverse/dplyr/issues/5955 why this is required
+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)
+}
+
 # S3: ab
 vec_ptype2.character.ab <- function(x, y, ...) {
   x
@@ -60,15 +72,3 @@ vec_ptype2.disk.integer <- function(x, 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/whocc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

R/zzz.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -57,15 +57,21 @@ if (utf8_supported && !is_latex) {
   s3_register("cleaner::freq", "mo")
   s3_register("cleaner::freq", "rsi")
   # 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")
+  if (pkg_is_available("skimr", also_load = FALSE, min_version = "2.0.0")) {
+    s3_register("skimr::get_skimmers", "mo")
+    s3_register("skimr::get_skimmers", "rsi")
+    s3_register("skimr::get_skimmers", "mic")
+    s3_register("skimr::get_skimmers", "disk")
+  }
   # Support for autoplot() from the ggplot2 package
   s3_register("ggplot2::autoplot", "rsi")
   s3_register("ggplot2::autoplot", "mic")
   s3_register("ggplot2::autoplot", "disk")
   s3_register("ggplot2::autoplot", "resistance_predict")
+  # Support for fortify from the ggplot2 package
+  s3_register("ggplot2::fortify", "rsi")
+  s3_register("ggplot2::fortify", "mic")
+  s3_register("ggplot2::fortify", "disk")
   # Support vctrs package for use in e.g. dplyr verbs
   s3_register("vctrs::vec_ptype2", "ab.character")
   s3_register("vctrs::vec_ptype2", "character.ab")
@@ -161,6 +167,5 @@ create_MO.old_lookup <- function() {
 
 create_intr_resistance <- function() {
   # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
-  paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
-        AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
+  paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
 }

README.md

@@ -2,17 +2,17 @@
 
 # `AMR` (for R)
 
-![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
+![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main)
 [![CodeFactor](https://www.codefactor.io/repository/github/msberends/amr/badge)](https://www.codefactor.io/repository/github/msberends/amr)
-[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
+[![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://app.codecov.io/gh/msberends/AMR?branch=main)
 
-<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
+<img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" />
 
-The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/master/data-raw).
+The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/main/data-raw).
 
 `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 150 countries.
  
-After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
+After installing this package, R knows ~71,000 distinct microbial species and all ~570 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
 
 This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.
 
@@ -33,7 +33,7 @@ It will be downloaded and installed automatically. For RStudio, click on the men
 
 ### Copyright
 
-This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
+This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/main/LICENSE). In a nutshell, this means that this package:
 
 - May be used for commercial purposes
 

_pkgdown.yml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -175,7 +175,7 @@ reference:
     - "`age_groups`"
     - "`age`"
     - "`availability`"
-    - "`get_locale`"
+    - "`get_AMR_locale`"
     - "`ggplot_pca`"
     - "`italicise_taxonomy`"
     - "`join`"
@@ -200,20 +200,6 @@ reference:
     contents:
     - "`AMR-deprecated`"
 
-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:
   bootstrap: 3
   opengraph:

codecov.yml

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -25,7 +25,7 @@
 
 codecov:
   require_ci_to_pass: no # allow fail
-  branch: master
+  branch: main
 
 comment: no
 

cran-comments.md

@@ -1 +1 @@
-* This package now has a data folder size of ~2.8 MB (this was ~5.6 MB), which will return a NOTE on R CMD CHECK. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, following 15 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.
+* This package has a data folder size of ~1.7 MB, which might return a NOTE on some R CMD CHECKs. This package size is needed to provide users reference data for the complete taxonomy of microorganisms - one of the most important features of this package, as it has been in the 16 previous releases of this package. All data sets were compressed using `compression = "xz"` to make them as small as possible.

data-raw/DRGLST.txt

@@ -1,549 +0,0 @@
-WHON5_CODE	WHON4_CODE	WHO_CODE	DIN_CODE	JAC_CODE	USER_CODE	ANTIBIOTIC	GUIDELINES	CLSI	EUCAST	SFM	SRGA	BSAC	DIN	NEO	AFA	ABX_NUMBER	POTENCY	BETALACTAM	CLASS	SUBCLASS	PROF_CLASS	CLSI_ORDER	HUMAN	VETERINARY	ANIMAL_GP	WHO_IMPORT	LOINCCOMP	LOINCGEN	LOINCDISK	LOINCMIC	LOINCETEST	LOINCSLOW	LOINCAFB	LOINCSBT	LOINCMLC	CLSI20_DR	CLSI20_DI	CLSI20_DS	CLSI20_MS	CLSI20_MR	CLSI19_DR	CLSI19_DI	CLSI19_DS	CLSI19_MS	CLSI19_MR	CLSI18_DR	CLSI18_DI	CLSI18_DS	CLSI18_MS	CLSI18_MR	CLSI17_DR	CLSI17_DI	CLSI17_DS	CLSI17_MS	CLSI17_MR	CLSI16_DR	CLSI16_DI	CLSI16_DS	CLSI16_MS	CLSI16_MR	CLSI15_DR	CLSI15_DI	CLSI15_DS	CLSI15_MS	CLSI15_MR	CLSI14_DR	CLSI14_DI	CLSI14_DS	CLSI14_MS	CLSI14_MR	CLSI13_DR	CLSI13_DI	CLSI13_DS	CLSI13_MS	CLSI13_MR	CLSI12_DR	CLSI12_DI	CLSI12_DS	CLSI12_MS	CLSI12_MR	CLSI11_DR	CLSI11_DI	CLSI11_DS	CLSI11_MS	CLSI11_MR	CLSI10_DR	CLSI10_DI	CLSI10_DS	CLSI10_MS	CLSI10_MR	EUCST20_DR	EUCST20_DI	EUCST20_DS	EUCST20_MS	EUCST20_MR	EUCST19_DR	EUCST19_DI	EUCST19_DS	EUCST19_MS	EUCST19_MR	EUCST18_DR	EUCST18_DI	EUCST18_DS	EUCST18_MS	EUCST18_MR	EUCST17_DR	EUCST17_DI	EUCST17_DS	EUCST17_MS	EUCST17_MR	EUCST16_DR	EUCST16_DI	EUCST16_DS	EUCST16_MS	EUCST16_MR	EUCST15_DR	EUCST15_DI	EUCST15_DS	EUCST15_MS	EUCST15_MR	EUCST14_DR	EUCST14_DI	EUCST14_DS	EUCST14_MS	EUCST14_MR	EUCST13_DR	EUCST13_DI	EUCST13_DS	EUCST13_MS	EUCST13_MR	ECV12_DR	ECV12_DI	ECV12_DS	ECV12_MS	ECV12_MR	EUCST11_DR	EUCST11_DI	EUCST11_DS	EUCST11_MS	EUCST11_MR	NEODK16_DR	NEODK16_DI	NEODK16_DS	NEODK16_MS	NEODK16_MR	NEODK13_DR	NEODK13_DI	NEODK13_DS	NEODK13_MS	NEODK13_MR	NEODK98_DR	NEODK98_DI	NEODK98_DS	NEODK98_MS	NEODK98_MR	SFM20_DR	SFM20_DI	SFM20_DS	SFM20_MS	SFM20_MR	SFM07_DR	SFM07_DI	SFM07_DS	SFM07_MS	SFM07_MR	DIN04_DR	DIN04_DI	DIN04_DS	DIN04_MS	DIN04_MR	CRG96_DR	CRG96_DI	CRG96_DS	CRG96_MS	CRG96_MR	AFA00_DR	AFA00_DI	AFA00_DS	AFA00_MS	AFA00_MR	MENS00_DR	MENS00_DI	MENS00_DS	MENS00_MS	MENS00_MR	SRGA98_DR	SRGA98_DI	SRGA98_DS	SRGA98_MS	SRGA98_MR	BSAC00_DR	BSAC00_DI	BSAC00_DS	BSAC00_MS	BSAC00_MR	OTHER_DR	OTHER_DI	OTHER_DS	OTHER_MS	OTHER_MR
-AMC	AUG	AMC	AMC	AMPC-CVA		Amoxicillin/Clavulanic acid	CLSI,EUCAST(Most bacteria)	X	X	X		X	X			2	20/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Amoxicilli	18862-3	21-6	20-8	6977-3		25310-4	22-4	19-0	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32	13	14-17	18	8	32																																														11		12	8	16																					13	14-20	21	4	32	20	21-27	28	2	16				2	32																17	-	18	8	16					
-APX	APX	APX	ASP	ASPC		Aspoxicillin										213		X	Penicillins	Ureidopenicillin	PEN	01c																																																																																																																																																																																		
-AMC	AU2	AMC	AMC	AMPC-CVA		Amoxicillin/Clavulanic acid	BSAC,EUCAST(Haemophilus)		X	X		X				306	2/1ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Amoxicilli	18862-3	21-6	20-8	6977-3		25310-4	22-4	19-0				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32				2	16				2	32																			8	16					
-BDP	BDP	BDP				Brodimoprim										220			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-BUT	BUC	BUT				Butoconazole										221			Antifungals		FUNG	29																																																																																																																																																																																		
-CAP	CAP		CPR			Capreomycin										128			Antimycobacterials		MYCO	28					Capreomyci	18872-2	57-0	56-2			23607-5	58-8	55-4																																																																																																																																																																					
-CRB	CAR	CB	CAR			Carbenicillin	CLSI,BSAC	X				X				9	100ug	X	Penicillins	Carboxypenicillin	PEN	01d	X				Carbenicil	18873-0	61-2	60-4	41668-5			62-0	59-6																																														19	20-22	23	16	64	19	20-22	23	16	64																																																																																																					12	-	13	128	256					
-CAR	CAM	CAR	CAM	CRMN		Carumonam										148		X	Monobactams		MONO	06																																																																																																																																																																																		
-CAS	CAS		CAS			Caspofungin	CLSI,NEO	X						X		441	5ug		Antifungals		FUNG	29					Caspofungi	32378-2																																																																																																																																																																												
-CAC	FAC	CAC	CAC			Cefacetrile										149	30ug	X	Cephems	Cephalosporin I	CEPH1	04a																																																																																																																																																																																		
-CEC	CFC	CEC	CEC	CCL		Cefaclor	CLSI,EUCAST	X	X	X		X	X			10	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefaclor	18874-8	85-1	84-4	6986-4			86-9	83-6	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																										2	16				1	8				4	32											13	14-34	35	1	16	34	-	35	1	2					
-BEK	BEK			AKM		Bekanamycin										444			Aminoglycosides		AG	09																																																																																																																																																																																		
-SAM	AS2	SAM	AMS	ABPC-SBT		Ampicillin/Sulbactam	DIN						X			211	20/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Ampicillin	18865-6	33-1	32-3	6980-7	20374-5	23618-2	34-9	31-5				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32	15	16-24	25	2	16																														
-SAM	AS3	SAM	AMS	ABPC-SBT		Ampicillin/Sulbactam	NEO							X		334	30/30ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Ampicillin	18865-6	33-1	32-3	6980-7	20374-5	23618-2	34-9	31-5				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32				2	16																														
-AMR	AMR					Amprolium										405			Coccidiostats		COCC	27																																																																																																																																																																																		
-ANI	ANI					Anidulafungin										477			Antifungals		FUNG	29																																																																																																																																																																																		
-APL	APA	APL	APL			Apalcillin										144		X	Penicillins	Ureidopenicillin	PEN	01c																																																																																																																																																																																		
-APR	AP1		APR			Apramycin	CLSI	X								400	15ug		Aminoglycosides		AG	09		X			Apramycin	23659-6	73653-8	73652-0																																																																																																																																																																										
-BAC	BAC	B	BTC	BC		Bacitracin zinc	CLSI	X		X						8	10units		Polypeptides		POLYPEP	26	X				Bacitracin	18870-6	10868-8	6827-0	6983-1																																																																																																																																		14	-	15	2	4																																			
-AMX	AX3	AMX	AMX	AMPC		Amoxicillin	NEO							X		330	30ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Amoxicilli	18861-5	17-4	16-6	6976-5			18-2	15-8																																																																																																																				14	15-27	28											4	32				2	16				2	32				2	32																				
-AMX	AMX	AMX	AMX	AMPC		Amoxicillin										485	2ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Amoxicilli	18861-5	17-4	16-6	6976-5			18-2	15-8																																																																																																																																	4	32				2	16				2	32				2	32																				
-CPC	CPC			CEPM-CVA		Cefepime/Clavulanic acid										432		X	Beta-lactam+Inhibitors		BL+INH	03					Cefepime+C	42353-3	42350-9	42351-7	35763-2																																																																																																																																																																									
-CCP	CEP			CFPN		Cefcapene										152	5ug	X	Cephems	Cephalosporin III	CEPH3	04c																																																																																																																																																																																		
-AMC	AU5	AMC	AMC	AMPC-CVA		Amoxicillin/Clavulanic acid										307	25/2ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Amoxicilli	18862-3	21-6	20-8	6977-3		25310-4	22-4	19-0				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32				2	16				2	32																			8	16					
-BES	BES					Besifloxacin	CLSI	X								486			Quinolones	Fluoroquinolone	FQ	11b	X					73606-6	73651-2	73628-0																																																																																																																																																																										
-BIA	BIA			BIPM		Biapenem	CLSI	X								218		X	Penems	Carbapenems	CARB	07a					Biapenem	41728-7	41666-9	41665-1	41667-7																																																																																																																																																																									
-BCZ	BCZ	BCZ				Bicyclomycin (Bicozamycin)										219			Rho factor inhibitors		RHO	27																																																																																																																																																																																		
-AMX	AMX	AMX	AMX	AMPC		Amoxicillin	CLSI	X		X						82	30ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Amoxicilli	18861-5	17-4	16-6	6976-5			18-2	15-8																																																																																																																														13	14-20	21	4	32				2	16				2	32				2	32																				
-CTL	CTL			CTZ		Ceftezole										450		X	Cephems	Cephalosporin I	CEPH1	04a																																																																																																																																																																																		
-AMX	AX1	AMX	AMX	AMPC		Amoxicillin	EUCAST		X	X			X			210	10ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Amoxicilli	18861-5	17-4	16-6	6976-5			18-2	15-8																																																																																																								8	16																								4	32	15	16-22	23	2	16				2	32				2	32																				
-CFR	DRX	CFR	CFR	CDX		Cefadroxil	EUCAST		X	X	X	X				70	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefadroxil	18875-5	65-3	64-6				66-1	63-8																																																																																																					11		12	16	32																					11	12-17	18	8	64																					13	14-29	30	1	16	24	-	25	1	2					
-RID	RID	CD	CLO			Cefaloridine										71	30ug	X	Cephems	Cephalosporin I	CEPH1	04a					Cephalorid	18899-5	158-6	157-8	41684-2				156-0																																																																																																																																																															1	2					
-MAN	MAN	MA	CMD	CMD		Cefamandole	CLSI,DIN,BSAC	X		X		X	X			11	30ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefamandol	18876-3	69-5	68-7	41669-3			70-3	67-9	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																							14	15-21	22	8	64				4	16				4	32																19	-	20	8	16					
-MAN	MA6	MA	CMD	CMD		Cefamandole	NEO							X		338	60ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefamandol	18876-3	69-5	68-7	41669-3			70-3	67-9				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										8	64				4	16				4	32																			8	16					
-APR	APR		APR			Apramycin	NEO							X		145	40ug		Aminoglycosides		AG	09					Apramycin	23659-6																																																																																																																																																																												
-CNX	CNX	CNX	CFX	CMNX		Cefminox										229		X	Cephems	Cephamycin	CEPHAM	04e																																																																																																																																																																																		
-CZO	CFZ	CZ	CEZ	CEZ		Cefazolin	CLSI,DIN	X					X			12	30ug	X	Cephems	Cephalosporin I	CEPH1	04a	X				Cefazolin	18878-9	77-8	76-0	41670-1			78-6	75-2	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	19	20-22	23	2	8	14	15-17	18	1	4																																																																												19	20-21	22	4	16																														
-CZO	CZ6	CZ		CEZ		Cefazolin	NEO							X		339	60ug	X	Cephems	Cephalosporin I	CEPH1	04a	X				Cefazolin	18878-9	77-8	76-0	41670-1			78-6	75-2				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																															4	16																														
-CFB	CFB	CFB	CBZ	CBPZ		Cefbuperazone										223		X	Cephems	Cephamycin	CEPHAM	04e																																																																																																																																																																																		
-CMZ	CMZ	CMZ	CMT	CMZ		Cefmetazole	CLSI	X								99	30ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefmetazol	18881-3	89-3	88-5	11575-8			90-1	87-7	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64																																																																																																														
-CCX	CCX		CCP			Cefcapene pivoxil										445		X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																																																		
-BAM	BAM		BAC	BAPC		Bacampicillin										147		X	Penicillins	Aminopenicillin	PEN	01b					Bacampicil	18869-8	49-7	48-9				50-5	47-1																																																																																																																																																																					
-AMC	AU3	AMC	AMC	AMPC-CVA		Amoxicillin/Clavulanic acid	NEO							X		331	30/15ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Amoxicilli	18862-3	21-6	20-8	6977-3		25310-4	22-4	19-0				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											4	32				2	16				2	32																			8	16					
-AXS	AXS		AMC	AMPC-SBT		Amoxicillin/Sulbactam										3		X	Beta-lactam+Inhibitors		BL+INH	03																																																																																																																																																																																		
-AMB	AMB	AB	APH	AMPH-B		Amphotericin B	CLSI,NEO	X						X		127	10ug		Antifungals		FUNG	29					Amphoteric	18863-1	25-7	24-0	6978-1			26-5	23-2																																																																																																																																																1	2																				
-AMP	AM2	AM	AMP	ABPC		Ampicillin	EUCAST(Other bacteria)		X	X		X				309	2ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Ampicillin	18864-9	29-9	28-1	6979-9			30-7	27-3				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																	8	16																								4	32				2	16				2	32				2	32									1	16				8	16					
-CRO	CRO	CRO	CRO	CTRX		Ceftriaxone	CLSI,EUCAST	X	X	X	X	X	X		X	20	30ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Ceftriaxon	18895-3	142-0	141-2	6998-9		25367-4	143-8	140-4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4																																														19	20-22	23	1	4											12	13-25	26								14	15-20	21	4	64	16	17-20	21	4	32						20	21-27	28	2	16						26	27-29	30	.5	2	27	-	28	1	2					
-AMP	AM5	AM	AMP	ABPC		Ampicillin	BSAC					X				308	25ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Ampicillin	18864-9	29-9	28-1	6979-9			30-7	27-3				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32				2	16				2	32				2	32									1	16				8	16					
-AMP	AM1	AM	AMP	ABPC		Ampicillin	NEO							X		332	2.5ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Ampicillin	18864-9	29-9	28-1	6979-9			30-7	27-3				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										4	32				2	16				2	32				2	32									1	16				8	16					
-AMP	AM3	AM	AMP	ABPC		Ampicillin	NEO							X		333	33ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Ampicillin	18864-9	29-9	28-1	6979-9			30-7	27-3				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											4	32				2	16				2	32				2	32									1	16				8	16					
-CRB	CA5	CB	CAR			Carbenicillin	NEO							X		337	115ug	X	Penicillins	Carboxypenicillin	PEN	01d	X				Carbenicil	18873-0	61-2	60-4	41668-5			62-0	59-6				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																													9	10-27	28																																									128	256					
-CTB	BUT	CTB	CIB	CETB		Ceftibuten	CLSI,EUCAST	X	X	X	X					140	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Ceftibuten	35779-8	35777-2	35778-0	6996-3					17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32	17	18-20	21	8	32																																														20		21	1	2																								2	16				1	8																23	24-26	27	1	8				1	2					
-CFM	FIX	CFM	CFI	CFIX		Cefixime	CLSI,EUCAST	X	X	X	X	X				69	5ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefixime	18880-5	81-0	80-2	35766-5			82-8	79-4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4																																														16		17	1	2																								1	4				1	4																					19	-	20	1	2					
-CFM	FI1	CFM	CFI	CFIX		Cefixime	DIN			X			X			186	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefixime	18880-5	81-0	80-2	35766-5			82-8	79-4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																							21	22-24	25	1	4	21	22-25	26	1	4																								1	2					
-CFM	FI3	CFM	CFI	CFIX		Cefixime	NEO							X		340	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefixime	18880-5	81-0	80-2	35766-5			82-8	79-4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										1	4				1	4																								1	2					
-CZP	CZP			CZX-AP		Ceftizoxime alapivoxil										447		X	Cephems	Cephalosporin III	CEPH3	04c																																																																																																																																																																																		
-CMX	ME0	CMX	CMX	CMX		Cefmenoxime	DIN						X			228	10ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefmenoxim	32375-8																																																																																																																																													2	16																			1	4										
-CTE	CTE	CH	CTE			Chlortetracycline										91			Tetracyclines		TETRA	24					Chlortetra	18904-3	178-4	177-6				179-2	176-8																																																																																																																																																																					
-CIC	CCL	CI		ACPC		Ciclacillin										159		X	Penicillins	Aminopenicillin	PEN	01b					Cyclacilli	18913-4	210-5	209-7				211-3	208-9																																																																																																																																																																					
-CIN	CI3	CIN	CIN	CINX		Cinoxacin	SRGA,NEO				X			X		191	30ug		Quinolones	Quinolone	QUIN	11a	X				Cinoxacin	18905-0	182-6	181-8				183-4	180-0				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																																																																15	16-19	20	8	32										
-CIN	CIN	CIN	CIN	CINX		Cinoxacin	CLSI	X								25	100ug		Quinolones	Quinolone	QUIN	11a	X				Cinoxacin	18905-0	182-6	181-8				183-4	180-0	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64	14	15-18	19	16	64																																																																																																			8	32										
-CIP	CI0		CIP	CPFX		Ciprofloxacin	AFA,SRGA,NEO				X			X	X	192	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ciprofloxa	18906-8	186-7	185-9	7002-9	20377-8	23621-6	187-5	184-2				0.25	1				0.25	1				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																													12	13-23	24											1	4				1	4				1	4	18	19-26	27	.25	4						17	18-23	24	.125	2				1	2					
-ARB	ARB		ARB	ABK		Arbekacin										212			Aminoglycosides		AG	09					Arbekacin	32373-3																																																																																																																																																																												
-CZD	CZD	CZD	CZD			Cefazedone										222		X	Cephems	Cephalosporin I	CEPH1	04a																																																																																																																																																																																		
-CIP	CI5		CIP	CPFX		Ciprofloxacin	NEO							X		346	.5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ciprofloxa	18906-8	186-7	185-9	7002-9	20377-8	23621-6	187-5	184-2				0.25	1				0.25	1				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										1	4				1	4				1	4				.25	4									.125	2				1	2					
-CIP	CI1		CIP	CPFX		Ciprofloxacin	BSAC					X				314	1ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ciprofloxa	18906-8	186-7	185-9	7002-9	20377-8	23621-6	187-5	184-2				0.25	1				0.25	1				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										1	4				1	4				1	4				.25	4									.125	2	17	-	18	1	2					
-CIP	CIP		CIP	CPFX		Ciprofloxacin	CLSI,EUCAST	X	X	X		X	X			26	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ciprofloxa	18906-8	186-7	185-9	7002-9	20377-8	23621-6	187-5	184-2	21	22-25	26	0.25	1	21	22-25	26	0.25	1	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4	15	16-20	21	1	4																																														18	19-21	22	0.5	2																					21	22-24	25	.5	2	18	19-22	23	1	4				1	4				.25	4									.125	2				1	2					
-CLR	CL3	CLR	CLR	CAM		Clarithromycin	NEO							X		347	30ug		Macrolides	14-Membered ring	MACRO	17	X				Clarithrom	18907-6	190-9	189-1	7003-7	20375-2	23619-0	191-7	188-3				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																													12	13-21	22																2	8				.5	4				1	4									.5	1				.5	1					
-CTZ	FAT	CTZ	CRI	CFT		Cefatrizine				X						151	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a					Cefatrizin	18877-1	73-7	72-9				74-5	71-1																																																																																																																														14	15-21	22	2	16																																			
-CLR	CLA	CLR	CLR	CAM		Clarithromycin	CLSI,EUCAST	X	X	X	X		X		X	103	15ug		Macrolides	14-Membered ring	MACRO	17a	X				Clarithrom	18907-6	190-9	189-1	7003-7	20375-2	23619-0	191-7	188-3	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8																																																																												16	17-20	21	2	8				.5	4	16	17-20	21	1	4						19	20-24	25	.5	1				.5	1					
-CLR	CR2	CLR	CLR	CAM		Clarithromycin						X				410	2ug		Macrolides	14-Membered ring	MACRO	17	X				Clarithrom	18907-6	190-9	189-1	7003-7	20375-2	23619-0	191-7	188-3				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																															2	8				.5	4				1	4									.5	1	19	-	20	.5	1					
-CED	RAD	CED	CED	CED		Cephradine	NEO							X		74	60ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a					Cephradine	18902-7	170-1	169-3				171-9	168-5																																																																																																																																	8	64									4	32																			2	4					
-CED	RA3	CED	CED	CED		Cephradine	BSAC			X		X				408	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a					Cephradine	18902-7	170-1	169-3				171-9	168-5																																																																																																																														11	12-17	18	8	64									4	32																11	-	12	2	4					
-CTB	BU1	CTB	CIB	CETB		Ceftibuten	DIN,BSAC			X		X	X			189	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Ceftibuten	35779-8	35777-2	35778-0	6996-3								8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																							15	16-19	20	2	16				1	8																			1	8	27	-	28	1	2					
-DIZ	DIZ	CDZ	CFO	CDZM		Cefodizime	DIN						X			100	10ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefodizime	18882-1	93-5	92-7	6988-0			94-3	91-9																																																																																																																																			15	16-17	18	4	16																														
-CHL	CH6	C	CMP	CP		Chloramphenicol	NEO							X		345	60ug		Phenicols		PHEN	22	X				Chloramphe	18903-5	174-3	173-5	7001-1			175-0	172-7				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											8	32				8	16				4	16				2	8									8	16				8	16					
-CMX	MEN	CMX	CMX	CMX		Cefmenoxime				X						85	30ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefmenoxim	32375-8																																																																																																																																													2	16																			1	4										
-CHL	CHL	C	CMP	CP		Chloramphenicol	CLSI,EUCAST	X	X	X	X	X	X		X	24	30ug		Phenicols		PHEN	22	X				Chloramphe	18903-5	174-3	173-5	7001-1			175-0	172-7	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32	12	13-17	18	8	32																																														16		17	8	16																					18	19-22	23	8	32	20	-	21	8	16				4	16	24	25-31	32	2	8						17	18-20	21	8	16	20	-	21	8	16					
-AVO	AVO		AVO			Avoparcin										215			Glycopeptides	Glycopeptide	GLYCO	21a																																																																																																																																																																																		
-FOX	FOX	FOX	COX	CFX		Cefoxitin	CLSI,EUCAST	X	X	X		X	X		X	17	30ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefoxitin	18888-8	117-2	116-4	6991-4		25366-6	118-0	115-6	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																							14	15-21	22	8	64	20	21-25	26	4	16				4	32	17	18-27	28	2	16						15	16-19	20	4	16	19	-	20	4	8					
-CPD	PO1	CPD	CPO	CPDX		Cefpodoxime										407	1ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Cefpodoxim	18890-4	121-4	120-6	6993-0			122-2	119-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	4																								1	4				1	2					
-AST	AST	AST	AST	ASTM		Astromicin										146			Aminoglycosides		AG	09																																																																																																																																																																																		
-CPD	PO5	CPD	CPO	CPDX		Cefpodoxime	BSAC					X				311	5ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefpodoxim	18890-4	121-4	120-6	6993-0			122-2	119-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	4																								1	4	33	-	34	1	2					
-CLI	CL1	CM	CLI	CLDM		Clindamycin	AFA,SRGA				X				X	193	15ug		Lincosamides		LINCO	15	X				Clindamyci	18908-4	194-1	193-3	7005-2			195-8	192-5				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4																																																																										2	4				1	8				1	8	17	18-23	24	1	4						19	20-27	28	.5	4				.5	1					
-CLI	CL2	CM	CLI	CLDM		Clindamycin	NEO							X		348	25ug		Lincosamides		LINCO	15	X				Clindamyci	18908-4	194-1	193-3	7005-2			195-8	192-5				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4				.5	4																																																													14	15-27	28											2	4				1	8				1	8				1	4									.5	4				.5	1					
-CLF	CLF					Clofazimine										482			Antimycobacterials		MYCO	28																																																																																																																																																																																		
-CTR	CLO	CTR	CTR			Clotrimazole	NEO							X		158	10ug		Antifungals		FUNG	29					Clotrimazo	18909-2		10653-4					10654-2																																																																																																																																																																					
-CLR	CL5	CLR	CLR	CAM		Clarithromycin						X				409	5ug		Macrolides	14-Membered ring	MACRO	17	X				Clarithrom	18907-6	190-9	189-1	7003-7	20375-2	23619-0	191-7	188-3				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																															2	8				.5	4				1	4									.5	1				.5	1					
-CLA	CLV	CLA	CLA	CVA		Clavulanic acid	CLSI	X								246		X	Beta-lactamase inhibitors		BL-INH	02					Clavulanat	41733-7	41686-7	41687-5	41685-9																																																																																																																																																																									
-CLX	CLN		CLN			Clinafloxacin	CLSI	X								157	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Clinafloxa	32376-6	35785-5	35786-3	7004-5																																																																																																																																																																									
-CHL	CH1	C	CMP	CP		Chloramphenicol	BSAC,NEO					X		X		313	10ug		Phenicols		PHEN	22	X				Chloramphe	18903-5	174-3	173-5	7001-1			175-0	172-7				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										8	32				8	16				4	16				2	8									8	16				8	16					
-CTT	CTN	CTT	CTT	CTT		Cefotetan	CLSI,BSAC	X		X		X				16	30ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefotetan	18887-0	113-1	112-3	6990-6			114-9	111-5	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64	12	13-15	16	16	64																																																													12	13-23	24								16	17-22	23	4	64				4	32				4	32																23	-	24	4	8					
-CTF	FOT	CTF	CTM	CTM		Cefotiam	DIN			X			X			86	30ug	X	Cephems	Cephamycin	CEPHAM	04e					Cefotiam	32374-1	35772-3	35773-1																																																																																																																																			14	15-21	22	4	64	16	17-19	20	4	16																														
-CHE	CHE		CTH	CTM-HE		Cefotiam hexetil				X						235	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																											18	19-21	22	1	4																																			
-CHE	CHE		CTH	CTM-HE		Cefotiam hexetil	DIN						X			435	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																20	21-25	26	1	8																														
-CLI	CLI	CM	CLI	CLDM		Clindamycin	CLSI,EUCAST	X	X	X		X				27	2ug		Lincosamides		LINCO	15	X				Clindamyci	18908-4	194-1	193-3	7005-2			195-8	192-5	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4	14	15-20	21	.5	4																																																																							14	-	15	2	4				1	8				1	8				1	4									.5	4	25	-	26	.5	1					
-FCT	5C1	FCT	5FC	5-FC		5-Fluorocytosine	CLSI,NEO	X						X		328	10ug		Antifungals		FUNG	29	X				5-Fluorocy	18855-7	254-3	253-5	7014-4			255-0	252-7														4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																																																									8	16																				
-FCT	5FC	FCT		5-FC		5-Fluorocytosine	CLSI,NEO	X						X		126	1ug		Antifungals		FUNG	29	X				5-Fluorocy	18855-7	254-3	253-5	7014-4			255-0	252-7														4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																																																									8	16																				
-ACM	ACM					Acetylmidecamycin										114			Macrolides		MACRO	17																																																																																																																																																																																		
-ASP	ASP					Acetylspiramycin										113			Macrolides		MACRO	17																																																																																																																																																																																		
-CTO	CTO	CTO				Cetocycline										245			Tetracyclines		TETRA	24																																																																																																																																																																																		
-ATM	ATM	ATM	AZT	AZT		Aztreonam	CLSI,EUCAST	X	X	X	X	X			X	7	30ug	X	Monobactams		MONO	06	X				Aztreonam	18868-0	45-5	44-8	6982-3			46-3	43-0	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16																																														20		25	1	16																					16	17-22	23	4	64				2	32				4	16	14	15-25	26	2	32						24	25-27	28	0.5	2	23	-	24	8	16					
-ATM	AT1	ATM	AZT	AZT		Aztreonam	DIN						X			217	10ug	X	Monobactams		MONO	06	X				Aztreonam	18868-0	45-5	44-8	6982-3			46-3	43-0				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	64				2	32				4	16				2	32									0.5	2				8	16					
-CID	CID	CID	CNI			Cefonicid	CLSI	X								13	30ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefonicid	18883-9	97-6	96-8				98-4	95-0	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																																																														
-CFP	CFP	CFP	CPZ	CPZ		Cefoperazone	CLSI	X								14	75ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefoperazo	18884-7	101-6	100-8	35767-3			102-4	99-2	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64	15	16-20	21	16	64																																																																										4	64				4	32																								4	8					
-CFP	CP1	CFP	CPZ	CPZ		Cefoperazone	DIN						X			230	10ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefoperazo	18884-7	101-6	100-8	35767-3			102-4	99-2				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																																										4	64	14	15-20	21	4	32																								4	8					
-CFP	CF3	CFP	CPZ	CPZ		Cefoperazone	BSAC			X		X				187	30ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefoperazo	18884-7	101-6	100-8	35767-3			102-4	99-2				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																																							13	14-20	21	4	64				4	32																					24	-	25	4	8					
-CFP	CF6	CFP	CPZ	CPZ		Cefoperazone	NEO							X		341	60ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefoperazo	18884-7	101-6	100-8	35767-3			102-4	99-2				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																																										4	64				4	32																								4	8					
-CSL	CFS		CPS	CPZ-SBT		Cefoperazone/Sulbactam	DIN						X			101	30/15ug	X	Beta-lactam+Inhibitors		BL+INH	03									35768-1																																																																																																																																							15	16-21	22																																
-CND	CND	CND				Ceforanide	NEO							X		231	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a					Ceforanide	18885-4	105-7	104-0				106-5	103-2																																																																																																																																																																					
-CSE	CSE					Cefoselis										448		X	Cephems	Cephalosporin IV	CEPH4	04d																																																																																																																																																																																		
-AMK	AMK	AN	AMK	AMK		Amikacin	CLSI,EUCAST	X	X	X	X	X	X			1	30ug		Aminoglycosides		AG	09	X				Amikacin	18860-7	13-3	12-5	6975-7	20373-7	23624-0	14-1	11-7	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64	14	15-16	17	16	64																																														12	13-15	16	8	32																					14	15-16	17	8	32	13	14-19	20	4	32				4	32											15	16-18	19	4	8	19	-	20	4	8					
-AMP	AMP	AM	AMP	ABPC		Ampicillin	CLSI,EUCAST(Enterobacterales)	X	X	X	X	X	X		X	4	10ug	X	Penicillins	Aminopenicillin	PEN	01b	X				Ampicillin	18864-9	29-9	28-1	6979-9			30-7	27-3	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32	13	14-16	17	8	32																																														11		12	8	16																					13	14-18	19	4	32	14	15-21	22	2	16				2	32	8	9-21	22	2	32						11	12-29	30	1	16	17	-	18	8	16					
-SAM	AMS	SAM	AMS	ABPC-SBT		Ampicillin/Sulbactam	CLSI,EUCAST	X	X	X						5	10/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Ampicillin	18865-6	33-1	32-3	6980-7	20374-5	23618-2	34-9	31-5	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32																																																	8	16																					13	14-18	19	4	32				2	16																														
-AVB	AVB					Avibactam	CLSI	X								496		X	Beta-lactamase inhibitors		BL-INH																																																																																																																																																																																			
-AVI	AVI	AVI	AVM			Avilamycin										214			Everninomycins		EVER	27					Avilamycin	35756-6	35754-1	35755-8																																																																																																																																																																										
-AZM	AZI	AZM	AZM			Azithromycin	CLSI,EUCAST	X	X	X	X	X	X		X	83	15ug		Macrolides	15-Membered ring	MACRO	17a	X				Azithromyc	18866-4	37-2	36-4	6981-5		23612-5	38-0	35-6	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8	13	14-17	18	2	8																																																																							16	17-21	22	.5	8	17	18-20	21	2	8						19	20-23	24	1	4						19	20-22	23	.5	1	19	-	20	1	2					
-AZM	AI3	AZM	AZM			Azithromycin	NEO							X		335	30ug		Macrolides	15-Membered ring	MACRO	17	X				Azithromyc	18866-4	37-2	36-4	6981-5		23612-5	38-0	35-6				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																													12	13-21	22											.5	8				2	8									1	4									.5	1				1	2					
-AZL	AZL	AZL	AZL			Azlocillin	CLSI	X		X						6	75ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Azlocillin	18867-2	41-4	40-6	41661-0			42-2	39-8	17	-	18	64	128	17	-	18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128	17		18	64	128																																																																							12	13-18	19	16	128														2	32																				
-AZL	AZ3	AZL	AZL			Azlocillin	AFA,DIN,NEO						X	X	X	216	30ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Azlocillin	18867-2	41-4	40-6	41661-0			42-2	39-8				64	128				64	128				64	128				64	128				64	128				64	128				64	128				64	128				64	128				64	128				64	128																																																													14	15-27	28											16	128	12	13-21	22								15	16-27	28	2	32																				
-CDR	DIN	CDR	CFD	CFDN		Cefdinir	CLSI	X								96	5ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefdinir	23636-4	35758-2	23637-2	35757-4					16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4																																																																																																														
-DIT	DIT		CDT	CDTR		Cefditoren	CLSI	X								153	5ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefditoren	35762-4	35759-0	35761-6	35760-8																																																																																																																																																																									
-DIX	DIX			CDTR-PI		Cefditoren pivoxil										446		X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																																																		
-FEP	FEP	FEP	CEP	CEPM		Cefepime	CLSI,EUCAST	X	X	X	X	X				97	30ug	X	Cephems	Cephalosporin IV	CEPH4	04d	X				Cefepime	18879-7	8272-7	6644-9	6987-2			8273-5	6643-1	18	19-24	25	2	16	18	19-24	25	2	16	18	19-24	25	2	16	18	19-24	25	2	16	18	19-24	25	2	16	18	19-24	25	2	16	18	19-24	25	2	16	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																														17	18-23	24	1	16											14	15-27	28								14	15-20	21	4	64				4	32																23	24-26	27	.5	2	31	-	32	2	4					
-FEP	FE1	FEP	CEP	CEPM		Cefepime	DIN						X			224	10ug	X	Cephems	Cephalosporin IV	CEPH4	04d	X				Cefepime	18879-7	8272-7	6644-9	6987-2			8273-5	6643-1				2	16				2	16				2	16				2	16				2	16				2	16				2	16				8	32				8	32				8	32				8	32																																																																										4	64	12	13-18	19	4	32																			.5	2				2	4					
-CTX	FTX	CTX	CTX	CTX		Cefotaxime	CLSI,SRGA,BSAC	X		X	X	X			X	15	30ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Cefotaxime	18886-2	109-9	108-1	6989-8			110-7	107-3	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4	22	23-25	26	1	4																																																													14	15-27	28								14	15-20	21	4	64				2	16				4	32	20	21-26	27	2	16						23	24-26	27	.5	2	29	-	30	1	2					
-CTX	FT5	CTX	CTX	CTX		Cefotaxime	EUCAST		X	X		X				406	5ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Cefotaxime	18886-2	109-9	108-1	6989-8			110-7	107-3				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																														17	18-20	21	1	4																								4	64				2	16				4	32				2	16									.5	2				1	2					
-CTX	FT1	CTX	CTX	CTX		Cefotaxime	DIN						X			232	10ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Cefotaxime	18886-2	109-9	108-1	6989-8			110-7	107-3				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										4	64	13	14-20	21	2	16				4	32				2	16									.5	2				1	2					
-CTC	CTC			CTX-CVA		Cefotaxime/Clavulanic acid	CLSI	X								394	30/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Cefotaxime	35771-5	35769-9	35770-7	41671-9																																																																																																																																																																									
-CTS	CTS		CTS	CTX-SBT		Cefotaxime/Sulbactam	DIN						X			233	10/15ug	X	Beta-lactam+Inhibitors		BL+INH	03																																																																																																																																																			2	16																														
-CTT	CT1	CTT	CTT	CTT		Cefotetan	DIN						X			234	10ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefotetan	18887-0	113-1	112-3	6990-6			114-9	111-5				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																																										4	64				4	32				4	32																			4	8					
-CAT	FET	CAT	CFT	CEMT		Cefetamet	CLSI	X								98	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefetamet	32377-4	35764-0	35765-7						14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16	14	15-17	18	4	16																																																																																																														
-CPI	CPI		CFP	CEMT-PI		Cefetamet pivoxil	DIN						X			225	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																19	20-25	26	1	8																														
-CCL	CET	CCL				Cefetecol (Cefcatacol)										226		X	Cephems	Cephalosporin IV	CEPH4	04d																																																																																																																																																																																		
-CZL	CZL	CZL				Cefetrizole										227		X	Cephems	Cephalosporin-new	CEPH?	04e																																																																																																																																																																																		
-CFS	SLD	CFS	CFS	CFS		Cefsulodin	DIN			X			X			73	30ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefsulodin	18892-0	129-7	128-9				130-5	127-1																																																																																																																				14	15-27	28								13	14-21	22	8	64	18	19-28	29						4	32																									
-CSU	CSU	CSU	CSM			Cefsumide										240		X	Cephems	Cephalosporin-new	CEPH?	04e																																																																																																																																																																																		
-CPT	CPT					Ceftaroline	CLSI	X								475	30ug	X	Cephems	Cephalosporin	CEPH	04b	X					73605-8	73650-4	73627-2						19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2	19	20-22	23	.5	2																																																																																																																													
-CPT	CPT					Ceftaroline	EUCAST		X	X						507	5ug		Cephems	Cephalosporin	CEPH	04b						73605-8	73650-4	73627-2																																																																																																																																																																										
-CPA	CPA					Ceftaroline/Avibactam	CLSI	X								497	30/15ug	X	Beta-lactam+Inhibitors		BL+INH	03	X					73604-1	73649-6	73626-4																																																																																																																																																																										
-BAC	BA4	B	BTC	BC		Bacitracin zinc	NEO							X		336	40units		Polypeptides		POLYPEP	26	X				Bacitracin	18870-6	10868-8	6827-0	6983-1																																																																																																																								12	13-21	22											2	4																																			
-CZX	ZOX	CZX	CZX	CZX		Ceftizoxime	CLSI,BSAC	X		X		X				19	30ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Ceftizoxim	18894-6	138-8	137-0	6997-1	20378-6	23622-4	139-6	136-2	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4	21	22-24	25	1	4																																																																							14	15-20	21	4	64				2	16																					29	-	30	1	2					
-CAZ	CAZ	CAZ	CAZ	CAZ		Ceftazidime	CLSI,SRGA,BSAC	X		X	X	X			X	18	30ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Ceftazidim	18893-8	134-7	133-9	6995-5			135-4	132-1	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16	17	18-20	21	4	16																																																													14	15-27	28								14	15-20	21	4	64				4	32				4	32	19	20-25	26	2	16						23	24-26	27	2	8	27	-	28	2	4					
-CAZ	CA1	CAZ	CAZ	CAZ		Ceftazidime	EUCAST		X	X			X			241	10ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Ceftazidim	18893-8	134-7	133-9	6995-5			135-4	132-1				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																														14	15-29	20	1	16																								4	64	10	11-15	16	4	32				4	32				2	16									2	8				2	4					
-CZA	CZA					Ceftazidime/Avibactam	CLSI	X								498	30/20ug	X	Beta-lactam+Inhibitors		BL+INH	03	X					73603-3	73648-8	73625-6						20		21	8	16	20		21	8	16	20		21	8	16																																																																																																																																																						
-TIO	TIO		CFL			Ceftiofur	CLSI	X								154	30ug	X	Cephems	Cephalosporin III	CEPH3	04c		X			Ceftiofur	23709-9	35780-6	35781-4						17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8																																																																																																														
-CZX	ZO5	CZX	CZX	CZX		Ceftizoxime	DIN						X			244	5ug	X	Cephems	Cephalosporin III	CEPH3	04c	X				Ceftizoxim	18894-6	138-8	137-0	6997-1	20378-6	23622-4	139-6	136-2				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										4	64	11	12-16	17	2	16																								1	2					
-BPR	BPR					Ceftobiprole	CLSI	X								474	30ug	X	Cephems	Cephalosporin	CEPH	04e	X				Ceftobipro	43272-4	43269-0	43271-6					43270-8																																																																																																																																																																					
-CZT	CZT					Ceftolozane/Tazobactam	CLSI,EUCAST	X	X	X						506	30/10ug	X	Beta-lactam+Inhibitors		BL+INH		X					73602-5	73647-0	73624-9						17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8				2	8				2	8																																																																																																																																												
-CCV	CCV			CAZ-CVA		Ceftazidime/Clavulanic acid	CLSI	X								242	30/4ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Ceftazidim	35776-4	35774-9	35775-6	42352-5																																																																																																																																																																									
-CEM	CEM	CEM	CFM			Cefteram										243		X	Cephems	Cephalosporin II	CEPH2	04b																																																																																																																																																																																		
-CPL	CPL			CFTM-PI		Cefteram pivoxil										449		X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																																																		
-CEC	CF1	CEC	CEC	CCL		Cefaclor				X						185	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefaclor	18874-8	85-1	84-4	6986-4			86-9	83-6				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																							15	16-21	22	2	16				1	8				4	32														1	16				1	2					
-CXM	FR5	CXM	CXM	CXM		Cefuroxime	BSAC					X				312	5ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefuroxime	18896-1	146-1	145-3	6999-7			147-9	144-6				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																										8	64				4	16				4	32				2	16									8	16				1	32					
-AMK	AK4	AN	AMK	AMK		Amikacin	NEO							X		329	40ug		Aminoglycosides		AG	09	X				Amikacin	18860-7	13-3	12-5	6975-7	20373-7	23624-0	14-1	11-7				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																													14	15-25	26											8	32				4	32				4	32														4	8				4	8					
-CXM	FRX	CXM	CXM	CXM		Cefuroxime	CLSI,EUCAST	X	X	X	X	X	X		X	21	30ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefuroxime	18896-1	146-1	145-3	6999-7			147-9	144-6	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																														17		18	8	16																					14	15-21	22	8	64				4	16				4	32	19	20-28	29	2	16						15	16-18	19	8	16	17	18-24	25	1	32					
-CXM	FR6	CXM	CXM	CXM		Cefuroxime	NEO							X		343	60ug	X	Cephems	Cephalosporin II	CEPH2	04b	X				Cefuroxime	18896-1	146-1	145-3	6999-7			147-9	144-6				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											8	64				4	16				4	32				2	16									8	16				1	32					
-CXA	FRA		CFA	CXM-AX		Cefuroxime axetil	CLSI,EUCAST	X	X	X		X	X			22	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefuroxime	35783-0	35782-2	20460-2						14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32	14	15-22	23	4	32																																														17		18	8	16																								1	8				1	8				1	32											24	25-28	29	1	4	24	-	25	1	2					
-CXA	FR1		CFA	CXM-AX		Cefuroxime axetil				X						190	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefuroxime	35783-0	35782-2	20460-2									4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																																							19	20-25	26	1	8				1	8				1	32														1	4				1	2					
-ZON	ZON		CFZ			Cefuzonam										155		X	Cephems	Cephamycin	CEPHAM	04e																																																																																																																																																																																		
-LEX	LEX	CN	CEX	CEX		Cephalexin	EUCAST		X	X		X			X	121	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cephalexin	18897-9	150-3	149-5	35784-8			151-1	148-7																																																																																																								16	32																					11	12-17	18	8	64											20	21-31	32								13	14-26	27	1	16	24	-	25	2	4					
-CEP	KE6	CF	CTN	CET		Cephalothin	NEO							X		344	66ug	X	Cephems	Cephalosporin I	CEPH1	04a	X				Cephalothi	18900-1	162-8	161-0	7000-3			163-6	160-2				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											8	64									4	32				2	16									1	16				1	2					
-CEP	KEF	CF	CTN	CET		Cephalothin	CLSI,EUCAST	X	X	X		X			X	23	30ug	X	Cephems	Cephalosporin I	CEPH1	04a	X				Cephalothi	18900-1	162-8	161-0	7000-3			163-6	160-2																										14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																							11	12-17	18	8	64									4	32	17	18-26	27	2	16						13	14-26	27	1	16	26	-	27	1	2					
-HAP	FAP	CP	CAP			Cephapirin				X						150	30ug	X	Cephems	Cephalosporin I	CEPH1	04a					Cephapirin	18901-9	166-9	165-1				167-7	164-4																																																																																																																																																																					
-GEH	GE2					Gentamicin-High	BSAC					X				318	200ug		Aminoglycosides		AG	09	X				Gentamicin	18929-0	7017-7	7018-5	35817-6								500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501																																																																										250	501														500	1000																				
-GEH	GEH					Gentamicin-High	CLSI	X								137	120ug		Aminoglycosides		AG	09	X				Gentamicin	18929-0	7017-7	7018-5	35817-6					6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513	6	7-9	10	512	513																																																																										250	501														500	1000																				
-GEH	G30					Gentamicin-High	EUCAST		X	X						488	30ug		Aminoglycosides		AG	09	X				Gentamicin	18929-0	7017-7	7018-5	35817-6								512	513				512	513				512	513				512	513				512	513				512	513				512	513				512	513				512	513				512	513				512	513																																																																										250	501														500	1000																				
-GRX	GRE		GRE	GPFX		Grepafloxacin	CLSI	X								141	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Grepafloxa	23638-0	35818-4	23639-8	21316-5					14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4																																																																																																														
-GRI	GRI		GRI	GRF		Griseofulvin	NEO							X		257	25ug		Antifungals		FUNG	29																																																																																																																																																																																		
-HAB	HAB	HAB				Habekacin										258			Aminoglycosides		AG	09																																																																																																																																																																																		
-CLO	CLX	CX		MCIPC		Cloxacillin										122	5ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e					Cloxacilli	18910-0	198-2	197-4				199-0	196-6																																																																																																																																											4	8																									
-FOX	FO6	FOX	COX	CFX		Cefoxitin	NEO							X		342	60ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefoxitin	18888-8	117-2	116-4	6991-4		25366-6	118-0	115-6				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											8	64				4	16				4	32				2	16									4	16				4	8					
-FOX	FOX	FOX	COX	CFX		Cefoxitin										439	10ug	X	Cephems	Cephamycin	CEPHAM	04e	X				Cefoxitin	18888-8	117-2	116-4	6991-4		25366-6	118-0	115-6				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																																																														
-ZOP	ZOP		COP	CZOP		Cefozopran										156		X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																																																																		
-CFZ	MIZ	CFZ	CMZ			Cefpimizole										236		X	Cephems	Cephalosporin III	CEPH3	04c																																																																																																																																																																																		
-CPM	CPM	CPM		CPM		Cefpiramide										237		X	Cephems	Cephalosporin III	CEPH3	04c																																																																																																																																																																																		
-CPO	PIR	CPO	CPI	CPR		Cefpirome	SRGA,NEO			X	X			X		72	30ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefpirome	18889-6	8276-8	8275-0	6992-2			6650-6	8274-3																																																																																																																				14	15-27	28								14	15-20	21	4	64														2	16						23	24-26	27	.5	2				1	2					
-CPO	PI2	CPO	CPI	CPR		Cefpirome	BSAC					X				310	20ug	X	Cephems	Cephalosporin III	CEPH3	04c					Cefpirome	18889-6	8276-8	8275-0	6992-2			6650-6	8274-3																																																																																																																																	4	64														2	16									.5	2	24	-	25	1	2					
-COL	CO1	CS	COL	CL		Colistin	NEO							X		349	150ug		Lipopeptides		LIPOPEP	16	X				Colistin	18912-6	206-3	205-5	33333-6			207-1	204-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																													12	13-21	22											2	4				0.5	4																								4	8					
-COL	COL	CS	COL	CL		Colistin	CLSI,EUCAST	X	X	X						28	10ug		Lipopeptides		LIPOPEP	16	X				Colistin	18912-6	206-3	205-5	33333-6			207-1	204-8	10	-	11	0.001	4	10	-	11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8	10		11	2	8																																																	2	4																								2	4				0.5	4																								4	8					
-COL	CO5	CS	COL	CL		Colistin				X						194	50ug		Lipopeptides		LIPOPEP	16	X				Colistin	18912-6	206-3	205-5	33333-6			207-1	204-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																							14	-	15	2	4				0.5	4																								4	8					
-COL	CO2	CS	COL	CL		Colistin	BSAC					X				315	25ug		Lipopeptides		LIPOPEP	16	X				Colistin	18912-6	206-3	205-5	33333-6			207-1	204-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										2	4				0.5	4																					14	-	15	4	8					
-CYC	CYC		CSE	CS		Cycloserine										129			Antimycobacterials		MYCO	28					Cycloserin	18914-2	214-7	213-9			23608-3	215-4	212-1																																																																																																																																																																					
-DAL	DAL					Dalbavancin	CLSI,EUCAST	X	X	X						467			Glycopeptides	Lipoglycopeptide	GLYCO	21b	X				Dalbavanci	41734-5	41688-3	41689-1	41690-9																																																																																																																																																																									
-DAN	DFX	DFX	DAN			Danofloxacin	CLSI	X								247	5ug		Quinolones	Fluoroquinolone	FQ	11b	X					73601-7	73646-2	73623-1																																																																																																																																																																										
-DAP	DAP		DPT			Daptomycin	CLSI	X								395	30ug		Lipopeptides		LIPOPEP	16	X				Daptomycin	35789-7	35787-1	35788-9	41691-7								1					1					1					1					1					1					1					1					1					1					1																																																																																																															
-DEM	DEM	DM		DMCTC		Demeclocycline										160			Tetracyclines		TETRA	24					Demeclocyc	18915-9	218-8	217-0	7006-0			219-6	216-2																																																																																																																																																																					
-DKB	DIB	DKB	DIB	DKB		Dibekacin				X						29	10ug		Aminoglycosides		AG	09																																																																																																																																											13	14-15	16	4	16																																			
-DIC	DIC	DX	DIC	MDIPC		Dicloxacillin	DIN						X			123	5ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e					Dicloxacil	18916-7	222-0	221-2				223-8	220-4																																																																																																																																						1	2																														
-DIF	DIF		DIF			Difloxacin	CLSI	X								248	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Difloxacin	35792-1	35790-5	35791-3						17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4	17	18-20	21	.5	4																																																																																																														
-DIR	DIR		DIR			Dirithromycin	CLSI	X		X						104	15ug		Macrolides		MACRO	17a	X				Dirithromy	35795-4	35793-9	35794-7	7007-8					15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8																																																																							15	16-27	28	.125	8																																			
-CPD	PO3	CPD	CPO	CPDX		Cefpodoxime	SRGA,NEO				X			X		188	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefpodoxim	18890-4	121-4	120-6	6993-0			122-2	119-8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	4																					23	24-26	27	1	4				1	2					
-CPD	POD	CPD	CPO	CPDX		Cefpodoxime	CLSI,EUCAST	X	X	X						87	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefpodoxim	18890-4	121-4	120-6	6993-0			122-2	119-8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8	17	18-20	21	2	8																																														20		21	1	2																					20	21-23	24	1	4																								1	4				1	2					
-CPX	CPX		CPP	CPDX-PR		Cefpodoxime proxetil	DIN			X			X			238	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a																																																																																																																																											20	21-23	24	1	4	18	19-24	25	1	8																														
-CDC	CDC			CPDX-CVA		Cefpodoxime/Clavulanic acid										429		X	Beta-lactam+Inhibitors		BL+INH	03					Cefpodoxim	41731-1	41680-0	41679-2	41678-4																																																																																																																																																																									
-CPR	PRO	CPR	CPY			Cefprozil	CLSI	X								102	30ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a	X				Cefprozil	18891-2	125-5	124-8	6994-8			126-3	123-0	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																																																														
-CEQ	CEQ					Cefquinome										481		X	Cephems	Cephalosporin ?	CEPH?	04d																																																																																																																																																																																		
-CRD	CRD	CRD		CXD		Cefroxadine										239		X	Cephems	Cephalosporin I	CEPH1	04a																																																																																																																																																																																		
-DOR	DOR			DRPM		Doripenem	CLSI,EUCAST	X	X	X						451	10ug	X	Penems	Carbapenems	CARB	07a	X				Doripenem	60535-2	72893-1	56031-8	58711-3					19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4																																																			17	18-23	24	1	8																																																												
-DOX	DOX	DO	DOX	DOXY		Doxycycline	CLSI,SRGA,BSAC	X		X	X	X			X	30	30ug		Tetracyclines		TETRA	24a	X				Doxycyclin	18917-5	226-1	225-3	7008-6	20379-4	23623-2	227-9	224-6	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16	10	11-13	14	4	16																																																																							16	17-18	19	4	16				1	8						19	20-24	25	1	4						19	20-22	23	1	2	28	-	29	1	2					
-DOX	DO8	DO	DOX	DOXY		Doxycycline	NEO							X		350	80ug		Tetracyclines		TETRA	24	X				Doxycyclin	18917-5	226-1	225-3	7008-6	20379-4	23623-2	227-9	224-6				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	16				1	8									1	4									1	2				1	2					
-ECO	ECO		ECO			Econazole	NEO							X		351	10ug		Antifungals		FUNG	29					Econazole	25595-0		25637-0																																																																																																																																																																										
-ENX	EN5	ENX	ENO	ENX		Enoxacin	DIN			X			X			249	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Enoxacin	18918-3	230-3	229-5	41692-5			231-1	228-7				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																							18	19-21	22	1	4	16	17-20	21	1	4																														
-ENX	ENX	ENX	ENO	ENX		Enoxacin	CLSI	X								31	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Enoxacin	18918-3	230-3	229-5	41692-5			231-1	228-7	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8																																																																										1	4				1	4																														
-GRN	GRN					Garenoxacin	CLSI	X								491	5ug		Quinolones	Quinolone	QUIN	11a	X				Garenoxaci	35813-5	35811-9	35812-7																																																																																																																																																																										
-GAT	GA2		GAT	GFLX		Gatifloxacin										412	2ug		Quinolones	Fluoroquinolone	FQ	11b	X				Gatifloxac	31038-3	31040-9	31036-7	31042-5		41494-6						2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	4				1	4																								1	2					
-GAT	GAT		GAT	GFLX		Gatifloxacin	CLSI,DIN	X		X			X			256	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Gatifloxac	31038-3	31040-9	31036-7	31042-5		41494-6			14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8	14	15-17	18	2	8																																																																							17	18-20	21	1	4	17	18-22	23	1	4																								1	2					
-GEM	GEM		GEM			Gemifloxacin	CLSI	X								393	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Gemifloxac	35816-8	35814-3	35815-0	41697-4					15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1	15	16-19	20	.25	1																																																																																																								1	2					
-GEM	GX1		GEM			Gemifloxacin						X				413	1ug		Quinolones	Fluoroquinolone	FQ	11b	X				Gemifloxac	35816-8	35814-3	35815-0	41697-4								.25	1				.25	1				.25	1				.25	1				.25	1				.25	1				.25	1				.25	1				.25	1				.25	1				.25	1																																																																																																					19	-	20	1	2					
-GEN	GE1	GM	GEN	GM		Gentamicin				X						196	15ug		Aminoglycosides		AG	09	X				Gentamicin	18928-2	268-3	267-5	7016-9			269-1	266-7				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																							15	16-17	18	2	8				1	8				1	8				2	8									2	4				1	2					
-JOS	JOS	JM	JOS	JM		Josamycin										115	100ug		Macrolides		MACRO	17					Josamycine	25597-6	41698-2	25702-2	41699-0																																																																																																																																																																									
-GEN	GEN	GM	GEN	GM		Gentamicin	CLSI,EUCAST	X	X	X		X	X			35	10ug		Aminoglycosides		AG	09	X				Gentamicin	18928-2	268-3	267-5	7016-9			269-1	266-7	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16																																														13	14-16	17	2	8																								4	16	14	15-20	21	1	8				1	8				2	8									2	4	19	-	20	1	2					
-GEN	GE4	GM	GEN	GM		Gentamicin	NEO							X		358	40ug		Aminoglycosides		AG	09	X				Gentamicin	18928-2	268-3	267-5	7016-9			269-1	266-7				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																													14	15-25	26											4	16				1	8				1	8				2	8									2	4				1	2					
-GEN	GE3	GM	GEN	GM		Gentamicin	AFA,SRGA,EUCAST(Enterococcus)				X				X	197	30ug		Aminoglycosides		AG	09	X				Gentamicin	18928-2	268-3	267-5	7016-9			269-1	266-7				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	16				1	8				1	8	18	19-21	22	2	8						17	18-20	21	2	4				1	2					
-GEH	GH2					Gentamicin-High	NEO							X		359	250ug		Aminoglycosides		AG	09	X				Gentamicin	18929-0	7017-7	7018-5	35817-6								500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501																																																																										250	501														500	1000																				
-GEH	GE5					Gentamicin-High				X						198	500ug		Aminoglycosides		AG	09	X				Gentamicin	18929-0	7017-7	7018-5	35817-6								500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501				500	501																																																																							10	11-16	17	250	501														500	1000																				
-HET	HET	H				Hetacillin										259		X	Penicillins	Aminopenicillin	PEN	01b					Hetacillin	18931-6	276-6	275-8				277-4	274-1																																																																																																																																																																					
-HYG	HYG					Hygromycin										414			Aminoglycosides		AG	09																																																																																																																																																																																		
-ICL	ICL					Iclaprim	CLSI	X								476	5ug		Folate pathway inhibitors		FOLATE	12a	X					73597-7	73642-1	73619-9																																																																																																																																																																										
-IPM	IMP	IPM	IMP			Imipenem	CLSI,EUCAST	X	X	X	X	X	X		X	36	10ug	X	Penems	Carbapenems	CARB	07a	X				Imipenem	18932-4	280-8	279-0	7019-3		23613-3	281-6	278-2	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	13	14-15	16	4	16																																														14	15-20	21	2	16																					16	17-21	22	4	16	19	20-22	23	2	8				2	16	22	23-25	26	4	16						16	17-22	23	1	16	22	-	23	4	8					
-IPM	IM1	IPM	IMP	IPM/CS		Imipenem	NEO							X		360	15ug	X	Penems	Carbapenems	CARB	07a	X				Imipenem	18932-4	280-8	279-0	7019-3		23613-3	281-6	278-2				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																													12	13-25	26											4	16														4	16														4	8					
-IPE	IPE					Imipenem/EDTA										433		X	Penems	Carbapenems	CARB	07a									35819-2																																																																																																																																																																									
-ISE	ISE	ISP	ISE	ISP		Isepamicin				X						75	30ug		Aminoglycosides		AG	09					Isepamicin	32381-6	35820-0	35821-8																																																																																																																																			14	15-16	17	8	32																																			
-ISO	ISO		ISL			Isoconazole	NEO							X		165	10ug		Antifungals		FUNG	29																																																																																																																																																																																		
-INH	INH		INH	INH		Isoniazid										132			Antimycobacterials		MYCO	28					Isoniazid	18934-0	288-1	287-3	7020-1	20383-6	23947-5	289-9	286-5																																																																																																																																																																					
-ENR	EN1		ENR			Enrofloxacin	NEO							X		352	10ug		Quinolones	Fluoroquinolone	FQ	11b					Enrofloxac	23712-3	35797-0	35798-8	35796-2								.25	2				.25	2				.25	2				.25	2				.25	2				.25	2				.25	2				.25	2				.25	2				.25	2				.25	2																																																																																																														
-ENR	ENR		ENR			Enrofloxacin	CLSI	X								161	5ug		Quinolones	Fluoroquinolone	FQ	11b		X			Enrofloxac	23712-3	35797-0	35798-8	35796-2					16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2	16	17-22	23	.25	2																																																																																																														
-ENV	ENV			EVM		Enviomycin (Tuberactinomycin)										452			Antimycobacterials		MYCO	28																																																																																																																																																																																		
-EPE	EPE					Eperozolid										250			Oxazolidinones		OXAZOLID	20																																																																																																																																																																																		
-EPP	EPP	EPP				Epiroprim										251			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-ETP	ETP		ERT			Ertapenem	CLSI,EUCAST	X	X	X						401	10ug	X	Penems	Carbapenems	CARB	07a	X				Ertapenem	35802-8	35799-6	35801-0	35800-2					18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	18	19-21	22	.5	2	19	20-22	23	.25	1	15	16-18	19	2	8																																														21	22-24	25	0.5	2																					19	20-22	23	2	8																																			
-ERY	ER5	E	ERY	EM		Erythromycin	BSAC					X				316	5ug		Macrolides		MACRO	17	X				Erythromyc	18919-1	234-5	233-7	7009-4	20380-2	23633-1	235-2	232-9				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8																																																																										1	8				1	8				1	4				1	4									.5	1	19	-	20	.5	1					
-ERY	ERY	E	ERY	EM		Erythromycin	CLSI,EUCAST	X	X	X	X		X		X	32	15ug		Macrolides	14-Membered ring	MACRO	17a	X				Erythromyc	18919-1	234-5	233-7	7009-4	20380-2	23633-1	235-2	232-9	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8	13	14-22	23	.5	8																																																																							16	17-21	22	1	8	16	17-20	21	1	8				1	4	19	20-23	24	1	4						19	20-24	25	.5	1				.5	1					
-ERY	ER7	E	ERY	EM		Erythromycin	NEO							X		353	78ug		Macrolides	14-Membered ring	MACRO	17	X				Erythromyc	18919-1	234-5	233-7	7009-4	20380-2	23633-1	235-2	232-9				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8				.5	8																																																													14	15-27	28											1	8				1	8				1	4				1	4									.5	1				.5	1					
-ETH	ETH	EB	EMB	EB		Ethambutol										130			Antimycobacterials		MYCO	28					Ethambutol	18921-7	242-8	241-0	7010-2	20381-0	23625-7	243-6	240-2																																																																																																																																																																					
-ETI	ETI	EA	ETH	ETH		Ethionamide										131			Antimycobacterials		MYCO	28					Ethionamid	18922-5	41693-3	16099-4	7011-0	20382-8	23617-4																																																																																																																																																																							
-ETO	ETO					Ethopabate										411			Coccidiostats		COCC	27																																																																																																																																																																																		
-FAR	FAR		FAR	FRPM		Faropenem	CLSI	X								428	5ug	X	Penems	Penem	PENEM	07b	X					73600-9	73645-4	73622-3																																																																																																																																																																										
-FDX	FDX					Fidaxomicin	CLSI	X								487						17	X					73599-3	73644-7	73621-5																																																																																																																																																																										
-FIN	FIN					Finafloxacin	CLSI	X								500			Quinolones	Fluoroquinolone	FQ	11b	X					73598-5	73643-9	73620-7																																																																																																																																																																										
-FLA	FLA					Flavomycin										252			Flavophospholipols		FLAVO	27																																																																																																																																																																																		
-FLE	FL1	FLE	FLO	FLRX		Fleroxacin	NEO							X		354	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Fleroxacin	32372-5	35806-9	25411-0	7012-8								2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																															1	8																														
-FLE	FLE	FLE	FLO	FLRX		Fleroxacin	CLSI,DIN	X					X			105	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Fleroxacin	32372-5	35806-9	25411-0	7012-8					15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8	15	16-18	19	2	8																																																													12	13-23	24													14	15-21	22	1	8																														
-FLO	FLO	FLO	FLX	FMOX		Flomoxef										162		X	Cephems	Oxacephem	OXACEPH	04f																																																																																																																																																																																		
-FLR	FLR		FLF			Florfenicol	CLSI	X								253	30ug		Phenicols		PHEN	22	X				Florfenico	23740-4	35807-7	35808-5						14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8	14	15-18	19	2	8																																																																																																														
-FLC	FLC	FU	FLU			Flucloxacillin	DIN						X			163		X	Penicillins	Penicillin (Stable)	PEN-S	01e																																																																																																																																																			1	2				4	8																									
-FLU	FL2		FCA	FLCZ		Fluconazole	CLSI,NEO	X						X		443	25ug		Antifungals		FUNG	29	X				Fluconazol	18924-1	250-1	249-3	7013-6			251-9	248-5											14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64	14	15-18	19	8	64																																																																																																														
-FLM	FLM	UB	FLM			Flumequine				X						88	30ug		Quinolones	Quinolone	QUIN	11a																																																																																																																																											20	21-24	25	4	16																																			
-FFL	FFL			F-FLCZ		Fosfluconazole										453			Antifungals		FUNG	29																																																																																																																																																																																		
-FOS	FO7	FOS	FOS	FOM		Fosfomycin	NEO							X		355	70ug		Fosfomycins	Fosfomycin	FOSFO	13	X				Fosfomycin	25596-8	35810-1	25653-7	35809-3																		64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256																																																													12	13-17	18											32	64																													128	256					
-FOS	FO2	FOS	FOS	FOM		Fosfomycin	BSAC									317	20ug		Fosfomycins	Fosfomycin	FOSFO	13	X				Fosfomycin	25596-8	35810-1	25653-7	35809-3																		64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256																																																																										32	64																													128	256					
-FOS	FOS	FOS	FOS	FOM		Fosfomycin	CLSI,EUCAST	X	X	X		X				254	200ug		Fosfomycins	Fosfomycin	FOSFO	13	X				Fosfomycin	25596-8	35810-1	25653-7	35809-3															12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256	12	13-15	16	64	256																																																	32	64																								32	64																										19	-	20	128	256					
-FOS	FO5	FOS	FOS	FOM		Fosfomycin				X						33	50ug		Fosfomycins	Fosfomycin	FOSFO	13	X				Fosfomycin	25596-8	35810-1	25653-7	35809-3																		64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256				64	256																																																																							13	-	14	32	64																													128	256					
-FMD	FMD	FMD				Fosmidomycin										255			Fosfomycins	Fosfomycin	FOSFO	13																																																																																																																																																																																		
-FRM	FRM	FY	FRA			Framycetin										164	30ug		Aminoglycosides		AG	09					Framycetin	18926-6	259-2	258-4				260-0	257-6																																																																																																																																																																					
-FRZ	FRZ		FUR			Furazolidone										434	100ug		Nitrofurans		FURAN	18																																																																																																																																																																																		
-FRZ	FRZ		FUR			Furazolidone	NEO							X		356	50ug		Nitrofurans		FURAN	18																																																																																																																																																																																		
-FUS	FU5	FA	FUS	FA		Fusidic acid	AFA,SRGA				X				X	195	50ug		Steroidals	Fusidane	FUSID	26	X				Fusidate	18927-4	263-4	262-6	7015-1			264-2	261-8																																																																																																																																	2	32									1	2	32	-	33	.5	1						26	27-29	30	.5	1				1	2					
-FUS	FUS	FA	FUS	FA		Fusidic acid	EUCAST	X	X	X		X				34	10ug		Steroidals	Fusidane	FUSID	26	X				Fusidate	18927-4	263-4	262-6	7015-1			264-2	261-8																																																																																																																														14	15-21	22	2	32									1	2				.5	1									.5	1	29	-	30	1	2					
-FUS	F00	FA	FUS	FA		Fusidic acid	NEO							X		357	100ug		Steroidals	Fusidane	FUSID	26	X				Fusidate	18927-4	263-4	262-6	7015-1			264-2	261-8																																																																																																																				14	15-27	28											2	32									1	2				.5	1									.5	1				1	2					
-KAN	KAN	K	KAN	KM		Kanamycin	CLSI	X		X						37	30ug		Aminoglycosides		AG	09	X				Kanamycin	18935-7	292-3	291-5	7022-7		23609-1	293-1	290-7	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64	13	14-17	18	16	64																																																																							14	15-16	17	8	32									4	32																									
-KAN	KA1	K		KM		Kanamycin	NEO							X		361	100ug		Aminoglycosides		AG	09	X				Kanamycin	18935-7	292-3	291-5	7022-7		23609-1	293-1	290-7				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64				16	64																																																													14	15-27	28											8	32									4	32																									
-KAH	KAH					Kanamycin-High	CLSI	X		X						138	1000ug		Aminoglycosides		AG	09	X				Kanamycin.	18936-5	7023-5	7024-3																																																																																																																																			9	10-13	14	250	501																																			
-KAH	KH5					Kanamycin-High	NEO							X		362	500ug		Aminoglycosides		AG	09	X				Kanamycin.	18936-5	7023-5	7024-3																																																																																																																																						250	501																																			
-KET	KET		KET	KCZ		Ketoconazole	NEO							X		134	15ug		Antifungals		FUNG	29					Ketoconazo	18937-3	296-4	295-6	7025-0			297-2	294-9																																																																																																																																																																					
-KIT	KIT	LU		LM		Kitasamycin (Leucomycin)										116			Macrolides		MACRO	17																																																																																																																																																																																		
-LAS	LAS					Lasalocid										415			Combinations	Coccidiostat/Ionophore	OTHER	28																																																																																																																																																																																		
-LEN	LEN		LEN	LAPC		Lenampicillin										454		X	Penicillins	Aminopenicillin	PEN	01b																																																																																																																																																																																		
-LVX	LEV		LEV	LVFX		Levofloxacin	CLSI,EUCAST	X	X	X	X	X				142	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Levofloxac	20629-2	21367-8	20396-8	7026-8					16	17-20	21	0.5	2	16	17-20	21	0.5	2	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8	13	14-16	17	2	8																																														18	19-21	22	1	4																					16	17-19	20	1	4				2	4																								2	4					
-LVX	LE1		LEV	LVFX		Levofloxacin	BSAC					X				319	1ug		Quinolones	Fluoroquinolone	FQ	11b	X				Levofloxac	20629-2	21367-8	20396-8	7026-8								0.5	2				0.5	2				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	8				2	4																					19	-	20	2	4					
-LIN	LIN	L	LIN	LCM		Lincomycin	AFA			X					X	38	15ug		Lincosamides		LINCO	15					Lincomycin	18938-1	300-4	299-8	41700-6			301-2	298-0																																																																																																																														16	17-20	21	2	16											17	18-23	24	1	4																				
-LIN	LI1	L	LIN	LCM		Lincomycin	NEO							X		363	19ug		Lincosamides		LINCO	15					Lincomycin	18938-1	300-4	299-8	41700-6			301-2	298-0																																																																																																																				14	15-27	28											2	16														1	4																				
-LSP	LSP					Linco-spectin (lincomycin/spectinomycin)	NEO							X		364	15/200ug		Combinations	Lincosamide/Aminocyclitol	OTHER	28																																																																																																																																																																																		
-LNZ	LNZ		LIZ	LZD		Linezolid	CLSI	X		X						260	30ug		Oxazolidinones		OXAZOLID	20	X				Linezolid	29258-1	29255-7	29254-0	33332-8		41500-0			20	-	21	4	8	20	-	21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8	20		21	4	8																																																																							23	24-27	28	2	8																													2	4					
-LNZ	LN1		LIZ	LZD		Linezolid	EUCAST		X	X		X				416	10ug		Oxazolidinones		OXAZOLID	20	X				Linezolid	29258-1	29255-7	29254-0	33332-8		41500-0						4	8				4	8				4	8				4	8				4	8				4	8				4	8				4	8				4	8				4	8				4	8																																																																										2	8																										22	-	23	2	4					
-LFE	LFE					Linoprist-flopristin	CLSI	X								483	10ug		Streptogramins		STREPTOG	23		X				55292-7	55294-3	55293-5																																																																																																																																																																										
-LOM	LOM	LOM	LOM	LFLX		Lomefloxacin	CLSI	X								107	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Lomefloxac	18939-9	304-6	303-8	41701-4			305-3	302-0	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8	18	19-21	22	2	8																																																																										1	4																																			
-LOM	LO5	LOM	LOM	LFLX		Lomefloxacin				X						261	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Lomefloxac	18939-9	304-6	303-8	41701-4			305-3	302-0				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																							18	19-21	22	1	4																																			
-LOR	LOR		LOR	LCBF		Loracarbef	CLSI,DIN	X					X			108	30ug	X	Cephems-Oral	Carbacephem	CEPH-ORAL	05b	X				Loracarbef	18940-7	308-7	307-9	7027-6					14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32	14	15-17	18	8	32																																																																										2	16	20	21-25	26	2	16																19	20-22	23	2	8										
-LOR	LO1		LOR	LCBF		Loracarbef				X						262	10ug	X	Cephems-Oral	Cephalosporin	CEPH-ORAL	05a					Loracarbef	18940-7	308-7	307-9	7027-6			309-5	306-1				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																																							14	15-22	23	2	16				2	16																			2	8										
-MAR	MAR		MAR			Marbofloxacin	CLSI	X								468	5ug		Quinolones	Fluoroquinolone	FQ	11b		X				73596-9	73641-3	73618-1						14	15-19	20	1	4	14	15-19	20	1	4	14	15-19	20	1	4	14	15-19	20	1	4	14	15-19	20	1	4	14	15-19	20	1	4																																																																																																																																							
-MEC	ME4	MEC	MCL			Mecillinam (Amdinocillin)	NEO							X		365	33ug	X	Penicillins	Amidinopenicillin	PEN	01f	X				Amdinocill	18859-9	9-1	8-3	7028-4			10-9	7-5				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-27	28											2	16														1	16									1	16				1	16					
-MEC	MEC	MEC	MCL			Mecillinam (Amdinocillin)	CLSI,EUCAST	X	X	X	X	X			X	80	10ug	X	Penicillins	Amidinopenicillin	PEN	01f	X				Amdinocill	18859-9	9-1	8-3	7028-4			10-9	7-5	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32	11	12-14	15	8	32																																														14		15	8	16																					17	18-21	22	2	16											14	15-23	24	1	16						13	14-23	24	1	16	13	14-23	24	1	16					
-MEL	MEL					Meleumycin										117			Macrolides		MACRO	17																																																																																																																																																																																		
-MEM	MER	MEM	MER	MEPM		Meropenem	CLSI,EUCAST	X	X	X	X	X	X		X	109	10ug	X	Penems	Carbapenems	CARB	07a	X				Meropenem	18943-1	6653-0	6652-2	7029-2			6654-8	6651-4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	19	20-22	23	1	4	13	14-15	16	4	16																																														15	16-21	22	2	16											16	17-19	20								14	15-19	20	4	16	13	14-21	22	2	16						16	17-22	23	4	16						19	20-28	29	.125	16	22	-	23	4	8					
-MES	MES	MES				Mesulfamide										263			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																								4	8																									
-MET	MET	ME	MET			Methicillin	CLSI,BSAC	X				X				39	5ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Methicilli	18945-6	324-4	323-6	7030-0			325-1	322-8	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16	9	10-13	14	8	16																																																																																																					13	-	14	4	8					
-MET	ME2	ME	MET			Methicillin	NEO							X		366	29ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Methicilli	18945-6	324-4	323-6	7030-0			325-1	322-8				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16																																																													14	15-27	28																																									4	8					
-MTP	MTP	MTP				Metioprim										264			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-MXT	MXT	MXT				Metioxate										265			Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-MTR	MTR	MTR	MTR			Metronidazole	SRGA				X					76	4ug		Nitroimidazoles		IMIDAZ	19					Metronidaz	18946-4	328-5	327-7	7031-8			329-3	326-9																																																																																																																																	4	32				4	8									4	16																				
-MTR	MT1	MTR	MTR			Metronidazole	NEO			X				X		367	16ug		Nitroimidazoles		IMIDAZ	19	X				Metronidaz	18946-4	328-5	327-7	7031-8			329-3	326-9																																																																																																																														20	-	21	4	32				4	8									4	16																				
-MTR	MTR	MTR	MTR			Metronidazole										430	5ug		Nitroimidazoles		IMIDAZ	19	X				Metronidaz	18946-4	328-5	327-7	7031-8			329-3	326-9																																																																																																																																	4	32				4	8									4	16																				
-MTR	ME1	MTR	MTR			Metronidazole	EUCAST		X	X						199	10ug		Nitroimidazoles		IMIDAZ	19	X				Metronidaz	18946-4	328-5	327-7	7031-8			329-3	326-9																																																																																																																																	4	32				4	8									4	16																				
-MEZ	MEZ	MZ	MZL			Mezlocillin	CLSI,BSAC	X		X		X				40	75ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Mezlocilli	18947-2	332-7	331-9	41702-2			333-5	330-1																																														17	18-20	21	16	128	17	18-20	21	16	128																																																																							15	16-20	21	8	64				4	32																			4	8	21	-	22	16	32					
-MEZ	ME3	MZ	MZL			Mezlocillin	DIN						X			266	30ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Mezlocilli	18947-2	332-7	331-9	41702-2			333-5	330-1				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																																																										8	64	16	17-22	23	4	32																			4	8				16	32					
-MSU	MSU		MZS			Mezlocillin/Sulbactam	DIN						X			267	30/15ug	X	Beta-lactam+Inhibitors		BL+INH	03																																																																																																																																																16	17-21	22	4	32																														
-MIF	MIF					Micafungin	CLSI	X								455	10ug		Antifungals		FUNG	29																																																																																																																																																																																		
-MCZ	MCZ	MCZ	MCZ	MCZ		Miconazole	NEO							X		268	10ug		Antifungals		FUNG	29					Miconazole	25607-3		25722-0																																																																																																																																																																										
-MCR	MCR	MCR	MCR	MCR		Micronomicin										269			Aminoglycosides		AG	09																																																																																																																																																																																		
-MID	MID		MID	MDM		Midecamycin										118	100ug		Macrolides		MACRO	17																																																																																																																																																																																		
-MIL	MIL	MIL				Miloxacin										270			Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-MNO	MIN	MNO	MNO	MINO		Minocycline	CLSI,EUCAST	X	X	X						41	30ug		Tetracyclines		TETRA	24a	X				Minocyclin	18948-0	336-8	335-0	7032-6			337-6	334-3	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16	12	13-15	16	4	16																																																																							16	17-18	19	4	16				1	8																														
-MNO	MI8	MNO	MNO	MINO		Minocycline	NEO							X		368	80ug		Tetracyclines		TETRA	24	X				Minocyclin	18948-0	336-8	335-0	7032-6			337-6	334-3				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	16				1	8																														
-MON	MON					Monensin sodium										417			Combinations	Coccidiostat/Ionophore	OTHER	28																																																																																																																																																																																		
-MOX	MOX	MOX	LMO	LMOX		Moxalactam (Latamoxef)	CLSI	X		X						42	30ug	X	Cephems	Oxacephem	OXACEPH	04f	X				Moxalactam	18950-6	344-2	343-4	41703-0			345-9	342-6	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64	14	15-22	23	8	64																																																																							16	17-22	23	4	64																																			
-MFX	MF1		MOX	MFLX		Moxifloxacin						X				418	1ug		Quinolones	Fluoroquinolone	FQ	11b	X				Moxifloxac	31039-1	31041-7	31037-5	31043-3		41502-6						.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2																																																																										1	4				1	4																					19	-	20	1	2					
-MFX	MFX		MOX	MFLX		Moxifloxacin	CLSI,EUCAST	X	X	X	X		X			392	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Moxifloxac	31039-1	31041-7	31037-5	31043-3		41502-6			20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2	20	21-23	24	.5	2																																														16	17-19	20	0.5	2																					20	21-23	24	.5	2	18	19-21	22	1	4																								1	2					
-MUP	MUP		MUP	MUP		Mupirocin	CLSI,NEO	X						X		124	10ug		Pseudomonic acids		PSEUDOM	27	X				Mupirocin	20389-3	35822-6	35823-4	7033-4																																																																																																																								19	-	20											2																														4	8					
-MUP	MU5		MUP	MUP		Mupirocin	BSAC			X		X				419	5ug		Pseudomonic acids		PSEUDOM	27	X				Mupirocin	20389-3	35822-6	35823-4	7033-4																																																																																																																																				19	2																											21	-	22	4	8					
-NAD	NAD			NDFX		Nadifloxacin										456			Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-NAF	NAF	NF	NCL			Nafcillin	CLSI	X								43	1ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Nafcillin	18951-4	348-3	347-5	41704-8			349-1	346-7	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4	10	11-12	13	2	4																																																																																																														
-NAL	NAL	NA	NAL	NA		Nalidixic acid	CLSI,EUCAST	X	X	X					X	44	30ug		Quinolones	Quinolone	QUIN	11a	X				Nalidixate	18952-2	352-5	351-7	7034-2			353-3	350-9	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32	13	14-18	19	16	32																																														15		16	16	32																					14	15-19	20	8	32											14	-	15	16	32						15	16-19	20	8	32										
-NAL	NA1	NA	NAL	NA		Nalidixic acid	NEO							X		369	130ug		Quinolones	Quinolone	QUIN	11a	X				Nalidixate	18952-2	352-5	351-7	7034-2			353-3	350-9				16	32				16	32				16	32				16	32				16	32				16	32				16	32				16	32				16	32				16	32				16	32																																																													14	15-27	28											8	32														16	32																				
-NAR	NAR					Narasin										402			Combinations	Coccidiostat/Ionophore	OTHER	28																																																																																																																																																																																		
-NEO	NEO	N	NEO	FRM		Neomycin	CLSI	X								45	30ug		Aminoglycosides		AG	09	X				Neomycin	18953-0	356-6	355-8	41705-5			357-4	354-1																																																																																																																																																																					
-NEO	NE0		NEO	FRM		Neomycin						X				420	10ug		Aminoglycosides		AG	09	X				Neomycin	18953-0	356-6	355-8	41705-5			357-4	354-1																																																																																																																																																												16	-	17							
-NEO	NE2	N	NEO	FRM		Neomycin	NEO							X		370	120ug		Aminoglycosides		AG	09	X				Neomycin	18953-0	356-6	355-8	41705-5			357-4	354-1																																																																																																																				14	15-27	28																																															
-NET	NET	NET	NET	NTL		Netilmicin	CLSI,SRGA	X		X	X				X	46	30ug		Aminoglycosides		AG	09	X				Netilmicin	18954-8	360-8	359-0	7035-9			361-6	358-2	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32	12	13-14	15	8	32																																																																							18	19-20	21	2	8				1	8				2	16	18	19-21	22	2	8						17	18-20	21	2	4				1	2					
-NET	NE1	NET	NET	NTL		Netilmicin	EUCAST		X	X		X	X			271	10ug		Aminoglycosides		AG	09	X				Netilmicin	18954-8	360-8	359-0	7035-9			361-6	358-2				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																														11	12-14	15	2	8																								4	16	16	17-21	22	1	8				2	16				2	8									2	4	24	-	25	1	2					
-NET	NE4	NET	NET	NTL		Netilmicin	NEO							X		371	40ug		Aminoglycosides		AG	09	X				Netilmicin	18954-8	360-8	359-0	7035-9			361-6	358-2				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													14	15-25	26											4	16				1	8				2	16				2	8						17	18-20	21	2	4				1	2					
-NIC	NIC					Nicarbazin										421			Coccidiostats		COCC	27																																																																																																																																																																																		
-NIF	NIF	NIF				Nifuroquine										272			Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-NTZ	NTZ					Nitazoxanide	CLSI	X								492			Thiazolides		THIAZ	30						73595-1	73640-5	73617-3																																																																																																																																																																										
-NIT	FU0	FT	NFT			Nitrofurantoin	BSAC									327	50ug		Nitrofurans		FURAN	18	X				Nitrofuran	18955-5	364-0	363-2	7036-7			365-7	362-4				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																																																										32	256				64	512				32	64				16	32									32	64				32	64					
-NIT	FU6	FT	NFT			Nitrofurantoin	NEO							X		372	260ug		Nitrofurans		FURAN	18	X				Nitrofuran	18955-5	364-0	363-2	7036-7			365-7	362-4				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																																													14	15-27	28											32	256				64	512				32	64				16	32									32	64				32	64					
-NIT	FU1	FT	NFT			Nitrofurantoin	EUCAST		X	X	X		X		X	200	100ug		Nitrofurans		FURAN	18	X				Nitrofuran	18955-5	364-0	363-2	7036-7			365-7	362-4				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																														10		11	64	128																								32	256	10	11-15	16	64	512				32	64	18	-	19	16	32						13	14-16	17	32	64				32	64					
-NIT	FUR	FT	NFT			Nitrofurantoin	CLSI	X		X						47	300ug		Nitrofurans		FURAN	18	X				Nitrofuran	18955-5	364-0	363-2	7036-7			365-7	362-4	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128	14	15-16	17	32	128																																																																							13	14-16	17	32	256				64	512				32	64				16	32									32	64				32	64					
-NIT	FU2	FT	NFT			Nitrofurantoin	BSAC					X				320	200ug		Nitrofurans		FURAN	18	X				Nitrofuran	18955-5	364-0	363-2	7036-7			365-7	362-4				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																																																										32	256				64	512				32	64				16	32									32	64	19	-	20	32	64					
-NIZ	NIZ	FC				Nitrofurazone										166			Nitrofurans		FURAN	18																																																																																																																																																																																		
-NTR	NIT	NI	NIT			Nitroxoline				X						89	20ug		Quinolones	Quinolone	QUIN	11a					Nitroxolin	25608-1		25723-8																																																																																																																																			11	12-29	30	1	64																																			
-NOR	NOR	NOR	NOR	NFLX		Norfloxacin	CLSI,EUCAST	X	X	X	X		X			48	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Norfloxaci	18956-3	368-1	367-3	7037-5		41504-2	369-9	366-5											12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16	12	13-16	17	4	16																																														18	19-21	22	0.5	2											12	13-25	26											1	4	23	24-26	27	1	4				1	4											17	18-23	24	.5	2				4	8					
-NOR	NO5	NOR	NOR	NFLX		Norfloxacin				X						201	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Norfloxaci	18956-3	368-1	367-3	7037-5		41504-2	369-9	366-5														4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																							21	22-24	25	.5	2				1	4				1	4														.5	2				4	8					
-NOR	NO2	NOR	NOR	NFLX		Norfloxacin	BSAC					X				321	2ug		Quinolones	Fluoroquinolone	FQ	11b	X				Norfloxaci	18956-3	368-1	367-3	7037-5		41504-2	369-9	366-5														4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										1	4				1	4				1	4														.5	2	16	-	17	4	8					
-NVA	NVA					Norvancomycin										119			Glycopeptides	Glycopeptide	GLYCO	21a																																																																																																																																																																																		
-NOV	NOV	NB				Novobiocin	CLSI,NEO	X						X		49	5ug		Polypeptides	Coumarin	POLYPEP	26	X				Novobiocin	18957-1	372-3	371-5	41706-3			373-1	370-7																																																																																																																				15	-	16																																															
-NOV	NO1	NB				Novobiocin	NEO							X		373	100ug		Polypeptides	Coumarin	POLYPEP	26	X				Novobiocin	18957-1	372-3	371-5	41706-3			373-1	370-7																																																																																																																				12	13-21	22																																															
-NYS	NYS	NY	NYS	NYS		Nystatin	NEO							X		273	50ug		Antifungals		FUNG	29					Nystatin	18958-9	35824-2	10697-1					10698-9																																																																																																																																																																					
-OFX	OFL		OFX	OFLX		Ofloxacin	CLSI,EUCAST	X	X	X			X			50	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ofloxacin	18959-7	376-4	375-6	7038-3	20384-4	23948-3	377-2	374-9	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8	12	13-15	16	2	8																																														18	19-21	22	0.5	2																					21	22-24	25	.5	1	17	18-21	22	1	4				1	8				.5	8									.5	2				2	4					
-OFX	OF1		OFX	OFLX		Ofloxacin	BSAC					X				322	1ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ofloxacin	18959-7	376-4	375-6	7038-3	20384-4	23948-3	377-2	374-9				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																										1	8				1	4				1	8				.5	8									.5	2	23	-	24	2	4					
-OFX	OF0		OFX	OFLX		Ofloxacin	AFA,SRGA,NEO				X			X	X	202	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Ofloxacin	18959-7	376-4	375-6	7038-3	20384-4	23948-3	377-2	374-9				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																													12	13-23	24											1	8				1	4				1	8	17	18-27	28	.5	8						17	18-23	24	.5	2				2	4					
-OLE	OLE	OL	OLE			Oleandomycin										167	15ug		Macrolides		MACRO	17					Oleandomyc	18960-5	380-6	379-8				381-4	378-0																																																																																																																																																																					
-OMC	OMC					Omadacycline	CLSI	X								502			Tetracyclines	Aminomethylcycline	TETRA	24c	X					73594-4	73639-7	73616-5																																																																																																																																																																										
-OPT	OPT					Optochin										168	5ug		Optochins		OPT	27																																																																																																																																																																																		
-ORB	ORB		ORB			Orbifloxacin	CLSI	X								469	10ug		Quinolones	Fluoroquinolone	FQ	11b		X			Orbifloxac	35827-5	35825-9	35826-7						17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8	17	18-22	23	1	8																																																																																																														
-ORI	ORI					Oritavancin	CLSI,EUCAST	X	X	X						442			Glycopeptides	Glycopeptide	LIPOGLYC	21a	X				Oritavanci	41736-0	41707-1	41708-9	41709-7																																																																																																																																																																									
-ORS	ORS					Ormetroprim/Sulfamethoxazole	CLSI	X								274	1.25/23.75ug		Folate pathway inhibitors		FOLATE	12a		X				73593-6	73638-9	73615-7																																																																																																																																																																										
-ORN	ORN	ORN	ORN			Ornidazole										169	4ug		Nitroimidazoles		IMIDAZ	19																																																																																																																																																																																		
-OXA	OXA	OX	OXA			Oxacillin	CLSI,EUCAST	X	X	X	X	X			X	51	1ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Oxacillin	18961-3	384-8	383-0	7039-1			385-5	382-2				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5																																																																										2	4				1	2									1	4						9	10-11	12			14	-	15	2	4					
-OXA	OX5	OX	OXA			Oxacillin	DIN,NEO			X			X	X		203	5ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Oxacillin	18961-3	384-8	383-0	7039-1			385-5	382-2				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5																																																													15	-	16								19	-	20	2	4	15	-	16	1	2									1	4														2	4					
-OXA	OX1	OX	OXA			Oxacillin	AFA								X	398	10ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e	X				Oxacillin	18961-3	384-8	383-0	7039-1			385-5	382-2				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5				.25	.5																																																																										2	4				1	2						19	-	20	1	4														2	4					
-OXO	OXO	OA	OXL			Oxolinic acid	CLSI	X								470	2ug		Quinolones	Quinolone	QUIN	11a		X			Oxolinate	55696-9	55697-7	55695-1	55698-5																																																																																																																																																																									
-OXO	OXO	OA	OXL			Oxolinic acid				X						90	10ug		Quinolones	Quinolone	QUIN	11a					Oxolinate	55696-9	55697-7	55695-1	55698-5																																																																																																																																		16	17-19	20	2	8																																			
-OXY	OXY	OT	OTE	OTC		Oxytetracycline	CLSI	X		X						170	30ug		Tetracyclines		TETRA	24					Oxytetracy	18962-1	388-9	387-1				389-7	386-3																																																																																																																														16	17-18	19	4	16																																			
-OXY	OX8	OT	OTE	OTC		Oxytetracycline	NEO							X		374	80ug		Tetracyclines		TETRA	24					Oxytetracy	18962-1	388-9	387-1				389-7	386-3																																																																																																																				14	15-27	28											4	16																																			
-PAS	PAS		PAS			P-Aminosalicylic acid										171			Antimycobacterials		MYCO	28					Para amino	23629-9		14332-1			23611-7																																																																																																																																																																							
-PAN	PAN		PAN	PAPM-BP		Panipenem										172		X	Penems	Carbapenems	CARB	07a																																																																																																																																																																																		
-PAR	PAR	PM	PAR			Paromomycin										275			Oligosaccharides		OLIGO	27																																																																																																																																																																																		
-PAZ	PAZ		PZF	PZFX		Pazufloxacin										457			Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-PEF	PEF		PEF			Pefloxacin				X						52	5ug		Quinolones	Fluoroquinolone	FQ	11b					Pefloxacin	18963-9	35828-3	390-5	7040-9																																																																																																																																		15	16-21	22	1	8									1	8																									
-PEF	PE0		PEF			Pefloxacin	NEO							X		375	10ug		Quinolones	Fluoroquinolone	FQ	11b					Pefloxacin	18963-9	35828-3	390-5	7040-9																																																																																																																																					1	8									1	8																									
-PEN	PEN	P	PEN	PCG		Penicillin G	CLSI,DIN,SRGA	X		X	X		X		X	53	10units	X	Penicillins	Penicillin	PEN	01a	X				Penicillin	18965-4	393-9	392-1	7041-7			394-7	391-3	28	-	29	.125	.25	28	-	29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25	28		29	.125	.25																																																																							7	8-28	29	.25	32	12	13-23	24	0.125	2				.25	8	10	11-22	23	1	32						30	31-33	34						.125	.25					
-PEN	PE1	P	PEN	PCG		Penicillin G	EUCAST		X	X		X				323	1unit	X	Penicillins	Penicillin	PEN	01a	X				Penicillin	18965-4	393-9	392-1	7041-7			394-7	391-3				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25																																																																										.25	32				0.125	2				.25	8				1	32											24	-	25	.125	.25					
-PEN	PE5	P	PEN	PCG		Penicillin G	NEO							X		376	5ug	X	Penicillins	Penicillin	PEN	01a	X				Penicillin	18965-4	393-9	392-1	7041-7			394-7	391-3				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25				.125	.25																																																													14	15-27	28											.25	32				0.125	2				.25	8				1	32														.125	.25					
-PNV	PNV	PV	PEN			Penicillin V	CLSI,EUCAST	X	X	X	X				X	81	10ug	X	Penicillins	Penicillin	PEN	01a	X				Penicillin	18966-2	397-0	396-2	7042-5			398-8	395-4																																																																																																																																						0.125	2						20	21-25	26	1	4						30	31-33	34												
-PNO	PNO					Penicillin/Novobiocin	CLSI	X								84	10units/30ug		Combinations	Penicillin/Polypeptide	OTHER	28		X			Penicillin	35874-7	35872-1	35873-9						14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4	14	15-17	18	1	4																																																																																																														
-PSU	PSU			PCG-SBT		Penicillin/Sulbactam	DIN						X			437	10/10	X	Beta-lactam+Inhibitors		BL+INH	03																																																																																																																																																20	21-25	26	0.125	2																														
-PIM	PIM	PIM				Pentisomicin										276			Aminoglycosides		AG	09																																																																																																																																																																																		
-PTZ	PTZ	PTZ				Pentizidone										277			Oxazolidinones		OXAZOLID	20																																																																																																																																																																																		
-PHE	PHE			PEPC		Phenethicillin										458		X	Penicillins	Penicillin	PEN	01a					Phenethici	18967-0	401-0	400-2				402-8	399-6																																																																																																																																																																					
-PMR	PMR			PMR		Pimaricin (Natamycin)										459			Antifungals		FUNG	29																																																																																																																																																																																		
-PPA	PPA	PI	PIM	PPA		Pipemidic acid	DIN			X			X			54	20ug		Quinolones	Quinolone	QUIN	11a					Pipemidate	18968-8	405-1	404-4				406-9	403-6																																																																																																																														13	14-18	19	8	32	16	-	17	4	8				8	16																									
-PPA	PP3	PI	PIM	PPA		Pipemidic acid	NEO							X		377	30ug		Quinolones	Quinolone	QUIN	11a					Pipemidate	18968-8	405-1	404-4				406-9	403-6																																																																																																																																	8	32				4	8				8	16																									
-PIP	PI7	PIP	PIP	PIPC		Piperacillin	BSAC			X		X				207	75ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Piperacill	18969-6	409-3	408-5	7043-3			410-1	407-7				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																																																							11	12-19	20	8	128				4	64				16	128														16	32	23	-	24	16	32					
-PIP	PIP	PIP	PIP	PIPC		Piperacillin	CLSI	X								55	100ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Piperacill	18969-6	409-3	408-5	7043-3			410-1	407-7	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128																																																													9	10-27	28											8	128				4	64				16	128														16	32				16	32					
-PIP	PI3	PIP	PIP	PIPC		Piperacillin	EUCAST		X	X	X		X			206	30ug	X	Penicillins	Ureidopenicillin	PEN	01c	X				Piperacill	18969-6	409-3	408-5	7043-3			410-1	407-7				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																														14	15-17	18	8	32																								8	128	12	13-21	22	4	64				16	128											17	18-20	21	16	32				16	32					
-PIS	PIS		PIS	PIPC-SBT		Piperacillin/Sulbactam	DIN						X			278	30/15ug	X	Beta-lactam+Inhibitors		BL+INH	03																																																																																																																																																13	14-21	22	4	64																														
-TZP	PTA		PIT	PIPC-TAZ		Piperacillin/Tazobactam	CLSI	X								92	100/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Piperacill	18970-4	413-5	412-7	7044-1			414-3	411-9	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128	17	18-20	21	16	128				16	128	17	18-20	21	16	128	17	18-20	21	16	128																																																													9	10-27	28											8	128				4	64				16	64				8	32									16	32				16	32					
-TZP	PT3		PIT	PIPC-TAZ		Piperacillin/Tazobactam	EUCAST		X	X	X					204	30/6ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Piperacill	18970-4	413-5	412-7	7044-1			414-3	411-9				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																														14	15-17	18	8	32																								8	128				4	64				16	64				8	32						17	18-20	21	16	32				16	32					
-TZP	PT7		PIT	PIPC-TAZ		Piperacillin/Tazobactam	BSAC			X		X				205	75/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Piperacill	18970-4	413-5	412-7	7044-1			414-3	411-9				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																																																							13	14-20	21	8	128				4	64				16	64				8	32									16	32	23	-	24	16	32					
-TZP	PT1		PIT	PIPC-TAZ		Piperacillin/Tazobactam	DIN						X			279	30/10ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Piperacill	18970-4	413-5	412-7	7044-1			414-3	411-9				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128				16	128																																																																										8	128	14	15-21	22	4	64				16	64				8	32									16	32				16	32					
-PRC	PRC	PRC				Piridicillin										280		X	Penicillins	?	PEN	01h																																																																																																																																																																																		
-PRL	PIL					Pirlimycin	CLSI	X								173	2ug		Lincosamides		LINCO	15		X			Pirlimycin	35831-7	35829-1	35830-9						12	-	13	2	4	12	-	13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4	12		13	2	4																																																																																																														
-PIR	PIA	PIR		PA		Piromidic acid				X						281	25ug		Quinolones	Quinolone	QUIN	11a																																																																																																																																											15	16-19	20	16	64																																			
-PME	PME			PMPC		Pivmecillinam (Amdinocillin pivoxil)										460		X	Penicillins	Amidinopenicillin	PEN	01f																																																																																																																																																																																		
-PLZ	PLZ					Plazomicin	CLSI	X								503			Aminoglycosides		AG	09	X					73592-8	73637-1	73614-0																																																																																																																																																																										
-POL	POL	PB	POL	PL-B		Polymixin B	CLSI	X								471	300units		Lipopeptides	Polymyxin	LIPOPEP	16	X				Polymyxin	18972-0	421-8	420-0	35832-5			422-6	419-2	11	-	12	2	8	11	-	12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8	11		12	2	8																																																																																																														
-POL	POL	PB	POL	PL-B		Polymixin B										56	50ug		Lipopeptides	Polymyxin	LIPOPEP	16	X				Polymyxin	18972-0	421-8	420-0	35832-5			422-6	419-2				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8				2	8																																																																																																														
-POS	POS					Posaconazole	CLSI,NEO	X						X		478	5ug		Antifungals		FUNG	29																																																																																																																																																																																		
-PRX	PRX		PRE			Premafloxacin	CLSI	X								403	1ug		Quinolones	Fluoroquinolone	FQ	11b	X					73591-0	73636-3	73613-2																																																																																																																																																																										
-PRM	PRM	PRM				Primycin										282			Macrolides		MACRO	17																																																																																																																																																																																		
-PRI	PR3	PT	PRI			Pristinamycin	NEO							X		378	30ug		Streptogramins		STREPTOG	23					Pristinamy	32383-2	35833-3	35834-1																																																																																																																																						1	4																																			
-PRI	PRI	PT				Pristinamycin				X						93	15ug		Streptogramins		STREPTOG	23					Pristinamy	32383-2	35833-3	35834-1																																																																																																																																			18	19-21	22	1	4																																			
-PRP	PRP	PR	PRO			Propicillin	DIN						X			174		X	Penicillins	Aminopenicillin	PEN	01b																																																																																																																																																			0.125	0.25																														
-PKA	PKA	PKA				Propikacin										283			Aminoglycosides		AG	09																																																																																																																																																																																		
-PTH	PRT		PTH	PTH		Prothionamide										175			Antimycobacterials		MYCO	28																																																																																																																																																																																		
-PRU	PRU			PUFX		Prulifloxacin										461			Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-PZA	PZA		PZA	PZA		Pyrazinamide										135			Antimycobacterials		MYCO	28					Pyrazinami	18973-8	425-9	424-2		20461-0	23632-3	426-7	423-4																																																																																																																																																																					
-QDA	QUI		QPD	QPR/DPR		Quinupristin/Dalfopristin	CLSI,EUCAST	X	X	X		X				176	15ug		Streptogramins		STREPTOG	23	X				Quinuprist	23640-6	35835-8	23641-4	33334-4					15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4	15	16-18	19	1	4																																																																							18	19-24	25	.5	4																										19	-	20	2	4					
-RAC	RAC					Ractopamine										422			Phenethylamines		PHEN	27			X																																																																																																																																																																															
-RAM	RAM					Ramoplanin	CLSI	X								493			Glycopeptides	Lipoglycopeptide	LIPOGLYC	21a	X				Ramoplanin	41737-8	41712-1	41710-5	41711-3																																																																																																																																																																									
-RZM	RZM					Razupenem	CLSI	X								489	10ug	X	Penems	Carbapenems	CARB	07a	X					73590-2	73635-5	73612-4																																																																																																																																																																										
-RST	RST			RSM		Ribostamycin										462			Aminoglycosides		AG	09																																																																																																																																																																																		
-RIB	RIB		RIB			Rifabutin										136			Ansamycins		RIF	10					Rifabutin	19149-4		16100-0		20386-9	23630-7																																																																																																																																																																							
-RIF	RI3	RA	RAM	RFP		Rifampin	NEO			X				X		58	30ug		Ansamycins		RIF	10	X				Rifampin	18974-6	429-1	428-3	7045-8	20385-1	23949-1	430-9	427-5				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																													14	15-27	28								13	14-18	19	4	32									1	2				1	2									1	2				.125	.06					
-RIF	RIF	RA	RAM	RFP		Rifampin	CLSI,EUCAST	X	X	X	X				X	57	5ug		Ansamycins		RIF	10	X				Rifampin	18974-6	429-1	428-3	7045-8	20385-1	23949-1	430-9	427-5	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4	16	17-19	20	1	4																																																																										4	32									1	2	25	26	27	1	2						21	22-24	25	1	2				.125	.06					
-RIF	RI2	RA	RAM	RFP		Rifampin	BSAC					X				324	2ug		Ansamycins		RIF	10	X				Rifampin	18974-6	429-1	428-3	7045-8	20385-1	23949-1	430-9	427-5				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4				1	4																																																																										4	32									1	2				1	2									1	2	29	-	30	.125	.06					
-						Rifaximin	CLSI	X								494			Ansamycins		RIF							73589-4	73634-8	73611-6																																																																																																																																																																										
-RIT	RIT			RIPM		Ritipenem										463		X	Penems	Carbapenems	CARB	07a																																																																																																																																																																																		
-RIA	RIA			RIPM-AC		Ritipenem acoxil										464		X	Penems	Carbapenems	CARB	07a																																																																																																																																																																																		
-ROK	ROK	ROK	ROK	RKM		Rokitamycin										284			Macrolides		MACRO	17																																																																																																																																																																																		
-ROS	ROS	ROS	ROS			Rosoxacin				X						94	5ug		Quinolones	Quinolone	QUIN	11a					Rosoxacin	18977-9	441-6	440-8				442-4	439-0																																																																																																																																	1	2																																			
-RXT	RO3	RXT	ROX	RXM		Roxithromicin	NEO							X		379	30ug		Macrolides		MACRO	17					Roxithromy	18978-7	445-7	444-0	7046-6			446-5	443-2																																																																																																																				12	13-17	18																					1	2														1	2										
-RXT	ROX	RXT	ROX	RXM		Roxithromicin	SRGA				X					77	15ug		Macrolides		MACRO	17					Roxithromy	18978-7	445-7	444-0	7046-6			446-5	443-2																																																																																																																																											1	2											19	20-24	25	1	2										
-SAL	SAL					Salinomycin										423			Combinations	Coccidiostat/Ionophore	OTHER	28					Salinomyci	35838-2	35836-6	35837-4																																																																																																																																																																										
-SAR	SAR		SAR			Sarafloxacin	CLSI	X								285	5ug		Quinolones	Fluoroquinolone	FQ	11b	X					73588-6	73633-0	73610-8																																																																																																																																																																										
-SRX	SRX	SRX				Sarmoxicillin										286		X	Penicillins	Aminopenicillin	PEN	01b																																																																																																																																																																																		
-SIS	SIS	SIS	SIS	SISO		Sisomicin				X						78	10ug		Aminoglycosides		AG	09					Sisomicin	18979-5	449-9	448-1				450-7	447-3																																																																																																																														13	14-15	16	4	16																																			
-SIT	SIT		SIT	STFX		Sitafloxacin										465			Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-SOL	SOL					Solithromycin	CLSI	X								504			Macrolides	Fluoroketolide	MACRO	17c	X					73587-8	73632-2	73609-0																																																																																																																																																																										
-SPX	SP2		SPF	SPFX		Sparfloxacin	BSAC									325	2ug		Quinolones	Fluoroquinolone	FQ	11b	X				Sparfloxac	23628-1	35839-0	20397-6	7047-4		23610-9						.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2																																																																										1	4				1	4																														
-SPX	SPA		SPF	SPFX		Sparfloxacin	CLSI,DIN	X		X			X			110	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Sparfloxac	23628-1	35839-0	20397-6	7047-4		23610-9			15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2	15	16-18	19	.5	2																																																																							15	16-19	20	1	4	18	19-22	23	1	4																														
-SPX	SP1		SPF	SPFX		Sparfloxacin	NEO							X		380	10ug		Quinolones	Fluoroquinolone	FQ	11b					Sparfloxac	23628-1	35839-0	20397-6	7047-4		23610-9						.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2				.5	2																																																																										1	4				1	4																														
-SPT	SP0	SPT	SPT	SPCM		Spectinomycin	NEO							X		381	200ug		Aminocyclitols		AMINOC	08	X				Spectinomy	18980-3	453-1	452-3	35840-8			454-9	451-5				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																																																										64	128														8	16														64	128					
-SPT	SPE	SPT	SPT	SPCM		Spectinomycin	CLSI,EUCAST	X	X	X						59	100ug		Aminocyclitols		AMINOC	08	X				Spectinomy	18980-3	453-1	452-3	35840-8			454-9	451-5																																														14	15-17	18	32	128	14	15-17	18	32	128																																																																							19	-	20	64	128														8	16														64	128					
-SPT	SP5		SPT	SPCM		Spectinomycin						X				424	25ug		Aminocyclitols		AMINOC	08	X				Spectinomy	18980-3	453-1	452-3	35840-8			454-9	451-5				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128				32	128																																																																										64	128														8	16											13	-	14	64	128					
-SPI	SPI	SP	SPM	SPM		Spiramycin				X						95	100ug		Macrolides		MACRO	17					Spiramycin	18981-1	457-2	456-4				458-0	455-6																																																																																																																														18	19-23	24	1	8																																			
-SPI	SM2	SP	SPM	SPM		Spiramycin	NEO							X		382	200ug		Macrolides	16-Membered ring	MACRO	17					Spiramycin	18981-1	457-2	456-4				458-0	455-6																																																																																																																																	1	8																																			
-STR	STR	S	STR	SM		Streptomycin	CLSI,BSAC	X		X		X				60	10ug		Aminoglycosides		AG	09	X				Streptomyc	18982-9	461-4	460-6	7048-2	20462-8	23626-5	462-2	459-8	11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15			11	12-14	15																																																																									12	13-14	15	8	32									4	32																12	-	13	8	16					
-STR	ST1	S	STR	SM		Streptomycin	NEO							X		383	100ug		Aminoglycosides		AG	09	X				Streptomyc	18982-9	461-4	460-6	7048-2	20462-8	23626-5	462-2	459-8				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																													14	15-27	28											8	32									4	32																			8	16					
-STH	STH					Streptomycin-High	CLSI	X								139	300ug		Aminoglycosides		AG	09	X				Streptomyc	18983-7	7049-0	6933-6	35841-6					6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025	6	7-9	10	1024	1025																																																																										250	501														500	1000																				
-STH	ST5					Streptomycin-High	NEO			X				X		208	500ug		Aminoglycosides		AG	09	X				Streptomyc	18983-7	7049-0	6933-6	35841-6								1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001				1000	1001																																																																							11	12-13	14	250	501														500	1000																				
-SUL	SBM		SUL	SBT		Sulbactam	CLSI	X		X						397		X	Beta-lactamase inhibitors		BL-INH	02					Sulbactam	41739-4	41716-2	41718-8	41717-0																																																																																																																																					8																																				
-SBC	SLB	SBC		SBPC		Sulbenicillin										125		X	Penicillins	Sulfonopenicillin	PEN	01g																																																																																																																																																																																		
-SUC	SUC	SUC				Sulconazole										287			Antifungals		FUNG	29																																																																																																																																																																																		
-SUP	SUP					Sulfachlorpyridazine										288			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SDI	SDI		SLD			Sulfadiazine										425			Folate pathway inhibitors		FOLATE	12a					Sulfadiazi	18984-5	465-5	464-8	7050-8			466-3	463-0																																																																																																																																																																					
-SUD	SUD	X				Sulfadimethoxine										289			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SDM	SDM	SDM				Sulfadimidine	AFA								X	290	250ug		Folate pathway inhibitors		FOLATE	12a																																																																																																																																																										12	13-25	26	16	256																				
-SZO	SZO	SZO				Sulfamazone										291			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SUM	SUM					Sulfamethazine										292			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SMX	SMX	SMX	SOZ			Sulfamethoxazole	CLSI	X		X						427	200-300ug		Folate pathway inhibitors		FOLATE	12a	X				Sulfametho	18985-2	469-7	468-9	11577-4			470-5	467-1	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512																																																													14	15-27	28								11	12-16	17	64	512									32	128																			32	64					
-SMX	SMX	SMX	SOZ			Sulfamethoxazole						X				293	100ug		Folate pathway inhibitors		FOLATE	12a	X				Sulfametho	18985-2	469-7	468-9	11577-4			470-5	467-1				256	512				256	512				256	512				256	512				256	512				256	512				256	512				256	512				256	512				256	512				256	512																																																																										64	512									32	128																13	-	14	32	64					
-SNA	SNA	SNA				Sulfasuccinamide										294			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SUT	SUT	ST				Sulfathiazole										295			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-SOX	SOX					Sulfisoxazole	CLSI	X								404	200-300ug		Folate pathway inhibitors		FOLATE	12a	X				Sulfisoxaz	18986-0	473-9	472-1	11578-2			474-7	471-3	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512																																																																										64	512																																			
-SSS	SUL	SSS	SSS			Sulfonamides	CLSI	X		X						61	200-300ug		Folate pathway inhibitors		FOLATE	12a	X				Sulfonamid	18987-8	477-0	476-2	35842-4			478-8	475-4	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512	12	13-16	17	256	512																																																													14	15-27	28								11	12-16	17	64	512									32	128																			32	64					
-SLP	SLP					Sulopenem	CLSI	X								484	2ug	X	Penems	Penem	PENEM	07b	X				Sulopenem	55289-3	55291-9	55290-1																																																																																																																																																																										
-TAL	TAL			TAPC		Talampicillin										466		X	Penicillins	Aminopenicillin	PEN	01b					Talampicil	18988-6	481-2	480-4				482-0	479-6																																																																																																																																																																					
-TLP	TLP	TLP				Talmetoprim										296			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-TAZ	TAZ		TAB	TAZ		Tazobactam	CLSI	X								297		X	Beta-lactamase inhibitors		BL-INH	02					Tazobactam	41740-2	41719-6	41721-2	41720-4																																																																																																																																																																									
-TZD	TED					Tedizolid	CLSI,EUCAST	X	X	X						505			Oxazolidinones		OXAZOLID	20						73586-0	73631-4	73608-2																																																																																																																																																																										
-TEC	TE6	TEC	TPL	TEIC		Teicoplanin	NEO							X		384	60ug		Glycopeptides	Lipoglycopeptide	GLYCO	21b	X				Teicoplani	18989-4	485-3	484-6	7051-6			486-1	483-8				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32				8	32																																																													12	13-21	22											4	32									2	8				4	16									4	8				4	8					
-TEC	TEI	TEC	TPL	TEIC		Teicoplanin	CLSI,EUCAST	X	X	X	X				X	79	30ug		Glycopeptides	Lipoglycopeptide	GLYCO	21b	X				Teicoplani	18989-4	485-3	484-6	7051-6					10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32																																																																									17	4	16									2	8	14	15	16	4	16						11	12-15	16	4	8	14	-	15	4	8					
-TCM	TCM			TEIC		Teicoplanin-Macromethod										440			Glycopeptides	Lipoglycopeptide	GLYCO	21b																																																																																																																																																																																		
-TLV	TLV					Telavancin	CLSI	X								472	30ug		Glycopeptides	Lipoglycopeptide	GLYCO	21b	X					72894-9	73630-6	72894-9																																																																																																																																																																										
-TLT	TLT		TEL	TEL		Telithromycin	CLSI,EUCAST	X	X	X						396	15ug		Macrolides	Ketolide	MACRO	17b	X				Telithromy	35845-7	35843-2	35844-0	41722-0					18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4	18	19-21	22	1	4																																																																							16	17-20	21	.5	4																																			
-TMX	TEM	TMX	TEM			Temafloxacin	CLSI	X								111	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Temafloxac	18990-2	489-5	488-7				490-3	487-9																																																																																																																																																																					
-TEM	TEL	TEM	TMO			Temocillin	NEO							X		298	30ug	X	Penicillins	Penicillin (Stable)	PEN-S	01e					Temocillin	18991-0	493-7	492-9				494-5	491-1																																																																																																																																																																					
-TRB	TRB					Terbinafine	NEO							X		479	30ug		Antifungals		FUNG	29																																																																																																																																																																																		
-TRC	TRC					Terconazole										480			Antifungals		FUNG	29																																																																																																																																																																																		
-TCY	TET	TE	TET	TC		Tetracycline	CLSI,EUCAST	X	X	X	X	X	X		X	62	30ug		Tetracyclines		TETRA	24a	X				Tetracycli	18993-6	497-8	496-0	7052-4			498-6	495-2	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16	11	12-14	15	4	16																																																																							16	17-18	19	4	16	16	17-21	22	1	8				1	8	19	20-24	25	1	4						21	22-24	25	2	4	33	-	34	1	2					
-TCY	TE8	TE	TET	TC		Tetracycline	NEO							X		399	80ug		Tetracyclines		TETRA	24	X				Tetracycli	18993-6	497-8	496-0	7052-4			498-6	495-2				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																													14	15-27	28											4	16				1	8				1	8				1	4									2	4				1	2					
-TCY	TE1	TE	TET	TC		Tetracycline	BSAC,NEO					X		X		326	10ug		Tetracyclines		TETRA	24	X				Tetracycli	18993-6	497-8	496-0	7052-4			498-6	495-2				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	16				1	8				1	8				1	4									2	4				1	2					
-TET	TEP	TET	TTP			Tetroxoprim										299			Folate pathway inhibitors		FOLATE	12a																																																																																																																																																																																		
-THA	THA					Thiacetazone										177			Antimycobacterials		MYCO	28					Thiacetazo	32384-0																																																																																																																																																																												
-THI	THI	TP	TPH	TP		Thiamphenicol										120	30ug		Phenicols		PHEN	22					Thiampheni		41723-8	41725-3	41724-6																																																																																																																																																																									
-THI	TH6	TP	TPH	TP		Thiamphenicol	NEO							X		385	60ug		Phenicols		PHEN	22					Thiampheni		41723-8	41725-3	41724-6																																																																																																																																																																									
-TIA	TIA		TIA			Tiamulin	CLSI,NEO	X						X		178	30ug		Pleuromutilins		OTHER	28		X			Tiamulin	35848-1	35846-5	35847-3						8	-	9	16	32	8	-	9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32	8		9	16	32																																																																																																														
-TIC	TIC	TIC	TIC			Ticarcillin	CLSI,EUCAST	X	X	X						63	75ug	X	Penicillins	Carboxypenicillin	PEN	01d	X				Ticarcilli	18994-4	501-7	500-9	7053-2			502-5	499-4																																														14	15-19	20	16	128	14	15-19	20	16	128																																														21	22	23	8	32											9	10-27	28								17	18-21	22	16	128									16	128																									
-TCC	TIM	TCC	TCC			Ticarcillin/Clavulanic acid	CLSI,EUCAST	X	X	X		X	X			64	75/10-15ug	X	Beta-lactam+Inhibitors		BL+INH	03	X				Ticarcilli	18995-1	505-8	504-1	7054-0			506-6	503-3	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128	14	15-19	20	16	128																																																	8	32											9	10-27	28								17	18-21	22	16	128	15	16-19	20						16	128																20	-	21	16	32					
-TGC	TGC		TGC			Tigecycline	CLSI,EUCAST	X	X	X						473	15ug		Tetracyclines	Glycylglycine	TETRA	24b	X				Tigecyclin	42357-4	42356-6	42355-8	42354-1																																																																																																									14	15-17	18	1	4																					21	-	22	.25	1																																			
-TBQ	TBQ	TBQ				Tilbroquinol										300			Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-TIL	TIL					Tilmicosin	CLSI	X								179	15ug		Macrolides	16-Membered ring	MACRO	17a		X			Tilmicosin	35851-5	35849-9	35850-7						10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32	10	11-13	14	8	32																																																																																																														
-TIN	TIN		TNZ			Tinidazole	CLSI	X								180	4ug		Nitroimidazoles		IMIDAZ	29					Tinidazole	54928-7	55721-5	55720-7	55722-3																																																																																																																																																																									
-TIN	TI1		TNZ			Tinidazole	CLSI,NEO							X		386	16ug		Nitroimidazoles		IMIDAZ	29					Tinidazole	54928-7	55721-5	55720-7	55722-3																																																																																																																																																																									
-TDC	TDC	TDC				Tiodonium chloride										301			Thiophenes		THIO	27																																																																																																																																																																																		
-TXC	TXC	TXC				Tioxacin										302			Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-TIZ	TIZ					Tizoxanide	CLSI	X								495			Thiazolides		THIAZ	30						73585-2	73629-8	73607-4																																																																																																																																																																										
-TOB	TO3	TM	TOB	TOB		Tobramycin	AFA,SRGA				X				X	209	30ug		Aminoglycosides		AG	09	X				Tobramycin	18996-9	509-0	508-2	7055-7		25800-4	510-8	507-4				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																																										4	16				1	8				1	8	18	19-22	23	2	8						17	18-20	21	2	4				1	2					
-TOB	TO4	TM	TOB	TOB		Tobramycin	NEO							X		387	40ug		Aminoglycosides		AG	09	X				Tobramycin	18996-9	509-0	508-2	7055-7		25800-4	510-8	507-4				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16				4	16																																																													14	15-25	26											4	16				1	8				1	8				2	8									2	4				1	2					
-TOB	TOB	TM	TOB	TOB		Tobramycin	CLSI,EUCAST	X	X	X		X	X			65	10ug		Aminoglycosides		AG	09	X				Tobramycin	18996-9	509-0	508-2	7055-7		25800-4	510-8	507-4	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16	12	13-14	15	4	16																																														11	12-14	15	2	8																					14	15-16	17	8	32	15	16-18	19	1	8				1	8				2	8									2	4	17	-	18	1	2					
-TFX	TFX	TFX	TOS	TFLX		Tosufloxacin										303			Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-TMP	TM2		TRP			Trimethoprim						X				426	2.5ug		Folate pathway inhibitors		FOLATE	12a	X				Trimethopr	18997-7	513-2	512-4	7056-5		23614-1	514-0	511-6				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16																																																																										4	16									1	4				2	8									2	8	14	15-19	20	.5	4					
-TMP	TMP	TMP	TRP			Trimethoprim	CLSI,EUCAST	X	X	X	X	X			X	66	5ug		Folate pathway inhibitors		FOLATE	12a	X				Trimethopr	18997-7	513-2	512-4	7056-5		23614-1	514-0	511-6	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16	10	11-15	16	8	16																																														14	15-17	18	2	8																					11	12-15	16	4	16									1	4	16	17-20	21	2	8						13	14-16	17	2	8				.5	4					
-TMP	TM5	TMP	TRP			Trimethoprim	NEO							X		388	5.2ug		Folate pathway inhibitors		FOLATE	12a	X				Trimethopr	18997-7	513-2	512-4	7056-5		23614-1	514-0	511-6				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16				8	16																																																													12	13-21	22											4	16									1	4				2	8									2	8				.5	4					
-SXT	SXT	SXT	SXT	ST		Trimethoprim/Sulfamethoxazole	CLSI,EUCAST	X	X	X	X	X	X		X	67	1.25/23.75ug		Folate pathway inhibitors		FOLATE	12a	X				Trimethopr	18998-5	517-3	516-5	7057-3	20387-7	23631-5	518-1	515-7	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4	10	11-15	16	2	4																																														12	13-15	16	2	8																					9	10-15	16	2	16	10	11-15	16	16	128				1	4	13	14-25	26	2	8						13	14-16	17	16	64	15	-	16	32	64					
-SXT	SX5	SXT	SXT	ST		Trimethoprim/Sulfamethoxazole	NEO							X		389	5.2/240ug		Folate pathway inhibitors		FOLATE	12a	X				Trimethopr	18998-5	517-3	516-5	7057-3	20387-7	23631-5	518-1	515-7				2	4				2	4				2	4				2	4				2	4				2	4				2	4				2	4				2	4				2	4				2	4																																																													14	15-27	28											2	16				16	128				1	4				2	8									16	64				32	64					
-TRL	TRL					Troleandomycin										181			Macrolides		MACRO	17					Troleandom	18999-3	521-5	520-7				522-3	519-9																																																																																																																																																																					
-TRO	TRO		TRS			Trospectomycin	CLSI	X								112	30ug		Aminocyclitols		AMINOC	08	X				Trospectin	35854-9	35852-3	35853-1																																																																																																																																																																										
-TVA	TRV		TRO			Trovafloxacin	CLSI	X		X						182	10ug		Quinolones	Fluoroquinolone	FQ	11b	X				Trovafloxa	23642-2	35855-6	23643-0	7058-1																																																																																																																																		16	17-19	20	1	4				1	4																			.25	2										
-TVA	TRV		TRO			Trovafloxacin	DIN						X			438	5ug		Quinolones	Fluoroquinolone	FQ	11b	X				Trovafloxa	23642-2	35855-6	23643-0	7058-1																																																																																																																																							16	17-19	20	1	4																														
-TYL	TYL	TI	TLS			Tylosin	NEO							X		304	150ug		Macrolides	16-Membered ring	MACRO	17		X			Tylosin	35858-0	35856-4	35857-2																																																																																																																																																																										
-PRU	PRU					Ulifloxacin (Prulifloxacin)										490	5ug		Quinolones	Fluoroquinolone	FQ	11b																																																																																																																																																																																		
-VAN	VA7	VA	VAN	VCM		Vancomycin	NEO							X		390	70ug		Glycopeptides	Glycopeptide	GLYCO	21a	X				Vancomycin	19000-9	525-6	524-9	7059-9		23615-8	526-4	523-1				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																													12	13-21	22											4	32				4	16				4	16				4	16									4	8				4	8					
-VAN	VAN	VA	VAN	VCM		Vancomycin	CLSI,AFA	X		X					X	68	30ug		Glycopeptides	Glycopeptide	GLYCO	21a	X				Vancomycin	19000-9	525-6	524-9	7059-9		23615-8	526-4	523-1				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																																									17	4	16				4	16				4	16	16	17-19	20	4	16									4	8				4	8					
-VAN	VA5	VA	VAN	VCM		Vancomycin	EUCAST,NEO		X	X	X	X		X		305	5ug		Glycopeptides	Glycopeptide	GLYCO	21a	X				Vancomycin	19000-9	525-6	524-9	7059-9		23615-8	526-4	523-1				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32				4	32																																																													15	-	16											4	32				4	16				4	16				4	16						9	10-10	11	4	8	11	-	12	4	8					
-VAM	VAM			VCM		Vancomycin-Macromethod										436			Glycopeptides	Glycopeptide	GLYCO	21a																																																																																																																																																																																		
-VIO	VIO		VIO			Viomycin										183			Antimycobacterials		MYCO	28					Viomycin	19001-7	529-8	528-0			23616-6	530-6	527-2																																																																																																																																																																					
-VIR	VI3	VG	VIR			Virginiamycine	NEO							X		391	30ug		Streptogramins		STREPTOG	23					Virginiamy	35861-4	35859-8	35860-6																																																																																																																																																																										
-VIR	VIR	VG	VIR			Virginiamycine				X						184	15ug		Streptogramins		STREPTOG	23					Virginiamy	35861-4	35859-8	35860-6																																																																																																																																																																										
-VOR	VOR			VRCZ		Voriconazole	CLSI,NEO	X						X		431	1ug		Antifungals		FUNG	29	X				Voriconazo	32379-0	41200-7	35863-0	35862-2				41199-1																																																																																																																																																																					
-AZA	AZA					Aztreonam/Avibactam	CLSI	X								510	30/20ug		Beta-lactam+inhibitors		BL+INH																																																																																																																																																																																			
-POP	POP					Polymyxin B/Polysorbate 80	CLSI	X								509	300units		Lipopeptides	Polymyxin	LIPOPEP	16	X																																																																																																																																																																																	
-SUR	SUR					Surotomycin	CLSI	X								514			Lipopeptides		LIPOPEP																																																																																																																																																																																			
-COP	COP					Colistin/Polysorbate	CLSI	X								508	10ug		Lipopeptides		LIPOPEP	16	X																																																																																																																																																																																	
-ERV	ERV					Eravacycline	CLSI	X								513	20ug		Fluorocyclines		OTHER	28																																																																																																																																																																																		
-DLM	DLM					Delamanid			X	X						512																																																																																																																																																																																								
-BDQ	BDQ					Bedaquiline			X	X						511																																																																																																																																																																																								
-FOV	FOV					Cefovecin	CLSI	X								515			Cephems	Cephalosporin III	CEPH3	04c		X																																																																																																																																																																																
-GAM	GAM					Gamithromycin	CLSI	X								516			Macrolides	15-Membered ring	MACRO			X																																																																																																																																																																																
-KAC	KAC					Kanamycin/Cephalexin	CLSI	X								517			Combinations	Aminoglycoside/Cephem	OTHER	28		X																																																																																																																																																																																
-TIP	TIP					Tildipirosin	CLSI	X								519	60ug		Macrolides	16-Membered ring	MACRO			X																																																																																																																																																																																
-PRA	PRA					Pradofloxacin	CLSI	X								518			Quinolones	Fluoroquinolone	FQ	11b		X																																																																																																																																																																																
-TUL	TUL					Tulathromycin	CLSI	X								520	30ug		Macrolides	15-Membered ring	MACRO			X												14	15-17	18	16	64	14	15-17	18	16	64	14	15-17	18	16	64	14	15-17	18	16	64	14	15-17	18	16	64	14	15-17	18	16	64																																																																																																																																							
-						Tylvalosin	CLSI	X								521			Macrolides	16-Membered ring	MACRO			X																																																																																																																																																																																
-AKF	AKF					Amikacin/Fosfomycin	CLSI	X								522			Combinations	Aminoglycoside/Fosfomycin	OTHER	28																																																																																																																																																																																		
-CDZ	CDZ					Cadazolid	CLSI	X								523			Quinolonyl oxazolidinones		OTHER	28																																																																																																																																																																																		
-FPT	FPT					Cefepime/Tazobactam	CLSI	X								524			Beta-lactam+Inhibitors		BL+INH	03c																																																																																																																																																																																		
-DFX	DFX					Delafloxacin	CLSI	X								525	5ug		Quinolones	Quinolone	QUIN	11a																																																																																																																																																																																		
-GEP	GEP					Gepotidacin	CLSI	X								526	10ug		Triazaacenaphylenes		OTHER	28																																																																																																																																																																																		
-IMR	IMR					Imipenem/relebactam	CLSI	X								527			Beta-lactam+Inhibitors		BL+INH	03c																																																																																																																																																																																		
-LMU	LMU					Lefamulin	CLSI	X								528	20ug		Pleuromutilins		OTHER	28																																																																																																																																																																																		
-LND	LND					Levonadifloxacin	CLSI	X								529	10ug		Quinolones	Benzoquinolizine	BQ	11c																																																																																																																																																																																		
-SEC	SEC					Secnidazole	CLSI	X								530			Nitroimidazoles		IMIDAZ																																																																																																																																																																																			
-ISV	ISV					Isavuconazole	EUCAST		X	X						531			Antifungals		FUNG																																																																																																																																																																																			
-MUP	MU2		MUP	MUP		Mupirocin	EUCAST		X	X						532	200ug		Pseudomonic acids		PSEUDOM	27	X				Mupirocin	20389-3	35822-6	35823-4	7033-4																																																																																																																																																																									
-MEV	MEV					Meropenem/Vaborbactam	CLSI	X								533	20/10ug		Beta-lactam+Inhibitors			03c	X													14	15-17	18	4	16	14	15-17	18	4	16																																																																																																																																																											
-ZWK	ZWK					Nafithromycin	CLSI	X								534	15ug		Macrolides	Ketolide	MACRO	17	X																																																																																																																																																																																	
-PEX	PEX					Pexiganan	CLSI	X								535			Peptsides	Magainin	PEPTIDE		X																																																																																																																																																																																	
-						Retapamulin	CLSI	X								538			Pleuromutilins																																																																																																																																																																																					
-						Rifapentine	CLSI	X								539			Ansamycins																																																																																																																																																																																					
-FDC	FDC					Cefiderocol	CLSI	X								537			Cephems	Siderophore																			4	16				4	16																																																																																																																																																											
-FPZ	FPZ					Cefepime/Zidebactam	CLSI	X								536																																																																																																																																																																																								
-ZID	ZID					Zidebactam	CLSI									540							X																																																																																																																																																																																	
-RID	RID					Ridinilazole	CLSI									541							X																																																																																																																																																																																	
-TBP	TBP					Tebipenem	CLSI	X									10ug		Penems	Carbapenems			X																																																																																																																																																																																	
-MNC	MNC					Meropenem/Nacubactam	CLSI	X											Beta-lactam+Inhibitors																																																																																																																																																																																					
-NAC	NAC					Nacubactam	CLSI	X											Beta-lactamase inhibitors																																																																																																																																																																																					
-TYL	TYL					Tylosin	CLSI,EUCAST	X	X							304	30ug		Macrolides	16-Membered ring		17																																																																																																																																																																																		
-ITR	ITR					Itraconazole	NEO	X						X		133	10ug		Antifungals		FUNG	29	X																																																																																																																																																																																	
-CZA	CZA					Ceftazidime/Avibactam	EUCAST									498	10/4ug		Beta-lactam+Inhibitors			03	X													20		21	8	16	20		21	8	16																																																																																																																																																											
-BPR	BPR					Ceftobiprole	EUCAST									474	5ug		Cephems	Cephalosporin		04e	X																																																																																																																																																																																	
-AMX	AMX					Amoxicillin				X						82	20ug		Penicillins	Aminopenicillin		01b	X																																																																																																																																																																																	
-ZFD						Zoliflodacin	CLSI	X								544			Spiropyrimidinetrione				X																																																																																																																																																																																	
-OZN						Ozenoxacin	CLSI	X								543			Quinolones	Fluoroquinolone	FQ		X																																																																																																																																																																																	
-EXE						Exebacase	CLSI	X								542			Antistaphylococcal lysin				X																																																																																																																																																																																	
-LIN	LIN	L	LIN	LCM		Lincomycin	CLSI	X								38	4ug		Lincosamides		LINCO	15					Lincomycin	18938-1	300-4	299-8	41700-6			301-2	298-0																																																																																																																														16	17-20	21	2	16											17	18-23	24	1	4																				

data-raw/_install_deps.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -24,14 +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", dependencies = c("Depends", "Imports"))
+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)
 
 pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
                      unlist(strsplit(unlist(packageDescription("AMR",
-                                                               fields = c("Suggests", "Enhances"))),
-                                     ", ?")))
+                                                               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) {
@@ -40,13 +48,23 @@ 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],
-                            type = ifelse(.Platform$OS.type == "unix", "source", "binary"),
+                            type = "source",
                             repos = "https://cran.rstudio.com/",
-                            dependencies = c("Depends", "Imports"),
+                            dependencies = c("Depends", "Imports", "LinkingTo"),
                             quiet = FALSE),
            # message = function(m) invisible(),
            warning = function(w) message(w$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)

data-raw/_internals.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 
@@ -68,7 +68,16 @@ TRANSLATIONS <- 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)[nchar(colnames(TRANSLATIONS)) == 2]))
+LANGUAGES_SUPPORTED <- c(Danish = "da",
+                         German = "de",
+                         English = "en",
+                         Spanish = "es",
+                         French = "fr",
+                         Italian = "it",
+                         Dutch = "nl",
+                         Portuguese = "pt",
+                         Russian = "ru",
+                         Swedish = "sv")
 
 # EXAMPLE_ISOLATES <- readRDS("data-raw/example_isolates.rds")
 
@@ -95,7 +104,9 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
                                            "pulvereri", "rostri", "saccharolyticus", "saprophyticus",
                                            "sciuri", "simulans", "stepanovicii", "succinus",
                                            "ureilyticus",
-                                           "vitulinus", "vitulus", "warneri", "xylosus")
+                                           "vitulinus", "vitulus", "warneri", "xylosus",
+                                           "caledonicus", "canis",
+                                           "durrellii", "lloydii")
                    | (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
              "mo", drop = TRUE]
   } else if (type == "CoPS") {
@@ -105,13 +116,15 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
                                            "delphini", "lutrae",
                                            "hyicus", "intermedius",
                                            "pseudintermedius", "pseudointermedius",
-                                           "schweitzeri", "simiae")
+                                           "schweitzeri", "simiae",
+                                           "roterodami")
                    | (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
              "mo", drop = TRUE]
   }
 }
 MO_CONS <- create_species_cons_cops("CoNS")
 MO_COPS <- create_species_cons_cops("CoPS")
+MO_STREP_ABCG <- as.mo(MO_lookup[which(MO_lookup$genus == "Streptococcus"), "mo", drop = TRUE], Lancefield = TRUE) %in% c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_GRPC", "B_STRPT_GRPG")
 
 # antibiotic groups
 # (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
@@ -155,6 +168,7 @@ usethis::use_data(EUCAST_RULES_DF,
                   # EXAMPLE_ISOLATES,
                   MO_CONS,
                   MO_COPS,
+                  MO_STREP_ABCG,
                   AB_AMINOGLYCOSIDES,
                   AB_AMINOPENICILLINS,
                   AB_ANTIFUNGALS,
@@ -265,15 +279,19 @@ if (changed_md5(av)) {
   try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
 }
 
-if (changed_md5(intrinsic_resistant)) {
+# give official names to ABs and MOs
+intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo),
+                         antibiotic = ab_name(intrinsic_resistant$ab),
+                         stringsAsFactors = FALSE)
+if (changed_md5(intrinsicR)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))
-  write_md5(intrinsic_resistant)
-  try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
-  try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
-  try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
-  try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
-  try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
-  try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
+  write_md5(intrinsicR)
+  try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
+  try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+  try(haven::write_sas(intrinsicR, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
+  try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
+  try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
+  try(openxlsx::write.xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
 }
 
 if (changed_md5(dosage)) {

data-raw/ab.md5

@@ -1 +1 @@
-9f708801889d2eaf974c6eb85c83a8e7
+4f082a7952a37133305f64d6f711e81e

data-raw/antibiotics.txt

@@ -31,6 +31,7 @@
 "AZL"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"J01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"az\", \"azl\", \"azlo\")"	""			12	"g"	""
 "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"				""	""					""
+"ANC"		"Aztreonam/nacubactam"	"Beta-lactams/penicillins"				""	""					""
 "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"	78358334	"Bacitracin zinc"	"Other antibacterials"	"R02AB04"			"baci"	""					""
 "BDQ"	5388906	"Bedaquiline"	"Other antibacterials"	"J04AK05"			""	"c(\"bedaquiline\", \"sirturo\")"	86	"mg"			"80637-2"
@@ -41,7 +42,7 @@
 )"			3.6	"g"	"3913-1"
 "BES"	10178705	"Besifloxacin"	"Quinolones"	"S01AE08"			""	"besifloxacin"					"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"	"Other antibacterials"				"c(\"\", \"bicozamycin\")"	"c(\"aizumycin\", \"bacfeed\", \"bacteron\", \"bicozamicina\", \"bicozamycin\", \"bicozamycine\", \"bicozamycinum\")"					"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"	"G01AF15"			""	"c(\"butaconazole\", \"butoconazol\", \"butoconazole\", \"butoconazolum\", \"compositenstarke\", \"dahlin\", \"femstat\", \"gynofort\", \"polyfructosanum\")"					"character(0)"
 "CDZ"	44242317	"Cadazolid"	"Oxazolidinones"				""	"cadazolid"					"character(0)"
@@ -67,11 +68,12 @@
 "DIX"	6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"				""	"c(\"cefditoren\", \"cefditoren pi voxil\", \"cefditoren pivoxil\", \"cefditorin\", \"cefditorin pivoxil\", \"meiact\", \"spectracef\")"					"character(0)"
 "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\")"	""					""
+"FNC"		"Cefepime/nacubactam"	"Beta-lactams/penicillins"				""	""					""
 "FPT"	9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"				""	""					""
 "FPZ"		"Cefepime/zidebactam"	"Other antibacterials"				""	""					""
 "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)"
-"CCL"	71719688	"Cefetecol (Cefcatacol)"	"Cephalosporins (4th gen.)"				""	""					""
+"CCL"	71719688	"Cefetecol"	"Cephalosporins (4th gen.)"				"c(\"\", \"cefcatacol\")"	""					""
 "CZL"	193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"				""	"c(\"cefetrizole\", \"cefetrizolum\")"					"character(0)"
 "FDC"	77843966	"Cefiderocol"	"Other antibacterials"	"J01DI04"			""	"cefiderocol"					"character(0)"
 "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\")"
@@ -176,7 +178,7 @@
 "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"	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)"
-"ENV"	135565326	"Enviomycin (Tuberactinomycin)"	"Antimycobacterials"				""	"c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")"					"character(0)"
+"ENV"	135565326	"Enviomycin"	"Antimycobacterials"				"c(\"\", \"tuberactinomycin\")"	"c(\"enviomicina\", \"enviomycin\", \"enviomycina\", \"enviomycinum\")"					"character(0)"
 "EPE"		"Eperozolid"	"Other antibacterials"				""	""					""
 "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)"
@@ -190,6 +192,7 @@
 "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)"
+"EXE"		"Exebacase"					""	""					""
 "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"	"A07AA12"			""	"c(\"dificid\", \"dificlir\", \"difimicin\", \"fidaxomicin\", \"lipiarmycin\", \"tiacumicin b\")"	0.4	"g"			"character(0)"
 "FIN"	11567473	"Finafloxacin"	"Quinolones"				""	"finafloxacin"					"character(0)"
@@ -214,7 +217,7 @@
 "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"	9571107	"Gemifloxacin"	"Quinolones"	"J01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")"	0.32	"g"			"character(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(\"gehi\", \"gehl\", \"genta high\", \"gentamicin high\")"	""					""
 "GEP"	25101874	"Gepotidacin"	"Other antibacterials"				""	"gepotidacin"					"character(0)"
 "GRX"	72474	"Grepafloxacin"	"Quinolones"	"J01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"grep\")"	"grepafloxacin"	0.4	"g"			"character(0)"
 "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\", 
@@ -223,6 +226,7 @@
 "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"	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)"
+"IBX"		"Ibrexafungerp"	"Antifungals"				""	""					""
 "ICL"	213043	"Iclaprim"	"Other antibacterials"	"J01EA03"			""	"c(\"iclaprim\", \"mersarex\")"					"character(0)"
 "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"				""	""					""
@@ -241,14 +245,14 @@
 "KAH"		"Kanamycin-high"	"Aminoglycosides"				"c(\"\", \"k_h\", \"kahl\")"	""					""
 "KAC"		"Kanamycin/cephalexin"	"Aminoglycosides"				""	""					""
 "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"	"Macrolides/lincosamides"				"c(\"\", \"leucomycin\")"	""					""
 "LAS"	5360807	"Lasalocid"	"Other antibacterials"				""	"c(\"avatec\", \"lasalocid\", \"lasalocid a\", \"lasalocide\", \"lasalocide a\", \"lasalocido\", \"lasalocidum\")"					"87598-9"
-"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)"
+"LTM"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"J01DD06"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"c(\"mox\", \"moxa\", \"moxalactam\")"	"c(\"disodium moxalactam\", \"festamoxin\", \"lamoxactam\", \"latamoxef\", \"latamoxefum\", \"shiomarin\")"			4	"g"	"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)"
 "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"	"J01MA24"			""	"levonadifloxacin"					"character(0)"
-"LSP"		"Linco-spectin (lincomycin/spectinomycin)"	"Other antibacterials"				""	""					""
+"LSP"		"Linco-spectin"	"Other antibacterials"				"c(\"\", \"lincomycin/spectinomycin\")"	""					""
 "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"	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"				""	""					""
@@ -256,8 +260,9 @@
 "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"	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"	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)"
+"MGX"		"Manogepix"	"Antifungals"				""	""					""
 "MAR"	60651	"Marbofloxacin"	"Quinolones"				""	"c(\"marbocyl\", \"marbofloxacin\", \"marbofloxacine\", \"marbofloxacino\", \"marbofloxacinum\", \"zeniquin\")"					"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)"
+"MEC"	36273	"Mecillinam"	"Beta-lactams/penicillins"	"J01CA11"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"c(\"\", \"amdinocillin\")"	"c(\"amdinocillin\", \"coactin\", \"hexacillin\", \"mecilinamo\", \"mecillinam\", \"mecillinamum\", \"micillinam\", \"penicillin hx\", \"selexidin\")"			1.2	"g"	"character(0)"
 "MEL"	71306732	"Meleumycin"	"Macrolides/lincosamides"				""	""					""
 "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"				""	""					""
@@ -324,6 +329,7 @@
 "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"	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\")"
+"OZN"		"Ozenoxacin"					""	""					""
 "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)"
 "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)"
@@ -338,7 +344,7 @@
 "PEX"	16132253	"Pexiganan"	"Other antibacterials"				""	"pexiganan"					"character(0)"
 "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"	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"	"Antifungals/antimycotics"				"c(\"\", \"natamycin\")"	"c(\"delvocid\", \"mycophyt\", \"myprozine\", \"natacyn\", \"natamicina\", \"natamycin\", \"natamycine\", \"natamycinum\", \"pimafucin\", \"pimaracin\", \"pimarizin\", \"synogil\", \"tennecetin\")"					"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"	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"				""	""					""
@@ -368,7 +374,8 @@
 "RAC"	56052	"Ractopamine"	"Other antibacterials"				""	"c(\"ractopamina\", \"ractopamine\", \"ractopaminum\")"					"character(0)"
 "RAM"	16132338	"Ramoplanin"	"Glycopeptides"				""	"ramoplanin"					"character(0)"
 "RZM"	10993211	"Razupenem"	"Carbapenems"				""	"razupenem"					"character(0)"
-"RTP"	6918462	"Retapamulin"	"Other antibacterials"	"D06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	""	"c(\"altabax\", \"altargo\", \"retapamulin\")"					"character(0)"
+"RTP"	6918462	"Retapamulin"	"Other antibacterials"	"D06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	"c(\"\", \"ret\")"	"c(\"altabax\", \"altargo\", \"retapamulin\")"					"character(0)"
+"RZF"		"Rezafungin"	"Antifungals"				""	""					""
 "RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"c(\"kisqali\", \"ribociclib\")"					"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)"
@@ -379,7 +386,7 @@
 "RPEI"		"Rifampicin/pyrazinamide/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM06"	"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"	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"	135403821	"Rifapentine"	"Antimycobacterials"	"J04AB05"	"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"	"c(\"rifp\", \"rpt\")"	"c(\"cyclopentyl rifampin\", \"priftin\", \"rifapentin\", \"rifapentina\", \"rifapentine\", \"rifapentinum\")"	0.11	"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)"
 "RIA"	163692	"Ritipenem acoxil"	"Carbapenems"				""	"ritipenem acoxil"					"character(0)"
@@ -403,7 +410,7 @@
 "SPM"		"Spiramycin/metronidazole"	"Other antibacterials"	"J01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "STR"		"Streptoduocin"	"Aminoglycosides"	"J01GA02"	"Aminoglycoside antibacterials"	"Streptomycins"	""	""			1	"g"	""
 "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(\"sthi\", \"sthl\", \"strepto high\", \"streptomycin high\")"	""					""
 "STI"		"Streptomycin/isoniazid"	"Antimycobacterials"	"J04AM01"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
 "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"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"J01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")"			15	"g"	"character(0)"
@@ -500,7 +507,7 @@
 "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)"
 "TYL"	5280440	"Tylosin"	"Macrolides/lincosamides"				""	"c(\"fradizine\", \"tilosina\", \"tylocine\", \"tylosin\", \"tylosin a\", \"tylosine\", \"tylosinum\")"					"87587-2"
-"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"				""	""					""
+"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"				"c(\"\", \"tvn\")"	""					""
 "PRU1"	124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"				""	"ulifloxacin"					"character(0)"
 "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"				""	""					""
@@ -509,3 +516,4 @@
 "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"	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)"
+"ZFD"		"Zoliflodacin"					""	""					""

data-raw/eucast_rules.tsv

@@ -7,7 +7,7 @@
 # The like.is.one_of column must be 'like' or 'is' or 'one_of' ('like' will read the 'this_value' column as regular expression)
 # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
-# -------------------------------------------------------------------------------------------------------------------------------				
+# -------------------------------------------------------------------------------------------------------------------------------			
 if_mo_property	like.is.one_of	this_value	and_these_antibiotics	have_these_values	then_change_these_antibiotics	to_value	reference.rule	reference.rule_group	reference.version	note
 order	is	Enterobacterales	AMP	S	AMX	S	Enterobacterales (Order)	Breakpoints	10	
 order	is	Enterobacterales	AMP	I	AMX	I	Enterobacterales (Order)	Breakpoints	10	
@@ -303,7 +303,7 @@ fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			am
 fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Enterobacter cloacae			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Escherichia hermannii			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
-genus_species	is	Hafnia alvei			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
+genus_species	is	Hafnia alvei			aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Klebsiella aerogenes			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Klebsiella oxytoca			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 fullname	like	^Klebsiella( pneumoniae| quasipneumoniae| variicola)?			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
@@ -367,7 +367,7 @@ genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	R	PIP	R	Expert Rule
 genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	S	PIP	S	Expert Rules on Enterobacterales	Expert Rules	3.2	
 fullname	like	^(Klebsiella(?! aerogenes)|Raoultella)			PIP	R	Expert Rules on Enterobacterales	Expert Rules	3.2	
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia)	CXM	S	CXM, cephalosporins_2nd	R	Expert Rules on Enterobacterales	Expert Rules	3.2	
-genus	one_of	Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Metakosakonia, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella	CIP	R	fluoroquinolones	R	Expert Rules on Enterobacterales	Expert Rules	3.2	This is Enterobacterales except Salmonella spp.
+genus	one_of	Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella	CIP	R	fluoroquinolones	R	Expert Rules on Enterobacterales	Expert Rules	3.2	This is Enterobacterales except Salmonella spp.
 fullname	like	^(Serratia|Providencia|Morganella morganii)			TGC	R	Expert Rules on Enterobacterales	Expert Rules	3.2	
 genus	is	Salmonella			cephalosporins_2nd	R	Expert Rules on Salmonella	Expert Rules	3.2	
 genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules	3.2	
@@ -415,3 +415,121 @@ fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacte
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+order	is	Enterobacterales			PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Enterobacter cloacae			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Escherichia hermannii			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Hafnia alvei			aminopenicillins, AMC, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Klebsiella aerogenes			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Klebsiella oxytoca			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Klebsiella( pneumoniae| quasipneumoniae| variicola)?			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Leclercia adecarboxylata			FOS	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Morganella morganii			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Plesiomonas shigelloides			aminopenicillins, AMC, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus mirabilis			DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus penneri			aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus vulgaris			aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Providencia rettgeri			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Providencia stuartii			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus	is	Raoultella			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Serratia marcescens			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Yersinia enterocolitica			aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Yersinia pseudotuberculosis			polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas hydrophila			aminopenicillins, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas veronii			aminopenicillins, SAM, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas dhakensis			aminopenicillins, SAM, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas caviae			aminopenicillins, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus	one_of	Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas			PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	
+fullname	like	^Acinetobacter (baumannii|pittii|nosocomialis)			aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus	is	Acinetobacter			DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Achromobacter xylosoxidans 			aminopenicillins, CRO, CTX, ETP, ATM	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+fullname	like	^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis)			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Elizabethkingia meningoseptica			aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Elizabethkingia anophelis			aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Brucella anthropi			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Pseudomonas aeruginosa			aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Stenotrophomonas maltophilia			aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus	is	Chryseobacterium			aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Haemophilus influenzae			FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis			TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus	is	Neisseria			TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+fullname	like	^Campylobacter (jejuni|coli)			FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+gramstain	is	Gram-positive			ATM, TEM, polymyxins, NAL	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus saprophyticus			FUS, CAZ, FOS, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus cohnii			CAZ, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus xylosus			CAZ, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus capitis			CAZ, FOS	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus			CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus coagulase-negative			CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	is	Streptococcus			FUS, CAZ, aminoglycosides	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Enterococcus faecalis			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+genus_species	is	Enterococcus faecalis	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecalis	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecalis	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+genus_species	is	Enterococcus faecium	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus	is	Corynebacterium			FOS	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Listeria monocytogenes			CAZ, cephalosporins_except_CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	one_of	Leuconostoc, Pediococcus			VAN, TEC	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	is	Lactobacillus			VAN, TEC	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+fullname	like	^Clostridium (ramosum|innocuum)			VAN	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	R	PIP	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	S	PIP	S	Expert Rules on Enterobacterales	Expert Rules	3.3	
+fullname	like	^(Klebsiella(?! aerogenes)|Raoultella)			PIP	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia)	CXM	S	CXM, cephalosporins_2nd	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus	one_of	Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella	CIP	R	fluoroquinolones	R	Expert Rules on Enterobacterales	Expert Rules	3.3	This is Enterobacterales except Salmonella spp.
+fullname	like	^(Serratia|Providencia|Morganella morganii)			TGC	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus	is	Salmonella			cephalosporins_2nd	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus	is	Salmonella	PEF	R	CIP	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX1	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX1	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	one_of	Staphylococcus aureus, Staphylococcus lugdunensis	PEN	R	AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC	R	Expert Rules on Staphylococcus	Expert Rules	3.3	all penicillins without beta-lactamse inhibitor
+genus	is	Staphylococcus	ERY, CLI	S	macrolides, lincosamides	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	NOR	S	CIP, LVX, MFX, OFX	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	LVX	R	fluoroquinolones	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	MFX	R	fluoroquinolones	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	TCY	S	DOX, MNO, TGC	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	TCY	R	DOX, MNO	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	VAN	S	lipoglycopeptides	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	LNZ	S	TZD	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+fullname	like	^Enterococcus (faecalis|faecium)	AMP	R	ureidopenicillins, IPM	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+fullname	like	^Enterococcus (faecalis|faecium)	AMX	R	ureidopenicillins, IPM	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus	is	Enterococcus	NOR	S	CIP, LVX	S	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus	is	Enterococcus	VAN	S	lipoglycopeptides	S	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus_species	is	Enterococcus faecium			CLI	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	PEN	S	aminopenicillins, cephalosporins, carbapenems	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	S	LVX, MFX	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	R	LVX, MFX	R	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	OXA	S	PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	NOR	S	LVX, MFX	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	NOR	R	LVX, MFX	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	LVX	R	fluoroquinolones	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	MFX	R	fluoroquinolones	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	TCY	S	DOX, MNO	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	TCY	R	DOX, MNO	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	VAN	S	lipoglycopeptides	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+fullname	like	^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	PEN	S	betalactams	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	NAL	S	fluoroquinolones	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	NAL	R	CIP, LVX, MFX	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	TCY	S	DOX, MNO	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	TCY	R	DOX, MNO	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis	NAL	S	fluoroquinolones	S	Expert Rules on Moraxella catarrhalis	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis	NAL	R	fluoroquinolones	R	Expert Rules on Moraxella catarrhalis	Expert Rules	3.3	
+genus	is	Campylobacter	ERY	S	CLR, AZM	S	Expert Rules on Campylobacter	Expert Rules	3.3	
+genus_species	is	Campylobacter	ERY	R	CLR, AZM	R	Expert Rules on Campylobacter	Expert Rules	3.3	
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument

data-raw/ex2.R

@@ -0,0 +1,13 @@
+ex2 <- example_isolates
+for (extra_id in seq_len(50)) {
+  ex2 <- ex2 %>% 
+    bind_rows(example_isolates %>% mutate(patient_id = paste0(patient_id, extra_id)))
+}
+# randomly clear antibibiograms of 2%
+clr <- sort(sample(x = seq_len(nrow(ex2)),
+                   size = nrow(ex2) * 0.02))
+for (row in which(is.rsi(ex2))) {
+  ex2[clr, row] <- NA_rsi_
+}
+
+

data-raw/intrinsicR.md5

@@ -0,0 +1 @@
+56b3cea0e28d8a54e0fcbd3e50af96fc

data-raw/intrinsic_resistant.md5

@@ -1 +1 @@
-9c58b2d894dbad7593cd44b78d04cd78
+d4e080899f438bc1eacb8ec9cfa117b8

data-raw/loinc.R

@@ -6,7 +6,7 @@
 # https://github.com/msberends/AMR                                     #
 #                                                                      #
 # LICENCE                                                              #
-# (c) 2018-2021 Berends MS, Luz CF et al.                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
 # Diagnostics & Advice, and University Medical Center Groningen.       # 

data-raw/microorganisms.old.md5

@@ -1 +1 @@
-8338ff5f079f4519fa3c44f8c5bace64
+ee4434541c7b6529b391d2684748e28b