Update DESCRIPTION

.github/prehooks/pre-commit

@@ -69,16 +69,10 @@ if [ "$currenttag" = "" ]; then
 else
   # there is a tag, so base version number on that
   currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
-  if (( "$currentcommit" == 0 )); then
-    # tag is new, so this must become the version number
-    currentversion="$currenttag"
-  fi
   echo "- latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
 fi
-if [ "$currentversion" = "" ]; then
-  # combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
-  currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
-fi
+# combine tag (e.g. 1.2.3) and commit number (like 5) increased by 9000 to indicate beta version
+currentversion="$currenttag.$((currentcommit + 9001))" # results in e.g. 1.2.3.9005
 echo "- ${currentpkg} pkg version set to ${currentversion}"
 
 # set version number and date to DESCRIPTION file

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.1.0
-Date: 2023-07-16 07:05:11 UTC
-SHA: 7a4628b73f91aad903f841c4275c8a68eea318b8
+Version: 2.1.1
+Date: 2023-10-20 16:05:16 UTC
+SHA: ca72a646d041f7f096c4e196e8ae2fb2b176019c

DESCRIPTION

@@ -1,13 +1,12 @@
 Package: AMR
-Version: 2.1.0
-Date: 2023-07-16
+Version: 2.1.1.9017
+Date: 2024-04-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by
   using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
 Authors@R: c(
   person(family = "Berends",     c("Matthijs", "S."), role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
-  person(family = "Luz",         c("Christian", "F."), role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-5809-5995")),
   person(family = "Souverein",   c("Dennis"), role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
   person(family = "Hassing",     c("Erwin", "E.", "A."), role = c("aut", "ctb")),
   person(family = "Albers",      c("Casper", "J."), role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
@@ -18,36 +17,40 @@ Authors@R: c(
   person(family = "Hazenberg",   c("Eric", "H.", "L.", "C.", "M."), role = "ctb"),
   person(family = "Knight",      c("Gwen"), role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
   person(family = "Lenglet",     c("Annick"), role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
+  person(family = "Luz",         c("Christian", "F."), role = c("ctb"), comment = c(ORCID = "0000-0001-5809-5995")),
   person(family = "Meijer",      c("Bart", "C."), role = "ctb"),
   person(family = "Mykhailenko", c("Dmytro"), role = "ctb"),
   person(family = "Mymrikov",    c("Anton"), role = "ctb"),
   person(family = "Norgan",      c("Andrew", "P."), role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
   person(family = "Ny",          c("Sofia"), role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
+  person(family = "Saab",        c("Matthew"), role = "ctb"),
   person(family = "Salm",        c("Jonas"), role = "ctb"),
+  person(family = "Sanchez",     c("Javier"), role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
   person(family = "Schade",      c("Rogier", "P."), role = "ctb"),
   person(family = "Sinha",       c("Bhanu", "N.", "M."), role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
+  person(family = "Stull",       c("Jason"), role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
   person(family = "Underwood",   c("Anthony"), role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
   person(family = "Williams",    c("Anita"), role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")))
 Depends: R (>= 3.0.0)
-Enhances:
-  cleaner,
-  ggplot2,
-  janitor,
-  skimr,
-  tibble,
-  tidyselect,
-  tsibble
 Suggests: 
+  cleaner,
   cli,
   curl,
   data.table,
   dplyr,
+  ggplot2,
+  janitor,
   knitr,
   progress,
   readxl,
   rmarkdown,
   rvest,
+  skimr,
+  tibble,
+  tidyselect,
   tinytest,
+  tsibble,
+  vctrs,
   xml2
 VignetteBuilder: knitr,rmarkdown
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
@@ -55,5 +58,5 @@ BugReports: https://github.com/msberends/AMR/issues
 License: GPL-2 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,22 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("!",mic)
 S3method("!=",ab_selector)
-S3method("!=",mic)
-S3method("%%",mic)
-S3method("%/%",mic)
 S3method("&",ab_selector)
-S3method("&",mic)
-S3method("*",mic)
-S3method("+",mic)
-S3method("-",mic)
-S3method("/",mic)
-S3method("<",mic)
-S3method("<=",mic)
 S3method("==",ab_selector)
-S3method("==",mic)
-S3method(">",mic)
-S3method(">=",mic)
 S3method("[",ab)
 S3method("[",av)
 S3method("[",disk)
@@ -27,7 +13,6 @@ S3method("[<-",av)
 S3method("[<-",disk)
 S3method("[<-",mic)
 S3method("[<-",mo)
-S3method("[<-",rsi)
 S3method("[<-",sir)
 S3method("[[",ab)
 S3method("[[",av)
@@ -39,44 +24,34 @@ S3method("[[<-",av)
 S3method("[[<-",disk)
 S3method("[[<-",mic)
 S3method("[[<-",mo)
-S3method("[[<-",rsi)
 S3method("[[<-",sir)
-S3method("^",mic)
 S3method("|",ab_selector)
-S3method("|",mic)
-S3method(abs,mic)
-S3method(acos,mic)
-S3method(acosh,mic)
+S3method(Complex,mic)
+S3method(Math,mic)
+S3method(Ops,mic)
+S3method(Summary,mic)
 S3method(all,ab_selector)
 S3method(all,ab_selector_any_all)
-S3method(all,mic)
 S3method(any,ab_selector)
 S3method(any,ab_selector_any_all)
-S3method(any,mic)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,av)
+S3method(as.data.frame,mic)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)
 S3method(as.list,custom_eucast_rules)
 S3method(as.list,custom_mdro_guideline)
+S3method(as.list,mic)
 S3method(as.matrix,mic)
 S3method(as.numeric,mic)
-S3method(as.rsi,data.frame)
-S3method(as.rsi,default)
-S3method(as.rsi,disk)
-S3method(as.rsi,mic)
 S3method(as.sir,data.frame)
 S3method(as.sir,default)
 S3method(as.sir,disk)
 S3method(as.sir,mic)
-S3method(asin,mic)
-S3method(asinh,mic)
-S3method(atan,mic)
-S3method(atanh,mic)
+S3method(as.vector,mic)
 S3method(barplot,antibiogram)
 S3method(barplot,disk)
 S3method(barplot,mic)
-S3method(barplot,rsi)
 S3method(barplot,sir)
 S3method(c,ab)
 S3method(c,ab_selector)
@@ -86,36 +61,15 @@ S3method(c,custom_mdro_guideline)
 S3method(c,disk)
 S3method(c,mic)
 S3method(c,mo)
-S3method(c,rsi)
 S3method(c,sir)
-S3method(ceiling,mic)
 S3method(close,progress_bar)
-S3method(cos,mic)
-S3method(cosh,mic)
-S3method(cospi,mic)
-S3method(cummax,mic)
-S3method(cummin,mic)
-S3method(cumprod,mic)
-S3method(cumsum,mic)
-S3method(digamma,mic)
 S3method(droplevels,mic)
-S3method(droplevels,rsi)
 S3method(droplevels,sir)
-S3method(exp,mic)
-S3method(expm1,mic)
-S3method(floor,mic)
 S3method(format,bug_drug_combinations)
-S3method(gamma,mic)
 S3method(hist,mic)
 S3method(kurtosis,data.frame)
 S3method(kurtosis,default)
 S3method(kurtosis,matrix)
-S3method(lgamma,mic)
-S3method(log,mic)
-S3method(log10,mic)
-S3method(log1p,mic)
-S3method(log2,mic)
-S3method(max,mic)
 S3method(mean,mic)
 S3method(mean_amr_distance,data.frame)
 S3method(mean_amr_distance,default)
@@ -123,12 +77,10 @@ S3method(mean_amr_distance,disk)
 S3method(mean_amr_distance,mic)
 S3method(mean_amr_distance,sir)
 S3method(median,mic)
-S3method(min,mic)
 S3method(plot,antibiogram)
 S3method(plot,disk)
 S3method(plot,mic)
 S3method(plot,resistance_predict)
-S3method(plot,rsi)
 S3method(plot,sir)
 S3method(print,ab)
 S3method(print,av)
@@ -141,46 +93,27 @@ S3method(print,mo)
 S3method(print,mo_renamed)
 S3method(print,mo_uncertainties)
 S3method(print,pca)
-S3method(print,rsi)
 S3method(print,sir)
-S3method(prod,mic)
 S3method(quantile,mic)
-S3method(range,mic)
 S3method(rep,ab)
 S3method(rep,av)
 S3method(rep,disk)
 S3method(rep,mic)
 S3method(rep,mo)
-S3method(rep,rsi)
 S3method(rep,sir)
-S3method(round,mic)
-S3method(sign,mic)
-S3method(signif,mic)
-S3method(sin,mic)
-S3method(sinh,mic)
-S3method(sinpi,mic)
 S3method(skewness,data.frame)
 S3method(skewness,default)
 S3method(skewness,matrix)
 S3method(sort,mic)
-S3method(sqrt,mic)
-S3method(sum,mic)
 S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,pca)
-S3method(summary,rsi)
 S3method(summary,sir)
-S3method(tan,mic)
-S3method(tanh,mic)
-S3method(tanpi,mic)
-S3method(trigamma,mic)
-S3method(trunc,mic)
 S3method(unique,ab)
 S3method(unique,av)
 S3method(unique,disk)
 S3method(unique,mic)
 S3method(unique,mo)
-S3method(unique,rsi)
 S3method(unique,sir)
 export("%like%")
 export("%like_case%")
@@ -188,7 +121,6 @@ export("%unlike%")
 export("%unlike_case%")
 export(NA_disk_)
 export(NA_mic_)
-export(NA_rsi_)
 export(NA_sir_)
 export(ab_atc)
 export(ab_atc_group1)
@@ -227,7 +159,6 @@ export(as.av)
 export(as.disk)
 export(as.mic)
 export(as.mo)
-export(as.rsi)
 export(as.sir)
 export(atc_online_ddd)
 export(atc_online_ddd_units)
@@ -273,21 +204,17 @@ export(custom_mdro_guideline)
 export(eucast_dosage)
 export(eucast_exceptional_phenotypes)
 export(eucast_rules)
-export(facet_rsi)
 export(facet_sir)
 export(filter_first_isolate)
 export(first_isolate)
 export(fluoroquinolones)
 export(full_join_microorganisms)
 export(g.test)
-export(geom_rsi)
 export(geom_sir)
 export(get_AMR_locale)
 export(get_episode)
 export(get_mo_source)
 export(ggplot_pca)
-export(ggplot_rsi)
-export(ggplot_rsi_predict)
 export(ggplot_sir)
 export(ggplot_sir_predict)
 export(glycopeptides)
@@ -298,8 +225,6 @@ export(is.av)
 export(is.disk)
 export(is.mic)
 export(is.mo)
-export(is.rsi)
-export(is.rsi.eligible)
 export(is.sir)
 export(is_new_episode)
 export(is_sir_eligible)
@@ -307,10 +232,10 @@ export(italicise_taxonomy)
 export(italicize_taxonomy)
 export(key_antimicrobials)
 export(kurtosis)
-export(labels_rsi_count)
 export(labels_sir_count)
 export(left_join_microorganisms)
 export(like)
+export(limit_mic_range)
 export(lincosamides)
 export(lipoglycopeptides)
 export(macrolides)
@@ -360,7 +285,6 @@ export(mo_uncertainties)
 export(mo_url)
 export(mo_year)
 export(mrgn)
-export(n_rsi)
 export(n_sir)
 export(not_intrinsic_resistant)
 export(oxazolidinones)
@@ -376,16 +300,16 @@ export(proportion_df)
 export(quinolones)
 export(random_disk)
 export(random_mic)
-export(random_rsi)
 export(random_sir)
 export(reset_AMR_locale)
 export(resistance)
 export(resistance_predict)
 export(right_join_microorganisms)
-export(rsi_df)
-export(rsi_predict)
-export(scale_rsi_colours)
+export(scale_colour_mic)
+export(scale_fill_mic)
 export(scale_sir_colours)
+export(scale_x_mic)
+export(scale_y_mic)
 export(scale_y_percent)
 export(semi_join_microorganisms)
 export(set_AMR_locale)
@@ -399,7 +323,6 @@ export(skewness)
 export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
-export(theme_rsi)
 export(theme_sir)
 export(translate_AMR)
 export(trimethoprims)

NEWS.md

@@ -1,3 +1,49 @@
+# AMR 2.1.1.9017
+
+*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
+
+#### A New Milestone: One Health Support (= Human + Veterinary + Environmental)
+This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
+
+## Breaking
+* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over a year ago
+
+## New
+* One Health implementation
+  * Function `as.sir()` now has extensive support for animal breakpoints from CLSI. Use `breakpoint_type = "animal"` and set the `host` argument to a variable that contains animal species names.
+  * The `clinical_breakpoints` data set contains all these breakpoints, and can be downloaded on our [download page](https://msberends.github.io/AMR/articles/datasets.html).
+  * The `antibiotics` data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
+  * `ab_atc()` now supports ATC codes of veterinary antibiotics (that all start with "Q")
+  * `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
+* The function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
+* Function `limit_mic_range()`, which allows to limit MIC values to a manually set range. This is the powerhouse behind the `scale_*_mic()` functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
+
+## Changed
+* For MICs:
+  * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
+  * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `limit_mic_range()` and `scale_*_mic()` functions.
+  * Comparisons of MIC values are now more strict. For example, `>32` is higher than (and never equal to) `32`. Thus, `as.mic(">32") == as.mic(32)` now returns `FALSE`, and `as.mic(">32") > as.mic(32)` now returns `TRUE`.
+* Updated `italicise_taxonomy()` to support HTML
+* Greatly improved `vctrs` integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as `dplyr`'s `bind_rows()`, `rowwise()` and `c_across()` are now supported for e.g. columns of class `mic`. Despite this, this `AMR` package is still zero-dependent on any other package, including `dplyr` and `vctrs`.
+* Updated all ATC codes from WHOCC
+* Updated all antibiotic DDDs from WHOCC
+
+## Other
+* Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
+
+
+# AMR 2.1.1
+
+* Fix for selecting first isolates using the phenotype-based method
+  * This included too many isolates when patients had altering antibiograms within the same bacterial species
+  * See for more info [our issue #122](https://github.com/msberends/AMR/issues/122)
+* Added 1,366 LOINC codes to the `antibiotics` data set and updated to the latest version (LOINC v2.76)
+* MICs can now be used in complex number calculations and allow scientific number format as input (e.g., `as.mic("1.28e-2")`)
+* Fix rounding MICs on latest R beta ('R-devel')
+* Removed unneeded note about the used language when option `AMR_locale` is set
+* Fixed non-ASCII characters in documentation, according to CRAN maintainers
+
+
 # AMR 2.1.0
 
 ## New
@@ -120,7 +166,7 @@ The new function `add_custom_antimicrobials()` allows users to add custom antimi
 
 The `antibiotics` data set was greatly updated:
 
-  * The following 20 antibiotics have been added (also includes the [new J01RA ATC group](https://www.whocc.no/atc_ddd_index/?code=J01RA&showdescription=no)): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)
+  * The following 20 antibiotics have been added (also includes the [new J01RA ATC group](https://atcddd.fhi.no/atc_ddd_index/?code=J01RA&showdescription=no)): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)
   * Added some missing ATC codes
   * Updated DDDs and PubChem Compound IDs
   * Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -> cefalexin, and phenethicillin -> pheneticillin)
@@ -133,7 +179,7 @@ Also, we added support for using antibiotic selectors in scoped `dplyr` verbs (w
 
 We now added extensive support for antiviral agents! For the first time, the `AMR` package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.
 
-* The `antivirals` data set has been extended with 18 new drugs (also from the [new J05AJ ATC group](https://www.whocc.no/atc_ddd_index/?code=J05AJ&showdescription=no)) and now also contains antiviral identifiers and LOINC codes
+* The `antivirals` data set has been extended with 18 new drugs (also from the [new J05AJ ATC group](https://atcddd.fhi.no/atc_ddd_index/?code=J05AJ&showdescription=no)) and now also contains antiviral identifiers and LOINC codes
 * A new data type `av` (*antivirals*) has been added, which is functionally similar to `ab` for antibiotics
 * Functions `as.av()`, `av_name()`, `av_atc()`, `av_synonyms()`, `av_from_text()` have all been added as siblings to their `ab_*()` equivalents
 
@@ -191,4 +237,4 @@ We now added extensive support for antiviral agents! For the first time, the `AM
 
 ----
 
-This changelog only contains changes from AMR v2.0 and later. For prior versions, please see [our archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).
+This changelog only contains changes from AMR v2.0 (January 2023) and later. For prior versions, please see [our archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).

R/aa_amr-package.R

@@ -34,9 +34,9 @@
 #'
 #' The `AMR` package is a [free and open-source](https://msberends.github.io/AMR/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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 AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. [Many different researchers](https://msberends.github.io/AMR/authors.html) from around the globe are continually helping us to make this a successful and durable project!
 #'
-#' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
+#' This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
 #'
-#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://msberends.github.io/AMR/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antibiotics) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://msberends.github.io/AMR/reference/antibiotics.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (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](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl).
+#' After installing this package, R knows [**`r format_included_data_number(AMR::microorganisms)` microorganisms**](https://msberends.github.io/AMR/reference/microorganisms.html) (updated `r format(TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r format_included_data_number(nrow(AMR::antibiotics) + nrow(AMR::antivirals))` antibiotic, antimycotic and antiviral drugs**](https://msberends.github.io/AMR/reference/antibiotics.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (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 public [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl).
 #'
 #' The `AMR` package is available in `r vector_and(vapply(FUN.VALUE = character(1), LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
 #' @section Reference Data Publicly Available:
@@ -44,7 +44,7 @@
 #' @source
 #' To cite AMR in publications use:
 #'
-#' Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). "AMR: An R Package for Working with Antimicrobial Resistance Data." _Journal of Statistical Software_, *104*(3), 1-31. \doi{10.18637/jss.v104.i03}.
+#' Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). "AMR: An R Package for Working with Antimicrobial Resistance Data." _Journal of Statistical Software_, *104*(3), 1-31. \doi{10.18637/jss.v104.i03}
 #'
 #' A BibTeX entry for LaTeX users is:
 #'

R/aa_globals.R

@@ -86,8 +86,8 @@ EUCAST_VERSION_EXPERT_RULES <- list(
 
 TAXONOMY_VERSION <- list(
   GBIF = list(
-    accessed_date = as.Date("2022-12-11"),
-    citation = "GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
+    accessed_date = as.Date("2024-01-08"),
+    citation = "GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
     url = "https://www.gbif.org"
   ),
   LPSN = list(
@@ -102,17 +102,18 @@ TAXONOMY_VERSION <- list(
   ),
   SNOMED = list(
     accessed_date = as.Date("2021-07-01"),
-    citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
+    citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
     url = "https://phinvads.cdc.gov"
   ),
   LOINC = list(
-    accessed_date = as.Date("2022-10-30"),
-    citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022).",
+    accessed_date = as.Date("2023-10-19"),
+    citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023).",
     url = "https://loinc.org"
   )
 )
 
 globalVariables(c(
+  ".GenericCallEnv",
   ".mo",
   ".rowid",
   ".syndromic_group",
@@ -145,6 +146,8 @@ globalVariables(c(
   "group",
   "guideline",
   "hjust",
+  "host_index",
+  "host_match",
   "input",
   "intrinsic_resistant",
   "isolates",

R/aa_helper_functions.R

@@ -237,7 +237,7 @@ addin_insert_like <- function() {
   }
 }
 
-search_type_in_df <- function(x, type, info = TRUE) {
+search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
   meet_criteria(x, allow_class = "data.frame")
   meet_criteria(type, allow_class = "character", has_length = 1)
 
@@ -280,7 +280,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
       if (!inherits(pm_pull(x, found), c("Date", "POSIXct"))) {
         stop(
           font_red(paste0(
-            "Found column '", font_bold(found), "' to be used as input for `col_", type,
+            "Found column '", font_bold(found), "' to be used as input for `", ifelse(add_col_prefix, "col_", ""), type,
             "`, but this column contains no valid dates. Transform its values to valid dates first."
           )),
           call. = FALSE
@@ -311,6 +311,14 @@ search_type_in_df <- function(x, type, info = TRUE) {
       found <- sort(colnames(x)[colnames_formatted %like_case% "^(specimen)"])
     }
   }
+  # -- host (animals)
+  if (type == "host") {
+    if (any(colnames_formatted %like_case% "^(host|animal)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "^(host|animal)"])
+    } else if (any(colnames_formatted %like_case% "((^|[^A-Za-z])host($|[^A-Za-z])|animal)")) {
+      found <- sort(colnames(x)[colnames_formatted %like_case% "((^|[^A-Za-z])host($|[^A-Za-z])|animal)"])
+    }
+  }
   # -- UTI (urinary tract infection)
   if (type == "uti") {
     if (any(colnames_formatted == "uti")) {
@@ -321,7 +329,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
     if (!is.null(found)) {
       # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
-        message_("Column '", font_bold(found), "' found as input for `col_", type,
+        message_("Column '", font_bold(found), "' found as input for `", ifelse(add_col_prefix, "col_", ""), type,
           "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
           add_fn = font_red
         )
@@ -334,9 +342,9 @@ search_type_in_df <- function(x, type, info = TRUE) {
 
   if (!is.null(found) && isTRUE(info)) {
     if (message_not_thrown_before("search_in_type", type)) {
-      msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
+      msg <- paste0("Using column '", font_bold(found), "' as input for `", ifelse(add_col_prefix, "col_", ""), type, "`.")
       if (type %in% c("keyantibiotics", "keyantimicrobials", "specimen")) {
-        msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
+        msg <- paste(msg, "Use", font_bold(paste0(ifelse(add_col_prefix, "col_", ""), type), "= FALSE"), "to prevent this.")
       }
       message_(msg)
     }
@@ -456,7 +464,8 @@ word_wrap <- function(...,
   ops <- "([,./><\\]\\[])"
   msg <- gsub(paste0(ops, " ", ops), "\\1\\2", msg, perl = TRUE)
   # we need to correct for already applied style, that adds text like "\033[31m\"
-  msg_stripped <- font_stripstyle(msg)
+  msg_stripped <- gsub("(.*)?\\033\\]8;;.*\\a(.*?)\\033\\]8;;\\a(.*)", "\\1\\2\\3", msg, perl = TRUE) # for font_url()
+  msg_stripped <- font_stripstyle(msg_stripped)
   # where are the spaces now?
   msg_stripped_wrapped <- paste0(
     strwrap(msg_stripped,
@@ -862,12 +871,20 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
       object <- tolower(object)
       is_in <- tolower(is_in)
     }
-    stop_ifnot(all(object %in% is_in, na.rm = TRUE), "argument `", obj_name, "` ",
+    is_in.bak <- is_in
+    if ("logical" %in% allow_class) {
+      is_in <- is_in[!is_in %in% c("TRUE", "FALSE")]
+    }
+    or_values <- vector_or(is_in, quotes = !isTRUE(any(c("numeric", "integer") %in% allow_class)))
+    if ("logical" %in% allow_class) {
+      or_values <- paste0(or_values, ", or TRUE or FALSE")
+    }
+    stop_ifnot(all(object %in% is_in.bak, na.rm = TRUE), "argument `", obj_name, "` ",
       ifelse(!is.null(has_length) && length(has_length) == 1 && has_length == 1,
         "must be either ",
         "must only contain values "
       ),
-      vector_or(is_in, quotes = !isTRUE(any(c("double", "numeric", "integer") %in% allow_class))),
+      or_values,
       ifelse(allow_NA == TRUE, ", or NA", ""),
       call = call_depth
     )
@@ -1551,7 +1568,7 @@ readRDS_AMR <- function(file, refhook = NULL) {
 match <- function(x, table, ...) {
   if (!is.null(AMR_env$chmatch) && inherits(x, "character") && inherits(table, "character")) {
     # data.table::chmatch() is much faster than base::match() for character
-    AMR_env$chmatch(x, table, ...)
+    tryCatch(AMR_env$chmatch(x, table, ...), error = function(e) base::match(x, table, ...))
   } else {
     base::match(x, table, ...)
   }
@@ -1559,7 +1576,7 @@ match <- function(x, table, ...) {
 `%in%` <- function(x, table) {
   if (!is.null(AMR_env$chin) && inherits(x, "character") && inherits(table, "character")) {
     # data.table::`%chin%`() is much faster than base::`%in%`() for character
-    AMR_env$chin(x, table)
+    tryCatch(AMR_env$chin(x, table), error = function(e) base::`%in%`(x, table))
   } else {
     base::`%in%`(x, table)
   }

R/aa_options.R

@@ -31,19 +31,19 @@
 #'
 #' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
 #' @section Options:
-#' * `AMR_custom_ab` \cr Allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
-#' * `AMR_custom_mo` \cr Allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
-#' * `AMR_eucastrules` \cr Used for setting the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
-#' * `AMR_guideline` \cr Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
+#' * `AMR_breakpoint_type` \cr A [character] to use in [as.sir()], to indicate which breakpoint type to use. This must be either `r vector_or(clinical_breakpoints$type)`.
+#' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
+#' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
+#' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
+#' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
+#' * `AMR_guideline` \cr A [character] to set the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
 #' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to ignore (i.e., make `NA`) any match given in [as.mo()] and all [`mo_*`][mo_property()] functions.
 #' * `AMR_include_PKPD` \cr A [logical] to use in [as.sir()], to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`.
-#' * `AMR_ecoff` \cr A [logical] use in [as.sir()], to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is `FALSE`.
 #' * `AMR_include_screening` \cr A [logical] to use in [as.sir()], to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`.
 #' * `AMR_keep_synonyms` \cr A [logical] to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`.
-#' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
-#' * `AMR_locale` \cr A language to use for the `AMR` package, can be one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. The default is the current system language (if supported).
+#' * `AMR_locale` \cr A [character] to set the language for the `AMR` package, can be one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. The default is the current system language (if supported, English otherwise).
 #' * `AMR_mo_source` \cr A file location for a manual code list to be used in [as.mo()] and all [`mo_*`][mo_property()] functions. This is explained in [set_mo_source()].
-#'
+#' 
 #' @section Saving Settings Between Sessions:
 #' Settings in \R are not saved globally and are thus lost when \R is exited. You can save your options to your own `.Rprofile` file, which is a user-specific file. You can edit it using:
 #'
@@ -51,18 +51,18 @@
 #'   utils::file.edit("~/.Rprofile")
 #' ```
 #'
-#' In this file, you can set options such as:
+#' In this file, you can set options such as...
 #'
 #' ```r
 #'  options(AMR_locale = "pt")
 #'  options(AMR_include_PKPD = TRUE)
 #'  ```
 #'
-#' to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with [as.sir()].
+#' ...to add Portuguese language support of antibiotics, and allow PK/PD rules when interpreting MIC values with [as.sir()].
 #'
 #' ### Share Options Within Team
 #'
-#' For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
+#' For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
 #'
 #' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
 #'

R/ab.R

@@ -51,7 +51,7 @@
 #'
 #' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
 #' @section Source:
-#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
+#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases ab
@@ -117,8 +117,8 @@ 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|gender|^dates?$)", "", x, ignore.case = TRUE, perl = TRUE)
-  # penicillin is a special case: we call it so, but then mean benzylpenicillin
+  x <- gsub("(specimen|specimen date|specimen_date|spec_date|gender|^dates?$|animal|host($|[a-z]))", "", x, ignore.case = TRUE, perl = TRUE)
+  # penicillin is a special case: we call it so, but then most often mean benzylpenicillin
   x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
   x_bak_clean <- x
   if (already_regex == FALSE) {

R/ab_property.R

@@ -245,7 +245,7 @@ ab_ddd <- function(x, administration = "oral", ...) {
     warning_(
       "in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
-      "www.whocc.no/ddd/list_of_ddds_combined_products/"
+      "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
   }
   out
@@ -265,7 +265,7 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
     warning_(
       "in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
-      "www.whocc.no/ddd/list_of_ddds_combined_products/"
+      "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
   }
   out
@@ -310,7 +310,10 @@ ab_url <- function(x, open = FALSE, ...) {
 
   ab <- as.ab(x = x, ...)
   atcs <- ab_atc(ab, only_first = TRUE)
-  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
+  u <- character(length(atcs))
+  # veterinary codes
+  u[atcs %like% "^Q"] <- paste0("https://atcddd.fhi.no/atcvet/atcvet_index/?code=", atcs[atcs %like% "^Q"], "&showdescription=no")
+  u[atcs %unlike% "^Q"] <- paste0("https://atcddd.fhi.no/atc_ddd_index//?code=", atcs[atcs %unlike% "^Q"], "&showdescription=no")
   u[is.na(atcs)] <- NA_character_
   names(u) <- ab_name(ab)
 

R/ab_selectors.R

@@ -226,10 +226,6 @@ ab_class <- function(ab_class,
   meet_criteria(ab_class, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec(NULL, only_sir_columns = only_sir_columns, ab_class_args = ab_class, only_treatable = only_treatable)
 }
 
@@ -242,10 +238,6 @@ ab_selector <- function(filter,
                         ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
 
   # 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
@@ -277,10 +269,6 @@ ab_selector <- function(filter,
 aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("aminoglycosides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
@@ -288,10 +276,6 @@ aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...
 #' @export
 aminopenicillins <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("aminopenicillins", only_sir_columns = only_sir_columns)
 }
 
@@ -299,10 +283,6 @@ aminopenicillins <- function(only_sir_columns = FALSE, ...) {
 #' @export
 antifungals <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("antifungals", only_sir_columns = only_sir_columns)
 }
 
@@ -310,10 +290,6 @@ antifungals <- function(only_sir_columns = FALSE, ...) {
 #' @export
 antimycobacterials <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("antimycobacterials", only_sir_columns = only_sir_columns)
 }
 
@@ -322,10 +298,6 @@ antimycobacterials <- function(only_sir_columns = FALSE, ...) {
 betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
@@ -334,10 +306,6 @@ betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
 carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("carbapenems", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
@@ -345,10 +313,6 @@ carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
 #' @export
 cephalosporins <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins", only_sir_columns = only_sir_columns)
 }
 
@@ -356,10 +320,6 @@ cephalosporins <- function(only_sir_columns = FALSE, ...) {
 #' @export
 cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins_1st", only_sir_columns = only_sir_columns)
 }
 
@@ -367,10 +327,6 @@ cephalosporins_1st <- function(only_sir_columns = FALSE, ...) {
 #' @export
 cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins_2nd", only_sir_columns = only_sir_columns)
 }
 
@@ -378,10 +334,6 @@ cephalosporins_2nd <- function(only_sir_columns = FALSE, ...) {
 #' @export
 cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns)
 }
 
@@ -389,10 +341,6 @@ cephalosporins_3rd <- function(only_sir_columns = FALSE, ...) {
 #' @export
 cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins_4th", only_sir_columns = only_sir_columns)
 }
 
@@ -400,10 +348,6 @@ cephalosporins_4th <- function(only_sir_columns = FALSE, ...) {
 #' @export
 cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("cephalosporins_5th", only_sir_columns = only_sir_columns)
 }
 
@@ -411,10 +355,6 @@ cephalosporins_5th <- function(only_sir_columns = FALSE, ...) {
 #' @export
 fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns)
 }
 
@@ -422,10 +362,6 @@ fluoroquinolones <- function(only_sir_columns = FALSE, ...) {
 #' @export
 glycopeptides <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("glycopeptides", only_sir_columns = only_sir_columns)
 }
 
@@ -433,10 +369,6 @@ glycopeptides <- function(only_sir_columns = FALSE, ...) {
 #' @export
 lincosamides <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("lincosamides", only_sir_columns = only_sir_columns)
 }
 
@@ -444,10 +376,6 @@ lincosamides <- function(only_sir_columns = FALSE, ...) {
 #' @export
 lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("lipoglycopeptides", only_sir_columns = only_sir_columns)
 }
 
@@ -455,10 +383,6 @@ lipoglycopeptides <- function(only_sir_columns = FALSE, ...) {
 #' @export
 macrolides <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("macrolides", only_sir_columns = only_sir_columns)
 }
 
@@ -466,10 +390,6 @@ macrolides <- function(only_sir_columns = FALSE, ...) {
 #' @export
 oxazolidinones <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("oxazolidinones", only_sir_columns = only_sir_columns)
 }
 
@@ -477,10 +397,6 @@ oxazolidinones <- function(only_sir_columns = FALSE, ...) {
 #' @export
 penicillins <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("penicillins", only_sir_columns = only_sir_columns)
 }
 
@@ -489,10 +405,6 @@ penicillins <- function(only_sir_columns = FALSE, ...) {
 polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("polymyxins", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
@@ -500,10 +412,6 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
 #' @export
 streptogramins <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
 }
 
@@ -511,10 +419,6 @@ streptogramins <- function(only_sir_columns = FALSE, ...) {
 #' @export
 quinolones <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
 }
 
@@ -522,10 +426,6 @@ quinolones <- function(only_sir_columns = FALSE, ...) {
 #' @export
 tetracyclines <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("tetracyclines", only_sir_columns = only_sir_columns)
 }
 
@@ -533,10 +433,6 @@ tetracyclines <- function(only_sir_columns = FALSE, ...) {
 #' @export
 trimethoprims <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("trimethoprims", only_sir_columns = only_sir_columns)
 }
 
@@ -544,10 +440,6 @@ trimethoprims <- function(only_sir_columns = FALSE, ...) {
 #' @export
 ureidopenicillins <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("ureidopenicillins", only_sir_columns = only_sir_columns)
 }
 
@@ -649,10 +541,10 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
     ),
     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))) {
+      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)
@@ -663,7 +555,7 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
       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))

R/atc_online.R

@@ -64,7 +64,7 @@
 #' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
 #' @export
 #' @rdname atc_online
-#' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
+#' @source <https://atcddd.fhi.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
 #' @examples
 #' \donttest{
 #' if (requireNamespace("curl") && requireNamespace("rvest") && requireNamespace("xml2")) {
@@ -81,9 +81,9 @@
 atc_online_property <- function(atc_code,
                                 property,
                                 administration = "O",
-                                url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
-                                url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
-  meet_criteria(atc_code, allow_class = "character")
+                                url = "https://atcddd.fhi.no/atc_ddd_index/?code=%s&showdescription=no",
+                                url_vet = "https://atcddd.fhi.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
+  meet_criteria(atc_code, allow_class = "character", allow_NA = TRUE)
   meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "unit", "Adm.R", "Note", "groups"), ignore.case = TRUE)
   meet_criteria(administration, allow_class = "character", has_length = 1)
   meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
@@ -128,6 +128,10 @@ atc_online_property <- function(atc_code,
 
   for (i in seq_len(length(atc_code))) {
     progress$tick()
+    
+    if (is.na(atc_code[i])) {
+      next
+    }
 
     if (atc_code[i] %like% "^Q") {
       # veterinary drugs, ATC_vet codes start with a "Q"
@@ -176,7 +180,7 @@ atc_online_property <- function(atc_code,
       colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
 
       if (length(out) == 0) {
-        warning_("in `atc_online_property()`: ATC not found: ", atc_code[i], ". Please check ", atc_url, ".")
+        message_("in `atc_online_property()`: no properties found for ATC ", atc_code[i], ". Please check ", font_url(atc_url, "this WHOCC webpage"), ".")
         returnvalue[i] <- NA
         next
       }
@@ -209,20 +213,20 @@ atc_online_property <- function(atc_code,
 #' @rdname atc_online
 #' @export
 atc_online_groups <- function(atc_code, ...) {
-  meet_criteria(atc_code, allow_class = "character")
+  meet_criteria(atc_code, allow_class = "character", allow_NA = TRUE)
   atc_online_property(atc_code = atc_code, property = "groups", ...)
 }
 
 #' @rdname atc_online
 #' @export
 atc_online_ddd <- function(atc_code, ...) {
-  meet_criteria(atc_code, allow_class = "character")
+  meet_criteria(atc_code, allow_class = "character", allow_NA = TRUE)
   atc_online_property(atc_code = atc_code, property = "ddd", ...)
 }
 
 #' @rdname atc_online
 #' @export
 atc_online_ddd_units <- function(atc_code, ...) {
-  meet_criteria(atc_code, allow_class = "character")
+  meet_criteria(atc_code, allow_class = "character", allow_NA = TRUE)
   atc_online_property(atc_code = atc_code, property = "unit", ...)
 }

R/av.R

@@ -49,7 +49,7 @@
 #'
 #' Note: the [as.av()] and [`av_*`][av_property()] functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
 #' @section Source:
-#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
+#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/}
 #'
 #' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
 #' @aliases av

R/av_property.R

@@ -164,7 +164,7 @@ av_ddd <- function(x, administration = "oral", ...) {
     warning_(
       "in `av_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
-      "www.whocc.no/ddd/list_of_ddds_combined_products/"
+      "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
   }
   out
@@ -184,7 +184,7 @@ av_ddd_units <- function(x, administration = "oral", ...) {
     warning_(
       "in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
-      "www.whocc.no/ddd/list_of_ddds_combined_products/"
+      "atcddd.fhi.no/ddd/list_of_ddds_combined_products/"
     )
   }
   out
@@ -227,7 +227,7 @@ av_url <- function(x, open = FALSE, ...) {
 
   av <- as.av(x = x, ...)
   atcs <- av_atc(av, only_first = TRUE)
-  u <- paste0("https://www.whocc.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
+  u <- paste0("https://atcddd.fhi.no/atc_ddd_index/?code=", atcs, "&showdescription=no")
   u[is.na(atcs)] <- NA_character_
   names(u) <- av_name(av)
 

R/custom_antimicrobials.R

@@ -96,7 +96,7 @@
 #'
 #'
 #' # Add Co-fluampicil, which is one of the many J01CR50 codes, see
-#' # https://www.whocc.no/ddd/list_of_ddds_combined_products/
+#' # https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/
 #' add_custom_antimicrobials(
 #'   data.frame(
 #'     ab = "COFLU",

R/data.R

@@ -45,10 +45,10 @@
 #' - `oral_units`\cr Units of `oral_ddd`
 #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs
 #' - `iv_units`\cr Units of `iv_ddd`
-#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
+#' - `loinc`\cr All codes associated with the name of the antimicrobial drug from `r TAXONOMY_VERSION$LOINC$citation` Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
 #'
 #' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
-#' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. *This is a unique identifier.*
+#' - `av`\cr Antiviral ID as used in this package (such as `ACI`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. *This is a unique identifier.* Combinations are codes that contain a `+` to indicate this, such as `ATA+COBI` for atazanavir/cobicistat.
 #' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO. *This is a unique identifier.*
 #' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
 #' - `cid`\cr Compound ID as found in PubChem. *This is a unique identifier.*
@@ -58,7 +58,7 @@
 #' - `oral_units`\cr Units of `oral_ddd`
 #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
 #' - `iv_units`\cr Units of `iv_ddd`
-#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.
+#' - `loinc`\cr All codes associated with the name of the antiviral drug from `r TAXONOMY_VERSION$LOINC$citation` Use [av_loinc()] to retrieve them quickly, see [av_property()].
 #' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
 #'
 #' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
@@ -67,7 +67,7 @@
 #' Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit [our website for the download links](https://msberends.github.io/AMR/articles/datasets.html). The actual files are of course available on [our GitHub repository](https://github.com/msberends/AMR/tree/main/data-raw).
 #' @source
 #'
-#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://www.whocc.no/atc_ddd_index/>
+#' * World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): <https://atcddd.fhi.no/atc_ddd_index/>
 #'
 #' * `r TAXONOMY_VERSION$LOINC$citation` Accessed from <`r TAXONOMY_VERSION$LOINC$url`> on `r documentation_date(TAXONOMY_VERSION$LOINC$accessed_date)`.
 #'
@@ -91,7 +91,7 @@
 #' - `status` \cr Status of the taxon, either `r vector_or(microorganisms$status)`
 #' - `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, `species`, `subspecies`\cr Taxonomic rank of the microorganism
 #' - `rank`\cr Text of the taxonomic rank of the microorganism, such as `"species"` or `"genus"`
-#' - `ref`\cr Author(s) and year of related scientific publication. This contains only the *first surname* and year of the *latest* authors, e.g. "Wallis *et al.* 2006 *emend.* Smith and Jones 2018" becomes "Smith *et al.*, 2018". This field is directly retrieved from the source specified in the column `source`. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "V`r "\u00e1\u0148ov\u00e1"`" becomes "Vanova".
+#' - `ref`\cr Author(s) and year of related scientific publication. This contains only the *first surname* and year of the *latest* authors, e.g. "Wallis *et al.* 2006 *emend.* Smith and Jones 2018" becomes "Smith *et al.*, 2018". This field is directly retrieved from the source specified in the column `source`. Moreover, accents were removed to comply with CRAN that only allows ASCII characters.
 #' - `lpsn`\cr Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, *Acetobacter ascendens* has LPSN Record number 7864 and 11011. Only the first is available in the `microorganisms` data set.
 #' - `oxygen_tolerance` \cr Oxygen tolerance, either `r vector_or(microorganisms$oxygen_tolerance)`. These data were retrieved from BacDive (see *Source*). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently `r round(length(microorganisms$oxygen_tolerance[which(!is.na(microorganisms$oxygen_tolerance))]) / nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]) * 100, 1)`% of all `r format_included_data_number(nrow(microorganisms[which(microorganisms$kingdom == "Bacteria"), ]))` bacteria in the data set contain an oxygen tolerance.
 #' - `lpsn_parent`\cr LPSN identifier of the parent taxon
@@ -100,7 +100,7 @@
 #' - `gbif_parent`\cr GBIF identifier of the parent taxon
 #' - `gbif_renamed_to`\cr GBIF identifier of the currently valid taxon
 #' - `source`\cr Either `r vector_or(microorganisms$source)` (see *Source*)
-#' - `prevalence`\cr Prevalence of the microorganism according to Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}), see [mo_matching_score()] for the full explanation
+#' - `prevalence`\cr Prevalence of the microorganism based on Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}), see [mo_matching_score()] for the full explanation
 #' - `snomed`\cr Systematized Nomenclature of Medicine (SNOMED) code of the microorganism, version of `r documentation_date(TAXONOMY_VERSION$SNOMED$accessed_date)` (see *Source*). Use [mo_snomed()] to retrieve it quickly, see [mo_property()].
 #' @details
 #' Please note that entries are only based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF) (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.
@@ -262,10 +262,17 @@
 
 #' Data Set with Clinical Breakpoints for SIR Interpretation
 #'
-#' Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`). Use [as.sir()] to transform MICs or disks measurements to SIR values.
+#' @description Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, `r length(unique(clinical_breakpoints$host[!clinical_breakpoints$host %in% clinical_breakpoints$type]))` different animal groups, and ECOFFs.
+#' 
+#' Currently available breakpoint guidelines for **clinical microbiology** are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`.
+#' 
+#' Currently available breakpoint guidelines for **veterinary microbiology** are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`.
+#' 
+#' Use [as.sir()] to transform MICs or disks measurements to SIR values.
 #' @format A [tibble][tibble::tibble] with `r format(nrow(clinical_breakpoints), big.mark = " ")` observations and `r ncol(clinical_breakpoints)` variables:
 #' - `guideline`\cr Name of the guideline
 #' - `type`\cr Breakpoint type, either `r vector_or(clinical_breakpoints$type)`
+#' - `host`\cr Host of infectious agent. This is mostly useful for veterinary breakpoints and is either `r vector_or(clinical_breakpoints$host)`
 #' - `method`\cr Testing method, either `r vector_or(clinical_breakpoints$method)`
 #' - `site`\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory"
 #' - `mo`\cr Microbial ID, see [as.mo()]

R/disk.R

@@ -165,11 +165,6 @@ pillar_shaft.disk <- function(x, ...) {
   create_pillar_column(out, align = "right", width = 2)
 }
 
-# will be exported using s3_register() in R/zzz.R
-type_sum.disk <- function(x, ...) {
-  "disk"
-}
-
 #' @method print disk
 #' @export
 #' @noRd

R/eucast_rules.R

@@ -103,7 +103,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @section Antibiotics:
 #' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
 #'
-#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
+#' The following antibiotics are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://atcddd.fhi.no/atc/structure_and_principles/))', sorted alphabetically:
 #'
 #' `r create_eucast_ab_documentation()`
 #' @aliases EUCAST
@@ -184,7 +184,6 @@ eucast_rules <- function(x,
   meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "sir"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
-  if ("only_rsi_columns" %in% names(list(...))) only_sir_columns <- list(...)$only_rsi_columns
 
   add_MO_lookup_to_AMR_env()
 

R/first_isolate.R

@@ -227,10 +227,6 @@ first_isolate <- function(x = NULL,
   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)
   meet_criteria(include_unknown, allow_class = "logical", has_length = 1)
-  if ("include_untested_rsi" %in% names(list(...))) {
-    deprecation_warning("include_untested_rsi", "include_untested_sir", is_function = FALSE)
-    include_untested_sir <- list(...)$include_untested_rsi
-  }
   meet_criteria(include_untested_sir, allow_class = "logical", has_length = 1)
 
   # remove data.table, grouping from tibbles, etc.
@@ -347,8 +343,8 @@ first_isolate <- function(x = NULL,
 
   # create original row index
   x$newvar_row_index <- seq_len(nrow(x))
-  x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE])
-  x$newvar_genus_species <- paste(mo_genus(x$newvar_mo), mo_species(x$newvar_mo))
+  x$newvar_mo <- as.mo(x[, col_mo, drop = TRUE], keep_synonyms = TRUE, info = FALSE)
+  x$newvar_genus_species <- paste(mo_genus(x$newvar_mo, keep_synonyms = TRUE, info = FALSE), mo_species(x$newvar_mo, keep_synonyms = TRUE, info = FALSE))
   x$newvar_date <- x[, col_date, drop = TRUE]
   x$newvar_patient_id <- as.character(x[, col_patient_id, drop = TRUE])
 
@@ -443,7 +439,7 @@ first_isolate <- function(x = NULL,
   # did find some isolates - add new index numbers of rows
   x$newvar_row_index_sorted <- seq_len(nrow(x))
 
-  scope.size <- nrow(x[which(x$newvar_row_index_sorted %in% c(row.start + 1:row.end) &
+  scope.size <- nrow(x[which(x$newvar_row_index_sorted %in% seq(row.start, row.end, 1) &
     !is.na(x$newvar_mo)), , drop = FALSE])
 
   # Analysis of first isolate ----
@@ -467,41 +463,45 @@ first_isolate <- function(x = NULL,
 
   x$other_pat_or_mo <- !(x$newvar_patient_id == pm_lag(x$newvar_patient_id) & x$newvar_genus_species == pm_lag(x$newvar_genus_species))
 
-  x$episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
-
+  x$newvar_episode_group <- paste(x$newvar_patient_id, x$newvar_genus_species)
+  
   x$more_than_episode_ago <- unlist(
     lapply(
       split(
         x$newvar_date,
-        x$episode_group
+        x$newvar_episode_group
       ),
       is_new_episode,
-      episode_days = episode_days
+      episode_days = episode_days,
+      drop = FALSE
     ),
     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$newvar_key_ab),
-      type = type,
-      ignore_I = ignore_I,
-      points_threshold = points_threshold
+    # using phenotypes
+    x$different_antibiogram <- !unlist(
+      lapply(
+        split(
+          x$newvar_key_ab,
+          x$newvar_episode_group
+        ),
+        duplicated_antibiogram,
+        points_threshold = points_threshold,
+        ignore_I = ignore_I,
+        type = type
+      ),
+      use.names = FALSE
     )
-    x$newvar_first_isolate <- x$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$other_key_ab)
   } else {
-    # no key antibiotics
-    x$newvar_first_isolate <- x$newvar_row_index_sorted >= row.start &
-      x$newvar_row_index_sorted <= row.end &
-      x$newvar_genus_species != "" &
-      (x$other_pat_or_mo | x$more_than_episode_ago)
+    x$different_antibiogram <- FALSE
   }
   
+  x$newvar_first_isolate <- x$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$different_antibiogram)
+  
   decimal.mark <- getOption("OutDec")
   big.mark <- ifelse(decimal.mark != ",", ",", " ")
   
@@ -664,3 +664,48 @@ coerce_method <- function(method) {
   method[method %like% "^(i$|iso)"] <- "isolate-based"
   method
 }
+
+duplicated_antibiogram <- function(antibiogram, points_threshold, ignore_I, type) {
+  if (length(antibiogram) == 1) {
+    # fast return, only 1 isolate
+    return(FALSE)
+  }
+  out <- rep(NA, length(antibiogram))
+  out[1] <- FALSE
+  out[2] <- antimicrobials_equal(antibiogram[1], antibiogram[2],
+                                 ignore_I = ignore_I, points_threshold = points_threshold,
+                                 type = type)
+  if (length(antibiogram) == 2) {
+    # fast return, no further check required
+    return(out)
+  }
+  
+  # sort after the second one (since we already determined AB equality of the first two)
+  original_sort <- c(1, 2, rank(antibiogram[3:length(antibiogram)]) + 2)
+  antibiogram.bak <- antibiogram
+  antibiogram <- c(antibiogram[1:2], sort(antibiogram[3:length(antibiogram)]))
+  
+  # we can skip the duplicates - they are never unique antibiograms of course
+  duplicates <- duplicated(antibiogram)
+  out[3:length(out)][duplicates[3:length(out)] == TRUE] <- TRUE
+  if (all(duplicates[3:length(out)] == TRUE, na.rm = TRUE)) {
+    # fast return, no further check required
+    return(c(out[1:2], rep(TRUE, length(out) - 2)))
+  }
+  
+  for (na in antibiogram[is.na(out)]) {
+    # check if this antibiogram has any change with other antibiograms
+    out[which(antibiogram == na)] <- all(
+      vapply(FUN.VALUE = logical(1),
+             antibiogram[!is.na(out) & antibiogram != na],
+             function(y) antimicrobials_equal(y = y, z = na,
+                                              ignore_I = ignore_I, points_threshold = points_threshold,
+                                              type = type)))
+  }
+  
+  out <- out[original_sort]
+  # rerun duplicated again
+  duplicates <- duplicated(antibiogram.bak)
+  out[duplicates == TRUE] <- TRUE
+  out
+}

R/get_episode.R

@@ -221,11 +221,11 @@ exec_episode <- function(x, episode_days, case_free_days, ...) {
 
   # running as.double() on a POSIXct object will return its number of seconds since 1970-01-01
   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
   case_free_seconds <- case_free_days * 60 * 60 * 24
-
+  
   if (length(x) == 1) { # this will also match 1 NA, which is fine
     return(1)
   } else if (length(x) == 2 && all(!is.na(x))) {
@@ -241,7 +241,7 @@ exec_episode <- function(x, episode_days, case_free_days, ...) {
     }
   }
 
-  run_episodes <- function(x, episode_seconds, case_free) {
+  run_episodes <- function(x, episode_sec, case_free_sec) {
     NAs <- which(is.na(x))
     x[NAs] <- 0
 
@@ -250,8 +250,8 @@ exec_episode <- function(x, episode_days, case_free_days, ...) {
     ind <- 1
     indices[ind] <- 1
     for (i in 2:length(x)) {
-      if ((length(episode_seconds) > 0 && (x[i] - start) >= episode_seconds) ||
-        (length(case_free_seconds) > 0 && (x[i] - x[i - 1]) >= case_free_seconds)) {
+      if ((length(episode_sec) > 0 && (x[i] - start) >= episode_sec) ||
+        (length(case_free_sec) > 0 && (x[i] - x[i - 1]) >= case_free_sec)) {
         ind <- ind + 1
         start <- x[i]
       }

R/ggplot_pca.R

@@ -85,16 +85,18 @@
 #'   summary(pca_result)
 #'
 #'   # old base R plotting method:
-#'   biplot(pca_result)
+#'   biplot(pca_result, main = "Base R biplot")
 #'
 #'   # new ggplot2 plotting method using this package:
 #'   if (require("ggplot2")) {
-#'     ggplot_pca(pca_result)
-#'
+#'     ggplot_pca(pca_result) +
+#'       labs(title = "ggplot2 biplot")
+#'   }
+#'   if (require("ggplot2")) {
 #'     # still extendible with any ggplot2 function
 #'     ggplot_pca(pca_result) +
 #'       scale_colour_viridis_d() +
-#'       labs(title = "Title here")
+#'       labs(title = "ggplot2 biplot")
 #'   }
 #' }
 #' }

R/italicise_taxonomy.R

@@ -31,11 +31,11 @@
 #'
 #' According to the binomial nomenclature, the lowest four taxonomic levels (family, genus, species, subspecies) should be printed in italics. This function finds taxonomic names within strings and makes them italic.
 #' @param string a [character] (vector)
-#' @param type type of conversion of the taxonomic names, either "markdown" or "ansi", see *Details*
+#' @param type type of conversion of the taxonomic names, either "markdown", "html" or "ansi", see *Details*
 #' @details
 #' This function finds the taxonomic names and makes them italic based on the [microorganisms] data set.
 #'
-#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or using ANSI colours by adding `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
+#' The taxonomic names can be italicised using markdown (the default) by adding `*` before and after the taxonomic names, or `<i>` and `</i>` when using html. When using 'ansi', ANSI colours will be added using `\033[3m` before and `\033[23m` after the taxonomic names. If multiple ANSI colours are not available, no conversion will occur.
 #'
 #' This function also supports abbreviation of the genus if it is followed by a species, such as "E. coli" and "K. pneumoniae ozaenae".
 #' @export
@@ -44,18 +44,21 @@
 #' italicise_taxonomy("An overview of S. aureus isolates")
 #'
 #' cat(italicise_taxonomy("An overview of S. aureus isolates", type = "ansi"))
-italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
+italicise_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
   if (missing(type)) {
     type <- "markdown"
   }
   meet_criteria(string, allow_class = "character")
-  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi"))
+  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("markdown", "ansi", "html"))
 
   add_MO_lookup_to_AMR_env()
 
   if (type == "markdown") {
     before <- "*"
     after <- "*"
+  } else if (type == "html") {
+    before <- "<i>"
+    after <- "</i>"
   } else if (type == "ansi") {
     if (!has_colour() && !identical(Sys.getenv("IN_PKGDOWN"), "true")) {
       return(string)
@@ -134,7 +137,7 @@ italicise_taxonomy <- function(string, type = c("markdown", "ansi")) {
 
 #' @rdname italicise_taxonomy
 #' @export
-italicize_taxonomy <- function(string, type = c("markdown", "ansi")) {
+italicize_taxonomy <- function(string, type = c("markdown", "ansi", "html")) {
   if (missing(type)) {
     type <- "markdown"
   }

R/key_antimicrobials.R

@@ -149,10 +149,6 @@ key_antimicrobials <- function(x = NULL,
   meet_criteria(gram_positive, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(antifungal, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
 
   # force regular data.frame, not a tibble or data.table
   x <- as.data.frame(x, stringsAsFactors = FALSE)

R/mdro.R

@@ -192,10 +192,6 @@ mdro <- function(x = NULL,
   meet_criteria(pct_required_classes, allow_class = "numeric", has_length = 1)
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
 
   if (!any(is_sir_eligible(x))) {
@@ -203,7 +199,7 @@ mdro <- function(x = NULL,
   }
 
   info.bak <- info
-  # don't thrown info's more than once per call
+  # don't throw info's more than once per call
   if (isTRUE(info)) {
     info <- message_not_thrown_before("mdro")
   }
@@ -1611,10 +1607,12 @@ mdro <- function(x = NULL,
     function(y) all(is.na(y))
   ))
   if (length(rows_empty) > 0) {
-    cat(font_italic(paste0(" (", length(rows_empty), " isolates had no test results)\n")))
+    if (isTRUE(info.bak)) {
+      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 {
+  } else if (isTRUE(info.bak)) {
     cat("\n")
   }
 

R/mean_amr_distance.R

@@ -175,8 +175,8 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
 #' @param row an index, such as a row number
 #' @export
 amr_distance_from_row <- function(amr_distance, row) {
-  meet_criteria(amr_distance, allow_class = c("double", "numeric"), is_finite = TRUE)
-  meet_criteria(row, allow_class = c("logical", "double", "numeric"))
+  meet_criteria(amr_distance, allow_class = "numeric", is_finite = TRUE)
+  meet_criteria(row, allow_class = c("logical", "numeric", "integer"))
   if (is.logical(row)) {
     row <- which(row)
   }

R/mic.R

@@ -27,48 +27,22 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-# these are allowed MIC values and will become [factor] levels
-operators <- c("<", "<=", "", ">=", ">")
-valid_mic_levels <- c(
-  c(t(vapply(
-    FUN.VALUE = character(6), operators,
-    function(x) paste0(x, "0.000", c(1:4, 6, 8))
-  ))),
-  c(t(vapply(
-    FUN.VALUE = character(90), operators,
-    function(x) paste0(x, "0.00", c(1:9, 11:19, 21:29, 31:39, 41:49, 51:59, 61:69, 71:79, 81:89, 91:99))
-  ))),
-  unique(c(t(vapply(
-    FUN.VALUE = character(106), operators,
-    function(x) {
-      paste0(x, sort(as.double(paste0(
-        "0.0",
-        sort(c(1:99, 125, 128, 156, 165, 256, 512, 625))
-      ))))
-    }
-  )))),
-  unique(c(t(vapply(
-    FUN.VALUE = character(103), operators,
-    function(x) {
-      paste0(x, sort(as.double(paste0(
-        "0.",
-        c(1:99, 125, 128, 256, 512)
-      ))))
-    }
-  )))),
-  c(t(vapply(
-    FUN.VALUE = character(10), operators,
-    function(x) paste0(x, sort(c(1:9, 1.5)))
-  ))),
-  c(t(vapply(
-    FUN.VALUE = character(45), operators,
-    function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])
-  ))),
-  c(t(vapply(
-    FUN.VALUE = character(17), operators,
-    function(x) paste0(x, sort(c(2^c(7:11), 192, 80 * c(2:12))))
-  )))
+# these are allowed MIC values and will become factor levels
+VALID_MIC_LEVELS <- c(
+  as.double(paste0("0.000", c(1:9))),
+  as.double(paste0("0.00", c(1:99, 1953125, 390625, 78125))),
+  as.double(paste0("0.0", c(1:99, 125, 128, 156, 165, 256, 512, 625, 3125, 15625))),
+  as.double(paste0("0.", c(1:99, 125, 128, 256, 512))),
+  1:9, 1.5,
+  c(10:98)[9:98 %% 2 == TRUE],
+  2^c(7:12), 192 * c(1:5), 80 * c(2:12)
 )
+VALID_MIC_LEVELS <- trimws(gsub("[.]?0+$", "", format(unique(sort(VALID_MIC_LEVELS)), scientific = FALSE), perl = TRUE))
+operators <- c("<", "<=", "", ">=", ">")
+VALID_MIC_LEVELS <- c(t(vapply(FUN.VALUE = character(length(VALID_MIC_LEVELS)),
+                               c("<", "<=", "", ">=", ">"),
+                               paste0,
+                               VALID_MIC_LEVELS)))
 
 #' Transform Input to Minimum Inhibitory Concentrations (MIC)
 #'
@@ -76,6 +50,7 @@ valid_mic_levels <- c(
 #' @rdname as.mic
 #' @param x a [character] or [numeric] vector
 #' @param na.rm a [logical] indicating whether missing values should be removed
+#' @param keep_operators a [character] specifying how to handle operators (such as `>` and `<=`) in the input. Accepts one of three values: `"all"` (or `TRUE`) to keep all operators, `"none"` (or `FALSE`) to remove all operators, or `"edges"` to keep operators only at both ends of the range.
 #' @param ... arguments passed on to methods
 #' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
 #'
@@ -115,12 +90,16 @@ valid_mic_levels <- c(
 #' #> 10    16        A
 #' ```
 #'
-#' The following [generic functions][groupGeneric()] are implemented for the MIC class: `!`, `!=`, `%%`, `%/%`, `&`, `*`, `+`, `-`, `/`, `<`, `<=`, `==`, `>`, `>=`, `^`, `|`, [abs()], [acos()], [acosh()], [all()], [any()], [asin()], [asinh()], [atan()], [atanh()], [ceiling()], [cos()], [cosh()], [cospi()], [cummax()], [cummin()], [cumprod()], [cumsum()], [digamma()], [exp()], [expm1()], [floor()], [gamma()], [lgamma()], [log()], [log1p()], [log2()], [log10()], [max()], [mean()], [min()], [prod()], [range()], [round()], [sign()], [signif()], [sin()], [sinh()], [sinpi()], [sqrt()], [sum()], [tan()], [tanh()], [tanpi()], [trigamma()] and [trunc()]. Some functions of the `stats` package are also implemented: [median()], [quantile()], [mad()], [IQR()], [fivenum()]. Also, [boxplot.stats()] is supported. Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
+#' All so-called [group generic functions][groupGeneric()] are implemented for the MIC class (such as `!`, `!=`, `<`, `>=`, [exp()], [log2()]). Some functions of the `stats` package are also implemented (such as [quantile()], [median()], [fivenum()]). Since [sd()] and [var()] are non-generic functions, these could not be extended. Use [mad()] as an alternative, or use e.g. `sd(as.numeric(x))` where `x` is your vector of MIC values.
 #'
 #' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users).
 #'
 #' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class.
-#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
+#' 
+#' With [limit_mic_range()], existing MIC ranges can be limited to a defined range of MIC values. This can be useful to better compare MIC distributions.
+#'
+#' For `ggplot2`, use one of the [`scale_*_mic()`][scale_x_mic()] functions to plot MIC values. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
+#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as a [numeric] vector. Bear in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
 #' @aliases mic
 #' @export
 #' @seealso [as.sir()]
@@ -136,6 +115,9 @@ valid_mic_levels <- c(
 #' fivenum(mic_data)
 #' quantile(mic_data)
 #' all(mic_data < 512)
+#' 
+#' # limit MICs using limit_mic_range()
+#' limit_mic_range(mic_data, mic_range = c(4, 16))
 #'
 #' # interpret MIC values
 #' as.sir(
@@ -161,113 +143,182 @@ valid_mic_levels <- c(
 #' if (require("ggplot2")) {
 #'   autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
 #' }
-#' if (require("ggplot2")) {
-#'   autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk") # Ukrainian
-#' }
-as.mic <- function(x, na.rm = FALSE) {
+as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   meet_criteria(x, allow_NA = TRUE)
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
-
-  if (is.mic(x)) {
-    x
+  meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
+  if (isTRUE(keep_operators)) {
+    keep_operators <- "all"
+  } else if (isFALSE(keep_operators)) {
+    keep_operators <- "none"
+  }
+  
+  if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
+    if (!identical(levels(x), VALID_MIC_LEVELS)) {
+      # from an older AMR version - just update MIC factor levels
+      x <- set_clean_class(factor(as.character(x), levels = VALID_MIC_LEVELS, ordered = TRUE),
+                           new_class = c("mic", "ordered", "factor"))
+    }
+    return(x)
+  }
+  
+  x.bak <- NULL
+  if (is.numeric(x)) {
+    x.bak <- format(x, scientific = FALSE)
+    # MICs never have more than 9 decimals, so:
+    x <- format(round(x, 9), scientific = FALSE)
   } else {
-    if (is.numeric(x)) {
-      x <- format(x, scientific = FALSE)
-    } else {
-      x <- as.character(unlist(x))
-    }
-    if (isTRUE(na.rm)) {
-      x <- x[!is.na(x)]
-    }
-    x[trimws2(x) == ""] <- NA
+    x <- as.character(unlist(x))
+  }
+  if (isTRUE(na.rm)) {
+    x <- x[!is.na(x)]
+  }
+  x <- trimws2(x)
+  x[x == ""] <- NA
+  if (is.null(x.bak)) {
     x.bak <- x
-
-    # comma to period
-    x <- gsub(",", ".", x, fixed = TRUE)
-    # 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 <=
-    x <- gsub("=<", "<=", x, fixed = TRUE)
-    x <- gsub("=>", ">=", x, fixed = TRUE)
-    # dots without a leading zero must start with 0
-    x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
-    # values like "<=0.2560.512" should be 0.512
-    x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
-    # remove ending .0
-    x <- gsub("[.]+0$", "", x, perl = TRUE)
-    # remove all after last digit
-    x <- gsub("[^0-9]+$", "", x, perl = TRUE)
-    # keep only one zero before dot
-    x <- gsub("0+[.]", "0.", x, perl = TRUE)
-    # starting 00 is probably 0.0 if there's no dot yet
-    x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
-    # remove last zeroes
-    x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
-    x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
-    # remove ending .0 again
-    x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
-    # never end with dot
-    x <- gsub("[.]$", "", x, perl = TRUE)
-    # trim it
-    x <- trimws2(x)
-
-    ## previously unempty values now empty - should return a warning later on
-    x[x.bak != "" & x == ""] <- "invalid"
-
-    na_before <- x[is.na(x) | x == ""] %pm>% length()
-    x[!x %in% valid_mic_levels] <- NA
-    na_after <- x[is.na(x) | x == ""] %pm>% length()
-
-    if (na_before != na_after) {
-      list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
-        unique() %pm>%
-        sort() %pm>%
-        vector_and(quotes = TRUE)
-      cur_col <- get_current_column()
-      warning_("in `as.mic()`: ", na_after - na_before, " result",
-        ifelse(na_after - na_before > 1, "s", ""),
-        ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
-        " truncated (",
-        round(((na_after - na_before) / length(x)) * 100),
-        "%) that were invalid MICs: ",
-        list_missing,
-        call = FALSE
-      )
-    }
-
-    set_clean_class(factor(x, levels = valid_mic_levels, ordered = TRUE),
-      new_class = c("mic", "ordered", "factor")
+  }
+  
+  # comma to period
+  x <- gsub(",", ".", x, fixed = TRUE)
+  # transform scientific notation
+  x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"])
+  # 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 <=
+  x <- gsub("=<", "<=", x, fixed = TRUE)
+  x <- gsub("=>", ">=", x, fixed = TRUE)
+  # dots without a leading zero must start with 0
+  x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
+  # values like "<=0.2560.512" should be 0.512
+  x <- gsub(".*[.].*[.]", "0.", x, perl = TRUE)
+  # remove ending .0
+  x <- gsub("[.]+0$", "", x, perl = TRUE)
+  # remove all after last digit
+  x <- gsub("[^0-9]+$", "", x, perl = TRUE)
+  # keep only one zero before dot
+  x <- gsub("0+[.]", "0.", x, perl = TRUE)
+  # starting 00 is probably 0.0 if there's no dot yet
+  x[x %unlike% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
+  # remove last zeroes
+  x <- gsub("([.].?)0+$", "\\1", x, perl = TRUE)
+  x <- gsub("(.*[.])0+$", "\\10", x, perl = TRUE)
+  # remove ending .0 again
+  x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
+  # never end with dot
+  x <- gsub("[.]$", "", x, perl = TRUE)
+  # trim it
+  x <- trimws2(x)
+  
+  ## previously unempty values now empty - should return a warning later on
+  x[x.bak != "" & x == ""] <- "invalid"
+  
+  na_before <- x[is.na(x) | x == ""] %pm>% length()
+  x[!x %in% VALID_MIC_LEVELS] <- NA
+  na_after <- x[is.na(x) | x == ""] %pm>% length()
+  
+  if (na_before != na_after) {
+    list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ""] %pm>%
+      unique() %pm>%
+      sort() %pm>%
+      vector_and(quotes = TRUE)
+    cur_col <- get_current_column()
+    warning_("in `as.mic()`: ", na_after - na_before, " result",
+             ifelse(na_after - na_before > 1, "s", ""),
+             ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+             " truncated (",
+             round(((na_after - na_before) / length(x)) * 100),
+             "%) that were invalid MICs: ",
+             list_missing,
+             call = FALSE
     )
   }
+  
+  if (keep_operators == "none" && !all(is.na(x))) {
+    x <- gsub("[>=<]", "", x)
+  } else if (keep_operators == "edges" && !all(is.na(x))) {
+    dbls <- as.double(gsub("[>=<]", "", x))
+    x[dbls == min(dbls, na.rm = TRUE)] <- paste0("<=", min(dbls, na.rm = TRUE))
+    x[dbls == max(dbls, na.rm = TRUE)] <- paste0(">=", max(dbls, na.rm = TRUE))
+    keep <- x[dbls == max(dbls, na.rm = TRUE) | dbls == min(dbls, na.rm = TRUE)]
+    x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
+  }
+  
+  set_clean_class(factor(x, levels = VALID_MIC_LEVELS, ordered = TRUE),
+                  new_class = c("mic", "ordered", "factor"))
 }
 
-all_valid_mics <- function(x) {
-  if (!inherits(x, c("mic", "character", "factor", "numeric", "integer"))) {
-    return(FALSE)
-  }
-  x_mic <- tryCatch(suppressWarnings(as.mic(x[!is.na(x)])),
-    error = function(e) NA
-  )
-  !any(is.na(x_mic)) && !all(is.na(x))
+#' @rdname as.mic
+#' @export
+is.mic <- function(x) {
+  inherits(x, "mic")
 }
 
 #' @rdname as.mic
 #' @details `NA_mic_` is a missing value of the new `mic` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
 #' @format NULL
 #' @export
-NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE),
+NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE),
   new_class = c("mic", "ordered", "factor")
 )
 
 #' @rdname as.mic
+#' @param mic_range a manual range to limit the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to set no limit on one side, e.g., `mic_range = c(NA, 32)`.
 #' @export
-is.mic <- function(x) {
-  inherits(x, "mic")
+limit_mic_range <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
+  meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
+  stop_ifnot(all(mic_range %in% c(VALID_MIC_LEVELS, NA)),
+             "Values in `mic_range` must be valid MIC values. Unvalid: ", vector_and(mic_range[mic_range %in% c(VALID_MIC_LEVELS, NA)]))
+  x <- as.mic(x)
+  if (is.null(mic_range)) {
+    mic_range <- c(NA, NA)
+  }
+  mic_range <- as.mic(mic_range)
+  
+  min_mic <- mic_range[1]
+  max_mic <- mic_range[2]
+  if (!is.na(min_mic)) {
+    x[x < min_mic] <- min_mic
+  }
+  if (!is.na(max_mic)) {
+    x[x > max_mic] <- max_mic
+  }
+  
+  x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators))
+  
+  if (isTRUE(as.mic)) {
+    if (keep_operators == "edges") {
+      x[x == min(x, na.rm = TRUE)] <- paste0("<=", x[x == min(x, na.rm = TRUE)])
+      x[x == max(x, na.rm = TRUE)] <- paste0(">=", x[x == max(x, na.rm = TRUE)])
+    }
+    return(x)
+  }
+  
+  # create a manual factor with levels only within desired range
+  expanded <- range_as_table(x,
+                                 expand = TRUE,
+                                 keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
+                                 mic_range = mic_range)
+  if (keep_operators == "edges") {
+    names(expanded)[1] <- paste0("<=", names(expanded)[1])
+    names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])
+  }
+  # MICs contain all MIC levels, so strip this to only existing levels and their intermediate values
+  out <- factor(names(expanded),
+                levels = names(expanded),
+                ordered = TRUE)
+  # and only keep the ones in the data
+  if (keep_operators == "edges") {
+    out <- out[match(x, as.double(as.mic(out, keep_operators = "all")))]  
+  } else {
+    out <- out[match(x, out)]  
+  }
+  out
 }
 
 #' @method as.double mic
@@ -289,6 +340,7 @@ as.numeric.mic <- function(x, ...) {
 #' @param as.mic a [logical] to indicate whether the `mic` class should be kept - the default is `FALSE`
 #' @export
 droplevels.mic <- function(x, as.mic = FALSE, ...) {
+  x <- as.mic(x) # make sure that currently implemented MIC levels are used
   x <- droplevels.factor(x, ...)
   if (as.mic == TRUE) {
     class(x) <- c("mic", "ordered", "factor")
@@ -296,6 +348,16 @@ droplevels.mic <- function(x, as.mic = FALSE, ...) {
   x
 }
 
+all_valid_mics <- function(x) {
+  if (!inherits(x, c("mic", "character", "factor", "numeric", "integer"))) {
+    return(FALSE)
+  }
+  x_mic <- tryCatch(suppressWarnings(as.mic(x[!is.na(x)])),
+                    error = function(e) NA
+  )
+  !any(is.na(x_mic)) && !all(is.na(x))
+}
+
 # will be exported using s3_register() in R/zzz.R
 pillar_shaft.mic <- function(x, ...) {
   crude_numbers <- as.double(x)
@@ -303,8 +365,8 @@ pillar_shaft.mic <- function(x, ...) {
   operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
   out[is.na(x)] <- font_na(NA)
-  # maketrailing zeroes almost invisible
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", font_white("\\1"), out[out %like% "[.]"], perl = TRUE)
+  # make trailing zeroes less visible
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", font_silver("\\1"), out[out %like% "[.]"], perl = TRUE)
   create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
 }
 
@@ -317,11 +379,10 @@ type_sum.mic <- function(x, ...) {
 #' @export
 #' @noRd
 print.mic <- function(x, ...) {
-  cat("Class 'mic'",
-    ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""),
-    "\n",
-    sep = ""
-  )
+  cat("Class 'mic'\n")
+  if(!identical(levels(x), VALID_MIC_LEVELS)) {
+    cat(font_red("This object has an outdated or altered structure - convert with `as.mic()` to update\n"))
+  }
   print(as.character(x), quote = FALSE)
   att <- attributes(x)
   if ("na.action" %in% names(att)) {
@@ -342,22 +403,44 @@ summary.mic <- function(object, ...) {
 as.matrix.mic <- function(x, ...) {
   as.matrix(as.double(x), ...)
 }
+#' @method as.vector mic
+#' @export
+#' @noRd
+as.vector.mic <- function(x, mode = "numneric", ...) {
+  y <- NextMethod()
+  y <- as.mic(y)
+  calls <- unlist(lapply(sys.calls(), as.character))
+  if (any(calls %in% c("rbind", "cbind")) && message_not_thrown_before("as.vector.mic")) {
+    warning_("Functions `rbind()` and `cbind()` cannot preserve the structure of MIC values. Use dplyr's `bind_rows()` or `bind_cols()` instead. To solve, you can also use `your_data %>% mutate_if(is.ordered, as.mic)`.", call = FALSE)
+  }
+  y
+}
+#' @method as.list mic
+#' @export
+#' @noRd
+as.list.mic <- function(x, ...) {
+  lapply(as.list(as.character(x), ...), as.mic)
+}
+#' @method as.data.frame mic
+#' @export
+#' @noRd
+as.data.frame.mic <- function(x, ...) {
+  as.data.frame.vector(as.mic(x), ...)
+}
 
 #' @method [ mic
 #' @export
 #' @noRd
 "[.mic" <- function(x, ...) {
   y <- NextMethod()
-  attributes(y) <- attributes(x)
-  y
+  as.mic(y)
 }
 #' @method [[ mic
 #' @export
 #' @noRd
 "[[.mic" <- function(x, ...) {
   y <- NextMethod()
-  attributes(y) <- attributes(x)
-  y
+  as.mic(y)
 }
 #' @method [<- mic
 #' @export
@@ -365,8 +448,7 @@ as.matrix.mic <- function(x, ...) {
 "[<-.mic" <- function(i, j, ..., value) {
   value <- as.mic(value)
   y <- NextMethod()
-  attributes(y) <- attributes(i)
-  y
+  as.mic(y)
 }
 #' @method [[<- mic
 #' @export
@@ -374,8 +456,7 @@ as.matrix.mic <- function(x, ...) {
 "[[<-.mic" <- function(i, j, ..., value) {
   value <- as.mic(value)
   y <- NextMethod()
-  attributes(y) <- attributes(i)
-  y
+  as.mic(y)
 }
 #' @method c mic
 #' @export
@@ -389,8 +470,7 @@ c.mic <- function(...) {
 #' @noRd
 unique.mic <- function(x, incomparables = FALSE, ...) {
   y <- NextMethod()
-  attributes(y) <- attributes(x)
-  y
+  as.mic(y)
 }
 
 #' @method rep mic
@@ -398,14 +478,14 @@ unique.mic <- function(x, incomparables = FALSE, ...) {
 #' @noRd
 rep.mic <- function(x, ...) {
   y <- NextMethod()
-  attributes(y) <- attributes(x)
-  y
+  as.mic(y)
 }
 
 #' @method sort mic
 #' @export
 #' @noRd
 sort.mic <- function(x, decreasing = FALSE, ...) {
+  x <- as.mic(x) # make sure that currently implemented MIC levels are used
   if (decreasing == TRUE) {
     ord <- order(-as.double(x))
   } else {
@@ -425,6 +505,7 @@ hist.mic <- function(x, ...) {
 
 # will be exported using s3_register() in R/zzz.R
 get_skimmers.mic <- function(column) {
+  column <- as.mic(column) # make sure that currently implemented MIC levels are used
   skimr::sfl(
     skim_type = "mic",
     p0 = ~ stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
@@ -462,399 +543,57 @@ quantile.mic <- function(x, probs = seq(0, 1, 0.25), na.rm = FALSE,
   quantile(as.double(x), probs = probs, na.rm = na.rm, names = names, type = type, ...)
 }
 
-# Math (see ?groupGeneric) ----------------------------------------------
+# Math (see ?groupGeneric) ------------------------------------------------
 
-#' @method abs mic
 #' @export
-#' @noRd
-abs.mic <- function(x) {
-  abs(as.double(x))
-}
-#' @method sign mic
-#' @export
-#' @noRd
-sign.mic <- function(x) {
-  sign(as.double(x))
-}
-#' @method sqrt mic
-#' @export
-#' @noRd
-sqrt.mic <- function(x) {
-  sqrt(as.double(x))
-}
-#' @method floor mic
-#' @export
-#' @noRd
-floor.mic <- function(x) {
-  floor(as.double(x))
-}
-#' @method ceiling mic
-#' @export
-#' @noRd
-ceiling.mic <- function(x) {
-  ceiling(as.double(x))
-}
-#' @method trunc mic
-#' @export
-#' @noRd
-trunc.mic <- function(x, ...) {
-  trunc(as.double(x), ...)
-}
-#' @method round mic
-#' @export
-#' @noRd
-round.mic <- function(x, digits = 0) {
-  round(as.double(x), digits = digits)
-}
-#' @method signif mic
-#' @export
-#' @noRd
-signif.mic <- function(x, digits = 6) {
-  signif(as.double(x), digits = digits)
-}
-#' @method exp mic
-#' @export
-#' @noRd
-exp.mic <- function(x) {
-  exp(as.double(x))
-}
-#' @method log mic
-#' @export
-#' @noRd
-log.mic <- function(x, base = exp(1)) {
-  log(as.double(x), base = base)
-}
-#' @method log10 mic
-#' @export
-#' @noRd
-log10.mic <- function(x) {
-  log10(as.double(x))
-}
-#' @method log2 mic
-#' @export
-#' @noRd
-log2.mic <- function(x) {
-  log2(as.double(x))
-}
-#' @method expm1 mic
-#' @export
-#' @noRd
-expm1.mic <- function(x) {
-  expm1(as.double(x))
-}
-#' @method log1p mic
-#' @export
-#' @noRd
-log1p.mic <- function(x) {
-  log1p(as.double(x))
-}
-#' @method cos mic
-#' @export
-#' @noRd
-cos.mic <- function(x) {
-  cos(as.double(x))
-}
-#' @method sin mic
-#' @export
-#' @noRd
-sin.mic <- function(x) {
-  sin(as.double(x))
-}
-#' @method tan mic
-#' @export
-#' @noRd
-tan.mic <- function(x) {
-  tan(as.double(x))
-}
-#' @method cospi mic
-#' @export
-#' @noRd
-cospi.mic <- function(x) {
-  cospi(as.double(x))
-}
-#' @method sinpi mic
-#' @export
-#' @noRd
-sinpi.mic <- function(x) {
-  sinpi(as.double(x))
-}
-#' @method tanpi mic
-#' @export
-#' @noRd
-tanpi.mic <- function(x) {
-  tanpi(as.double(x))
-}
-#' @method acos mic
-#' @export
-#' @noRd
-acos.mic <- function(x) {
-  acos(as.double(x))
-}
-#' @method asin mic
-#' @export
-#' @noRd
-asin.mic <- function(x) {
-  asin(as.double(x))
-}
-#' @method atan mic
-#' @export
-#' @noRd
-atan.mic <- function(x) {
-  atan(as.double(x))
-}
-#' @method cosh mic
-#' @export
-#' @noRd
-cosh.mic <- function(x) {
-  cosh(as.double(x))
-}
-#' @method sinh mic
-#' @export
-#' @noRd
-sinh.mic <- function(x) {
-  sinh(as.double(x))
-}
-#' @method tanh mic
-#' @export
-#' @noRd
-tanh.mic <- function(x) {
-  tanh(as.double(x))
-}
-#' @method acosh mic
-#' @export
-#' @noRd
-acosh.mic <- function(x) {
-  acosh(as.double(x))
-}
-#' @method asinh mic
-#' @export
-#' @noRd
-asinh.mic <- function(x) {
-  asinh(as.double(x))
-}
-#' @method atanh mic
-#' @export
-#' @noRd
-atanh.mic <- function(x) {
-  atanh(as.double(x))
-}
-#' @method lgamma mic
-#' @export
-#' @noRd
-lgamma.mic <- function(x) {
-  lgamma(as.double(x))
-}
-#' @method gamma mic
-#' @export
-#' @noRd
-gamma.mic <- function(x) {
-  gamma(as.double(x))
-}
-#' @method digamma mic
-#' @export
-#' @noRd
-digamma.mic <- function(x) {
-  digamma(as.double(x))
-}
-#' @method trigamma mic
-#' @export
-#' @noRd
-trigamma.mic <- function(x) {
-  trigamma(as.double(x))
-}
-#' @method cumsum mic
-#' @export
-#' @noRd
-cumsum.mic <- function(x) {
-  cumsum(as.double(x))
-}
-#' @method cumprod mic
-#' @export
-#' @noRd
-cumprod.mic <- function(x) {
-  cumprod(as.double(x))
-}
-#' @method cummax mic
-#' @export
-#' @noRd
-cummax.mic <- function(x) {
-  cummax(as.double(x))
-}
-#' @method cummin mic
-#' @export
-#' @noRd
-cummin.mic <- function(x) {
-  cummin(as.double(x))
+Math.mic <- function(x, ...) {
+  x <- as.double(x)
+  # set class to numeric, because otherwise NextMethod will be factor (since mic is a factor)
+  .Class <- class(x)
+  NextMethod(.Generic)
 }
 
-# Ops (see ?groupGeneric) -----------------------------------------------
+# Ops (see ?groupGeneric) -------------------------------------------------
 
-is_greater <- function(el) {
-  el %like_case% ">[0-9]"
-}
-is_lower <- function(el) {
-  el %like_case% "<[0-9]"
+#' @export
+Ops.mic <- function(e1, e2) {
+  e1_chr <- as.character(e1)
+  e2_chr <- character(0)
+  e1 <- as.double(e1)
+  if (!missing(e2)) {
+    # when e1 is `!`, e2 is missing
+    e2_chr <- as.character(e2)
+    e2 <- as.double(e2)
+  }
+  if (as.character(.Generic) %in% c("<", "<=", "==", "!=", ">", ">=")) {
+    # make sure that <0.002 is lower than 0.002
+    # and that >32 is higher than 32, but equal to >=32
+    e1[e1_chr %like% "<" & e1_chr %unlike% "="] <- e1[e1_chr %like% "<" & e1_chr %unlike% "="] - 0.000001
+    e1[e1_chr %like% ">" & e1_chr %unlike% "="] <- e1[e1_chr %like% ">" & e1_chr %unlike% "="] + 0.000001
+    e2[e2_chr %like% "<" & e2_chr %unlike% "="] <- e2[e2_chr %like% "<" & e2_chr %unlike% "="] - 0.000001
+    e2[e2_chr %like% ">" & e2_chr %unlike% "="] <- e2[e2_chr %like% ">" & e2_chr %unlike% "="] + 0.000001
+  }
+  # set .Class to numeric, because otherwise NextMethod will be factor (since mic is a factor)
+  .Class <- class(e1)
+  NextMethod(.Generic)
 }
 
-#' @method + mic
+# Complex (see ?groupGeneric) ---------------------------------------------
+
 #' @export
-#' @noRd
-`+.mic` <- function(e1, e2) {
-  as.double(e1) + as.double(e2)
+Complex.mic <- function(z) {
+  z <- as.double(z)
+  # set class to numeric, because otherwise NextMethod will be factor (since mic is a factor)
+  .Class <- class(z)
+  NextMethod(.Generic)
 }
 
-#' @method - mic
-#' @export
-#' @noRd
-`-.mic` <- function(e1, e2) {
-  as.double(e1) - as.double(e2)
-}
+# Summary (see ?groupGeneric) ---------------------------------------------
 
-#' @method * mic
 #' @export
-#' @noRd
-`*.mic` <- function(e1, e2) {
-  as.double(e1) * as.double(e2)
-}
-
-#' @method / mic
-#' @export
-#' @noRd
-`/.mic` <- function(e1, e2) {
-  as.double(e1) / as.double(e2)
-}
-
-#' @method ^ mic
-#' @export
-#' @noRd
-`^.mic` <- function(e1, e2) {
-  as.double(e1)^as.double(e2)
-}
-
-#' @method %% mic
-#' @export
-#' @noRd
-`%%.mic` <- function(e1, e2) {
-  as.double(e1) %% as.double(e2)
-}
-
-#' @method %/% mic
-#' @export
-#' @noRd
-`%/%.mic` <- function(e1, e2) {
-  as.double(e1) %/% as.double(e2)
-}
-
-#' @method & mic
-#' @export
-#' @noRd
-`&.mic` <- function(e1, e2) {
-  as.double(e1) & as.double(e2)
-}
-
-#' @method | mic
-#' @export
-#' @noRd
-`|.mic` <- function(e1, e2) {
-  as.double(e1) | as.double(e2)
-}
-
-#' @method ! mic
-#' @export
-#' @noRd
-`!.mic` <- function(x) {
-  !as.double(x)
-}
-
-#' @method == mic
-#' @export
-#' @noRd
-`==.mic` <- function(e1, e2) {
-  as.double(e1) == as.double(e2)
-}
-
-#' @method != mic
-#' @export
-#' @noRd
-`!=.mic` <- function(e1, e2) {
-  as.double(e1) != as.double(e2)
-}
-
-#' @method < mic
-#' @export
-#' @noRd
-`<.mic` <- function(e1, e2) {
-  as.double(e1) < as.double(e2)
-}
-
-#' @method <= mic
-#' @export
-#' @noRd
-`<=.mic` <- function(e1, e2) {
-  as.double(e1) <= as.double(e2)
-}
-
-#' @method >= mic
-#' @export
-#' @noRd
-`>=.mic` <- function(e1, e2) {
-  as.double(e1) >= as.double(e2)
-}
-
-#' @method > mic
-#' @export
-#' @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) -------------------------------------------
-
-#' @method all mic
-#' @export
-#' @noRd
-all.mic <- function(..., na.rm = FALSE) {
-  all(as.double(c(...)), na.rm = na.rm)
-}
-#' @method any mic
-#' @export
-#' @noRd
-any.mic <- function(..., na.rm = FALSE) {
-  any(as.double(c(...)), na.rm = na.rm)
-}
-#' @method sum mic
-#' @export
-#' @noRd
-sum.mic <- function(..., na.rm = FALSE) {
-  sum(as.double(c(...)), na.rm = na.rm)
-}
-#' @method prod mic
-#' @export
-#' @noRd
-prod.mic <- function(..., na.rm = FALSE) {
-  prod(as.double(c(...)), na.rm = na.rm)
-}
-#' @method min mic
-#' @export
-#' @noRd
-min.mic <- function(..., na.rm = FALSE) {
-  min(as.double(c(...)), na.rm = na.rm)
-}
-#' @method max mic
-#' @export
-#' @noRd
-max.mic <- function(..., na.rm = FALSE) {
-  max(as.double(c(...)), na.rm = na.rm)
-}
-#' @method range mic
-#' @export
-#' @noRd
-range.mic <- function(..., na.rm = FALSE) {
-  range(as.double(c(...)), na.rm = na.rm)
+Summary.mic <- function(..., na.rm = FALSE) {
+  # NextMethod() cannot be called from an anonymous function (`...`), so we get() the generic directly:
+  fn <- get(.Generic, envir = .GenericCallEnv)
+  fn(as.double(c(...)),
+     na.rm = na.rm)
 }

R/mo.R

@@ -250,7 +250,7 @@ as.mo <- function(x,
     x_unique <- unique(x[is.na(out) & !is.na(x)])
     
     # set up progress bar
-    progress <- progress_ticker(n = length(x_unique), n_min = 10, print = info)
+    progress <- progress_ticker(n = length(x_unique), n_min = 10, print = info, title = "Converting microorganism input")
     on.exit(close(progress))
     
     msg <- character(0)

R/mo_property.R

@@ -245,7 +245,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
   # unknown species etc.
   shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
 
-  shortnames[mo_rank(x.mo) %in% c("kingdom", "phylum", "class", "order", "family")] <- mo_name(x.mo, language = NULL, keep_synonyms = keep_synonyms)
+  shortnames[mo_rank(x.mo) %in% c("kingdom", "phylum", "class", "order", "family")] <- mo_name(x.mo[mo_rank(x.mo) %in% c("kingdom", "phylum", "class", "order", "family")], language = NULL, keep_synonyms = keep_synonyms)
 
   shortnames[is.na(x.mo)] <- NA_character_
   load_mo_uncertainties(metadata)

R/mo_source.R

@@ -125,14 +125,13 @@
 #' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
 #' @export
 set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
+  stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their file system.")
+
   meet_criteria(path, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(destination, allow_class = "character", has_length = 1)
   stop_ifnot(destination %like% "[.]rds$", "the `destination` must be a file location with file extension .rds.")
-
   mo_source_destination <- path.expand(destination)
 
-  stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their file system.")
-
   if (is.null(path) || path %in% c(FALSE, "")) {
     AMR_env$mo_source <- NULL
     if (file.exists(mo_source_destination)) {
@@ -247,6 +246,12 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
     }
     return(NULL)
   }
+  if (destination %unlike% "[.]rds$") {
+    current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
+    current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
+    vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
+    stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If `\"", basename(destination), "\"` was meant as your input file, use `set_mo_source()` on this file. In any case, the option `AMR_mo_source` must be set to another path.")
+  }
   if (is.null(AMR_env$mo_source)) {
     AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
   }

R/plot.R

@@ -29,8 +29,10 @@
 
 #' Plotting for Classes `sir`, `mic` and `disk`
 #'
+#' @description
 #' Functions to plot classes `sir`, `mic` and `disk`, with support for base \R and `ggplot2`.
-
+#' 
+#' Especially the `scale_*_mic()` functions are relevant wrappers to plot MIC values for `ggplot2`. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
 #' @param x,object values created with [as.mic()], [as.disk()] or [as.sir()] (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 drug code with [as.ab()]
@@ -65,10 +67,36 @@
 #' # when providing the microorganism and antibiotic, colours will show interpretations:
 #' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
 #' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
-#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "uk")
-#'
+#' plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
+#' 
+#' 
+#' # Plotting using scale_x_mic()
 #' \donttest{
 #' if (require("ggplot2")) {
+#'   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
+#'                                 counts = c(1, 1, 2, 2, 3, 3)),
+#'                      aes(mics, counts)) +
+#'     geom_col()
+#'   mic_plot +
+#'     labs(title = "without scale_x_mic()")
+#' }
+#' if (require("ggplot2")) {
+#'   mic_plot +
+#'     scale_x_mic() +
+#'     labs(title = "with scale_x_mic()")
+#' }
+#' if (require("ggplot2")) {
+#'   mic_plot +
+#'     scale_x_mic(keep_operators = "all") +
+#'     labs(title = "with scale_x_mic() keeping all operators")
+#' }
+#' if (require("ggplot2")) {
+#'   mic_plot +
+#'     scale_x_mic(mic_range = c(1, 128)) +
+#'     labs(title = "with scale_x_mic() using a manual range")
+#' }
+#' 
+#' if (require("ggplot2")) {
 #'   autoplot(some_mic_values)
 #' }
 #' if (require("ggplot2")) {
@@ -80,6 +108,59 @@
 #' }
 NULL
 
+#' @export
+#' @inheritParams as.mic
+#' @param drop a [logical] to remove intermediate MIC values, defaults to `FALSE`
+#' @rdname plot
+scale_x_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_x_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_y_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_colour_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_colour_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_fill_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    limit_mic_range(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
 #' @method plot mic
 #' @importFrom graphics barplot axis mtext legend
 #' @export
@@ -97,16 +178,13 @@ plot.mic <- function(x,
                      include_PKPD = getOption("AMR_include_PKPD", TRUE),
                      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                      ...) {
+  x <- as.mic(x) # make sure that currently implemented MIC levels are used
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
   meet_criteria(xlab, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -116,8 +194,7 @@ plot.mic <- function(x,
   }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
-  x <- plot_prepare_table(x, expand = expand)
-
+  x <- range_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -187,16 +264,13 @@ barplot.mic <- function(height,
                         language = get_AMR_locale(),
                         expand = TRUE,
                         ...) {
+  height <- as.mic(height) # make sure that currently implemented MIC levels are used
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
   meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -233,16 +307,13 @@ autoplot.mic <- function(object,
                          breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                          ...) {
   stop_ifnot_installed("ggplot2")
+  object <- as.mic(object) # make sure that currently implemented MIC levels are used
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
   meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
   meet_criteria(xlab, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -254,7 +325,7 @@ autoplot.mic <- function(object,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
 
-  x <- plot_prepare_table(object, expand = expand)
+  x <- range_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -316,12 +387,14 @@ autoplot.mic <- function(object,
 #' @rdname plot
 # will be exported using s3_register() in R/zzz.R
 fortify.mic <- function(object, ...) {
+  object <- as.mic(object) # make sure that currently implemented MIC levels are used
   stats::setNames(
-    as.data.frame(plot_prepare_table(object, expand = FALSE)),
+    as.data.frame(range_as_table(object, expand = FALSE)),
     c("x", "y")
   )
 }
 
+
 #' @method plot disk
 #' @export
 #' @importFrom graphics barplot axis mtext legend
@@ -345,10 +418,6 @@ plot.disk <- function(x,
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -358,8 +427,7 @@ plot.disk <- function(x,
   }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
-  x <- plot_prepare_table(x, expand = expand)
-
+  x <- range_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -435,10 +503,6 @@ barplot.disk <- function(height,
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -481,10 +545,6 @@ autoplot.disk <- function(object,
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -496,7 +556,7 @@ autoplot.disk <- function(object,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
 
-  x <- plot_prepare_table(object, expand = expand)
+  x <- range_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -560,7 +620,7 @@ autoplot.disk <- function(object,
 # 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)),
+    as.data.frame(range_as_table(object, expand = FALSE)),
     c("x", "y")
   )
 }
@@ -635,10 +695,6 @@ barplot.sir <- function(height,
   meet_criteria(xlab, allow_class = "character", has_length = 1)
   meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
   meet_criteria(ylab, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -714,22 +770,31 @@ fortify.sir <- function(object, ...) {
   )
 }
 
-plot_prepare_table <- function(x, expand) {
+range_as_table <- function(x, expand, keep_operators = "all", mic_range = NULL) {
   x <- x[!is.na(x)]
-  stop_if(length(x) == 0, "no observations to plot", call = FALSE)
   if (is.mic(x)) {
+    x <- as.mic(x, keep_operators = keep_operators)
     if (expand == TRUE) {
       # expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
-      valid_lvls <- levels(x)
-      extra_range <- max(x) / 2
-      while (min(extra_range) / 2 > min(x)) {
+      extra_range <- max(x)
+      min_range <- min(x)
+      if (!is.null(mic_range)) {
+        if (!is.na(mic_range[2])) {
+          extra_range <- as.mic(mic_range[2]) * 2
+        }
+        if (!is.na(mic_range[1])) {
+          min_range <- as.mic(mic_range[1])
+        }
+      }
+      extra_range <- extra_range / 2
+      while (min(extra_range) / 2 > min_range) {
         extra_range <- c(min(extra_range) / 2, extra_range)
       }
       nms <- extra_range
       extra_range <- rep(0, length(extra_range))
       names(extra_range) <- nms
       x <- table(droplevels(x, as.mic = FALSE))
-      extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
+      extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% VALID_MIC_LEVELS]
       x <- as.table(c(x, extra_range))
     } else {
       x <- table(droplevels(x, as.mic = FALSE))
@@ -751,6 +816,15 @@ plot_prepare_table <- function(x, expand) {
   as.table(x)
 }
 
+ggplot2_get_from_dots <- function(arg, default, ...) {
+  dots <- list(...)
+  if (!arg %in% names(dots)) {
+    default
+  } else {
+    dots[[arg]]
+  }
+}
+
 plot_name_of_I <- function(guideline) {
   if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
     # interpretation since 2019
@@ -762,6 +836,8 @@ plot_name_of_I <- function(guideline) {
 }
 
 plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, fn, language, method, breakpoint_type, include_PKPD, ...) {
+  stop_if(length(x) == 0, "no observations to plot", call = FALSE)
+  
   guideline <- get_guideline(guideline, AMR::clinical_breakpoints)
   
   # store previous interpretations to backup

R/proportion.R

@@ -46,13 +46,13 @@
 #' @param collapse a [logical] to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing
 #' @inheritSection as.sir Interpretation of SIR
 #' @details
+#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
+#' 
 #' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
 #'
 #' Use [sir_confidence_interval()] to calculate the confidence interval, which relies on [binom.test()], i.e., the Clopper-Pearson method. This function returns a vector of length 2 at default for antimicrobial *resistance*. Change the `side` argument to "left"/"min" or "right"/"max" to return a single value, and change the `ab_result` argument to e.g. `c("S", "I")` to test for antimicrobial *susceptibility*, see Examples.
 #'
-#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
-#'
-#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [`count()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to `count_susceptible() / count_all()`. *Low counts can influence the outcome - the `proportion` functions may camouflage this, since they only return the proportion (albeit being dependent on the `minimum` argument).*
+#' These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the [`count_*()`][AMR::count()] functions to count isolates. The function [susceptibility()] is essentially equal to [count_susceptible()]` / `[count_all()]. *Low counts can influence the outcome - the `proportion_*()` functions may camouflage this, since they only return the proportion (albeit dependent on the `minimum` argument).*
 #'
 #' The function [proportion_df()] takes any variable from `data` that has an [`sir`] class (created with [as.sir()]) and calculates the proportions S, I, and R. It also supports grouped variables. The function [sir_df()] works exactly like [proportion_df()], but adds the number of isolates.
 #' @section Combination Therapy:
@@ -294,7 +294,7 @@ sir_confidence_interval <- function(...,
 
   # this applies the Clopper-Pearson method
   out <- stats::binom.test(x = x, n = n, conf.level = confidence_level)$conf.int
-  out <- set_clean_class(out, "double")
+  out <- set_clean_class(out, "numeric")
 
   if (side %in% c("left", "l", "lower", "lowest", "less", "min")) {
     out <- out[1]

R/random.R

@@ -83,10 +83,6 @@ random_disk <- function(size = NULL, mo = NULL, ab = NULL, ...) {
 #' @export
 random_sir <- function(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...) {
   meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
-  if ("prob_RSI" %in% names(list(...))) {
-    deprecation_warning("prob_RSI", "prob_SIR", is_function = FALSE)
-    prob_SIR <- list(...)$prob_RSI
-  }
   meet_criteria(prob_SIR, allow_class = c("numeric", "integer"), has_length = 3)
   if (is.null(size)) {
     size <- NROW(get_current_data(arg_name = "size", call = -3))

R/sir.R

@@ -29,10 +29,13 @@
 
 #' Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data
 #'
-#' @description Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing SIR values. This transforms the input to a new class [`sir`], which is an ordered [factor] with levels `S < I < R`.
+#' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor].
+#' 
+#' Currently breakpoints are available:
+#' - For **clinical microbiology** from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
+#' - For **veterinary microbiology** from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
+#' - ECOFFs (Epidemiological cut-off values) from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
 #' 
-#' Currently available **breakpoint guidelines** are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, and available **breakpoint types** are `r vector_and(clinical_breakpoints$type)`.
-#'
 #' All breakpoints used for interpretation are publicly available in the [clinical_breakpoints] data set.
 #' @rdname as.sir
 #' @param x vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
@@ -45,16 +48,17 @@
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
 #' @param include_screening a [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the [package option][AMR-options] [`AMR_include_screening`][AMR-options].
 #' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the [package option][AMR-options] [`AMR_include_PKPD`][AMR-options].
-#' @param breakpoint_type the type of breakpoints to use, either `r vector_or(clinical_breakpoints$type)`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the [package option][AMR-options] [`AMR_breakpoint_type`][AMR-options].
+#' @param breakpoint_type the type of breakpoints to use, either `r vector_or(clinical_breakpoints$type)`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the [package option][AMR-options] [`AMR_breakpoint_type`][AMR-options]. If `host` is set to values of veterinary species, this will automatically be set to `"animal"`.
+#' @param host a vector (or column name) with [character]s to indicate the host. Only useful for veterinary breakpoints, as it requires `breakpoint_type = "animal"`. The values can be any text resembling the animal species, even in any of the `r length(LANGUAGES_SUPPORTED)` supported languages of this package. For foreign languages, be sure to set the language with [set_AMR_locale()] (though it will be automatically guessed based on the system language).
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [clinical_breakpoints] 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 [clinical_breakpoints] 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.sir()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
 #' @details
-#' *Note: The clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org) and the public use of this `AMR` package has been endorsed by CLSI and EUCAST, please see [clinical_breakpoints] for more information.*
+#' *Note: The clinical breakpoints in this package were validated through, and imported from, [WHONET](https://whonet.org). The public use of this `AMR` package has been endorsed by both CLSI and EUCAST. See [clinical_breakpoints] for more information.*
 #' 
 #' ### How it Works
 #'
-#' The [as.sir()] function works in four ways:
+#' The [as.sir()] function can work in four ways:
 #'
 #' 1. For **cleaning raw / untransformed data**. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with SIR interpretations and MIC values such as `"<0.25; S"` will be coerced to `"S"`. Combined interpretations for multiple test methods (as seen in laboratory records) such as `"S; S"` will be coerced to `"S"`, but a value like `"S; I"` will return `NA` with a warning that the input is unclear.
 #'
@@ -63,6 +67,9 @@
 #'      ```
 #'      your_data %>% mutate_if(is.mic, as.sir)
 #'      your_data %>% mutate(across(where(is.mic), as.sir))
+#'      
+#'      # for veterinary breakpoints, also set `host`:
+#'      your_data %>% mutate_if(is.mic, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
 #'      ```
 #'    * Operators like "<=" will be stripped before interpretation. When using `conserve_capped_values = TRUE`, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (`conserve_capped_values = FALSE`) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
 #' 3. For **interpreting disk diffusion diameters** according to EUCAST or CLSI. You must clean your disk zones first using [as.disk()], that also gives your columns the new data class [`disk`]. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the `mo` argument.
@@ -70,6 +77,9 @@
 #'      ```
 #'      your_data %>% mutate_if(is.disk, as.sir)
 #'      your_data %>% mutate(across(where(is.disk), as.sir))
+#'      
+#'      # for veterinary breakpoints, also set `host`:
+#'      your_data %>% mutate_if(is.disk, as.sir, host = "column_with_animal_hosts", guideline = "CLSI")
 #'      ```
 #' 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.sir(your_data)`.
 #'
@@ -77,7 +87,7 @@
 #'
 #' ### Supported Guidelines
 #'
-#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
+#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`, and for **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`.
 #'
 #' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #'
@@ -90,6 +100,13 @@
 #'   # or to reset:
 #'   options(AMR_guideline = NULL)
 #' ```
+#' 
+#' For veterinary guidelines, these might be the best options:
+#' 
+#' ```
+#'   options(AMR_guideline = "CLSI")
+#'   options(AMR_breakpoint_type = "animal")
+#' ```
 #'
 #' ### After Interpretation
 #'
@@ -124,9 +141,10 @@
 #' @source
 #' For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:
 #'
-#' - **M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m39/>.
-#' - **M100 Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>.
-#' - **Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>.
+#' - **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m39/>.
+#' - **CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type != "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/microbiology/documents/m100/>.
+#' - **CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`, *Clinical and Laboratory Standards Institute* (CLSI). <https://clsi.org/standards/products/veterinary-medicine/documents/vet01//>.
+#' - **EUCAST Breakpoint tables for interpretation of MICs and zone diameters**, `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, *European Committee on Antimicrobial Susceptibility Testing* (EUCAST). <https://www.eucast.org/clinical_breakpoints>.
 #' @inheritSection AMR Reference Data Publicly Available
 #' @examples
 #' example_isolates
@@ -226,6 +244,7 @@ as.sir <- function(x, ...) {
 
 #' @rdname as.sir
 #' @details `NA_sir_` is a missing value of the new `sir` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
 #' @export
 NA_sir_ <- set_clean_class(factor(NA_character_, levels = c("S", "I", "R"), ordered = TRUE),
   new_class = c("sir", "ordered", "factor")
@@ -237,12 +256,7 @@ is.sir <- function(x) {
   if (inherits(x, "data.frame")) {
     unname(vapply(FUN.VALUE = logical(1), x, is.sir))
   } else {
-    rsi <- inherits(x, "rsi")
-    sir <- inherits(x, "sir")
-    if (isTRUE(rsi) && message_not_thrown_before("is.sir-rsi")) {
-      deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns to 'sir' with `as.sir()`, e.g.:\n  your_data %>% mutate_if(is.rsi, as.sir)")
-    }
-    isTRUE(rsi) || isTRUE(sir)
+    isTRUE(inherits(x, "sir"))
   }
 }
 
@@ -312,7 +326,7 @@ as.sir.default <- function(x, ...) {
   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))) {
+  if (inherits(x.bak, c("numeric", "integer")) && all(x %in% c(1:3, NA))) {
     # support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
     lbls <- attributes(x.bak)$labels
     if (!is.null(lbls) && all(c("S", "I", "R") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
@@ -329,7 +343,7 @@ as.sir.default <- function(x, ...) {
     x[x.bak == "2"] <- "I"
     x[x.bak == "3"] <- "R"
   } else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("S", "I", "R", NA))) {
-    if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
+    if (all(x %unlike% "(S|I|R)", na.rm = TRUE)) {
       # check if they are actually MICs or disks
       if (all_valid_mics(x)) {
         warning_("in `as.sir()`: the input seems to contain MIC values. You can transform them with `as.mic()` before running `as.sir()` to interpret them.")
@@ -434,6 +448,7 @@ as.sir.mic <- function(x,
                        include_screening = getOption("AMR_include_screening", FALSE),
                        include_PKPD = getOption("AMR_include_PKPD", TRUE),
                        breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+                       host = NULL,
                        ...) {
   as_sir_method(
     method_short = "mic",
@@ -449,6 +464,7 @@ as.sir.mic <- function(x,
     include_screening = include_screening,
     include_PKPD = include_PKPD,
     breakpoint_type = breakpoint_type,
+    host = host,
     ...
   )
 }
@@ -465,6 +481,7 @@ as.sir.disk <- function(x,
                         include_screening = getOption("AMR_include_screening", FALSE),
                         include_PKPD = getOption("AMR_include_PKPD", TRUE),
                         breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+                        host = NULL,
                         ...) {
   as_sir_method(
     method_short = "disk",
@@ -480,6 +497,7 @@ as.sir.disk <- function(x,
     include_screening = include_screening,
     include_PKPD = include_PKPD,
     breakpoint_type = breakpoint_type,
+    host = NULL,
     ...
   )
 }
@@ -496,7 +514,8 @@ as.sir.data.frame <- function(x,
                               reference_data = AMR::clinical_breakpoints,
                               include_screening = getOption("AMR_include_screening", FALSE),
                               include_PKPD = getOption("AMR_include_PKPD", TRUE),
-                              breakpoint_type = getOption("AMR_breakpoint_type", "human")) {
+                              breakpoint_type = getOption("AMR_breakpoint_type", "human"),
+                              host = NULL) {
   meet_criteria(x, allow_class = "data.frame") # will also check for dimensions > 0
   meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
@@ -507,7 +526,7 @@ as.sir.data.frame <- function(x,
   meet_criteria(include_screening, allow_class = "logical", has_length = 1)
   meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
   meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1)
-
+  meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE)
   x.bak <- x
   for (i in seq_len(ncol(x))) {
     # don't keep factors, overwriting them is hard
@@ -521,11 +540,20 @@ as.sir.data.frame <- function(x,
   if (is.null(col_mo)) {
     col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
   }
-
+  
+  # -- host
+  if (breakpoint_type == "animal") {
+    if (is.null(host)) {
+      host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE)
+    } else if (length(host) == 1 && as.character(host) %in% colnames(x)) {
+      host <- x[[as.character(host)]]
+    }
+  }
+  
   # -- UTIs
   col_uti <- uti
   if (is.null(col_uti)) {
-    col_uti <- search_type_in_df(x = x, type = "uti")
+    col_uti <- search_type_in_df(x = x, type = "uti", add_col_prefix = FALSE)
   }
   if (!is.null(col_uti)) {
     if (is.logical(col_uti)) {
@@ -639,6 +667,7 @@ as.sir.data.frame <- function(x,
           include_screening = include_screening,
           include_PKPD = include_PKPD,
           breakpoint_type = breakpoint_type,
+          host = host,
           is_data.frame = TRUE
         )
     } else if (types[i] == "disk") {
@@ -657,6 +686,7 @@ as.sir.data.frame <- function(x,
           include_screening = include_screening,
           include_PKPD = include_PKPD,
           breakpoint_type = breakpoint_type,
+          host = host,
           is_data.frame = TRUE
         )
     } else if (types[i] == "sir") {
@@ -666,7 +696,7 @@ as.sir.data.frame <- function(x,
       if (!all(x[, ab_cols[i], drop = TRUE] %in% c("S", "I", "R", NA), na.rm = TRUE)) {
         show_message <- TRUE
         # only print message if values are not already clean
-        message_("=> Cleaning values in column '", font_bold(ab), "' (",
+        message_("Cleaning values in column '", font_bold(ab), "' (",
           ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
           ab_name(ab_coerced, tolower = TRUE), ")... ",
           appendLF = FALSE,
@@ -675,7 +705,7 @@ as.sir.data.frame <- function(x,
       } else if (!is.sir(x.bak[, ab_cols[i], drop = TRUE])) {
         show_message <- TRUE
         # only print message if class not already set
-        message_("=> Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
+        message_("Assigning class 'sir' to already clean column '", font_bold(ab), "' (",
           ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
           ab_name(ab_coerced, tolower = TRUE, language = NULL), ")... ",
           appendLF = FALSE,
@@ -684,7 +714,7 @@ as.sir.data.frame <- function(x,
       }
       x[, ab_cols[i]] <- as.sir.default(x = as.character(x[, ab_cols[i], drop = TRUE]))
       if (show_message == TRUE) {
-        message_(" OK.", add_fn = list(font_green), as_note = FALSE)
+        message(font_green_bg(" OK "))
       }
     }
   }
@@ -714,6 +744,20 @@ get_guideline <- function(guideline, reference_data) {
   guideline_param
 }
 
+convert_host <- function(x, lang = get_AMR_locale()) {
+  x <- trimws2(tolower(as.character(x)))
+  x_out <- rep(NA_character_, length(x))
+  # this order is based on: clinical_breakpoints |> filter(type == "animal") |> count(host, sort = TRUE)
+  x_out[is.na(x_out) & (x %like% "dog|canine" | x %like% translate_AMR("dog|dogs|canine", lang))] <- "dogs"
+  x_out[is.na(x_out) & (x %like% "cattle|bovine" | x %like% translate_AMR("cattle|bovine", lang))] <- "cattle"
+  x_out[is.na(x_out) & (x %like% "swine|suida(e)?" | x %like% translate_AMR("swine|swines", lang))] <- "swine"
+  x_out[is.na(x_out) & (x %like% "cat|feline" | x %like% translate_AMR("cat|cats|feline", lang))] <- "cats"
+  x_out[is.na(x_out) & (x %like% "horse|equine" | x %like% translate_AMR("horse|horses|equine", lang))] <- "horse"
+  x_out[is.na(x_out) & (x %like% "aqua|fish" | x %like% translate_AMR("aquatic|fish", lang))] <- "aquatic"
+  x_out[is.na(x_out) & (x %like% "bird|chicken|poultry|avia" | x %like% translate_AMR("bird|birds|poultry", lang))] <- "poultry"
+  x_out
+}
+
 as_sir_method <- function(method_short,
                           method_long,
                           x,
@@ -727,6 +771,7 @@ as_sir_method <- function(method_short,
                           include_screening,
                           include_PKPD,
                           breakpoint_type,
+                          host,
                           ...) {
   meet_criteria(x, allow_NA = TRUE, .call_depth = -2)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE, .call_depth = -2)
@@ -740,11 +785,43 @@ as_sir_method <- function(method_short,
   meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
   check_reference_data(reference_data, .call_depth = -2)
   meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1, .call_depth = -2)
-
+  meet_criteria(host, allow_class = c("character", "factor"), allow_NULL = TRUE, allow_NA = TRUE, .call_depth = -2)
+  
+  # backward compatibilty
+  dots <- list(...)
+  dots <- dots[which(!names(dots) %in% c("warn", "mo.bak", "is_data.frame"))]
+  if (length(dots) != 0) {
+    warning_("These arguments in `as.sir()` are no longer used: ", vector_and(names(dots), quotes = "`"), ".", call = FALSE)
+  }
+  
   guideline_coerced <- get_guideline(guideline, reference_data)
   
+  if (breakpoint_type == "animal") {
+    if (is.null(host)) {
+      host <- AMR_env$host_preferred_order[1]
+      if (message_not_thrown_before("as.sir", "host_missing")) {
+        message_("Animal hosts not set in `host`, assuming `host = \"", host, "\"`, since these have the highest breakpoint availability.\n\n")  
+      }
+    }
+  } else {
+    if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
+      if (message_not_thrown_before("as.sir", "assumed_breakpoint_animal")) {
+        message_("Assuming `breakpoint_type = \"animal\"`, since `host` is set.", ifelse(guideline_coerced %like% "EUCAST", " Do you also need to set `guideline = \"CLSI\"`?", ""), "\n\n")
+      }
+      breakpoint_type <- "animal"
+    } else {
+      host <- NA_character_
+    }
+  }
+  host <- convert_host(host)
+  host <- tolower(host)
+  host[host == "ecoff"] <- "ECOFF"
+  
   if (message_not_thrown_before("as.sir", "sir_interpretation_history")) {
-    message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations. Note that some microorganisms might not have breakpoints for each antimicrobial drug in ", guideline_coerced, ".\n\n")  
+    message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations. Note that some ", ifelse(breakpoint_type == "animal", "animal hosts and ", ""), "microorganisms might not have breakpoints for each antimicrobial drug in ", guideline_coerced, ".\n\n")
+  }
+  if (breakpoint_type == "animal" && message_not_thrown_before("as.sir", "host_preferred_order")) {
+    message_("Please note that in the absence of specific veterinary breakpoints for certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse, aquatic, and poultry, in that order, are used as substitutes.\n\n")
   }
   
   # for dplyr's across()
@@ -817,7 +894,9 @@ as_sir_method <- function(method_short,
   if (length(uti) == 1) {
     uti <- rep(uti, length(x))
   }
-
+  if (length(host) == 1) {
+    host <- rep(host, length(x))
+  }
   if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
     if (message_not_thrown_before("as.sir", "intrinsic")) {
       warning_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
@@ -870,6 +949,7 @@ as_sir_method <- function(method_short,
     mo = mo,
     result = NA_sir_,
     uti = uti,
+    host = host,
     stringsAsFactors = FALSE
   )
   if (method == "mic") {
@@ -879,7 +959,7 @@ as_sir_method <- function(method_short,
     # when as.sir.disk is called directly
     df$values <- as.disk(df$values)
   }
-  df_unique <- unique(df[ , c("mo", "uti"), drop = FALSE])
+  df_unique <- unique(df[ , c("mo", "uti", "host"), drop = FALSE])
 
   rise_warning <- FALSE
   rise_note <- FALSE
@@ -918,7 +998,7 @@ as_sir_method <- function(method_short,
     # apparently no breakpoints found
     message(
       paste0(font_rose_bg(" WARNING "), "\n"),
-      font_black(paste0("  ", AMR_env$bullet_icon, " No ", method_coerced, " breakpoints available for ",
+      font_black(paste0("  ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
         suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
         " (", ab_coerced, ").")))
     
@@ -935,7 +1015,7 @@ as_sir_method <- function(method_short,
   has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
   on.exit(close(p))
   
-  # run the rules
+  # run the rules (df_unique is a row combination per mo/ab/uti/host)
   for (i in seq_len(nrow(df_unique))) {
     p$tick()
     mo_current <- df_unique[i, "mo", drop = TRUE]
@@ -972,9 +1052,9 @@ as_sir_method <- function(method_short,
       suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
       " (", ab_coerced, ")"
     )
-
-    # gather all available breakpoints for current MO and sort on taxonomic rank
-    # (this will prefer species breakpoints over order breakpoints)
+    
+   
+    # gather all available breakpoints for current MO
     breakpoints_current <- breakpoints %pm>%
       subset(mo %in% c(
         mo_current, mo_current_genus, mo_current_family,
@@ -982,23 +1062,45 @@ as_sir_method <- function(method_short,
         mo_current_species_group,
         mo_current_other
       ))
-
+    # set the host index according to most available breakpoints (see R/zzz.R where this is set in the pkg environment)
+    breakpoints_current$host_index <- match(breakpoints_current$host, c("human", "ECOFF", AMR_env$host_preferred_order))
+    
+    # sort on host and taxonomic rank
+    # (this will prefer species breakpoints over order breakpoints)
     if (is.na(unique(uti_current))) {
       breakpoints_current <- breakpoints_current %pm>%
         # this will put UTI = FALSE first, then UTI = TRUE, then UTI = NA
-        pm_arrange(rank_index, uti) # 'uti' is a column in data set 'clinical_breakpoints'  
+        pm_arrange(host_index, rank_index, uti) # 'uti' is a column in data set 'clinical_breakpoints'  
     } else if (unique(uti_current) == TRUE) {
       breakpoints_current <- breakpoints_current %pm>%
         subset(uti == TRUE) %pm>%
         # be as specific as possible (i.e. prefer species over genus):
-        pm_arrange(rank_index)
+        pm_arrange(host_index, rank_index)
     } else if (unique(uti_current) == FALSE) {
       breakpoints_current <- breakpoints_current %pm>%
         subset(uti == FALSE) %pm>%
         # be as specific as possible (i.e. prefer species over genus):
-        pm_arrange(rank_index)
+        pm_arrange(host_index, rank_index)
     }
-
+    
+    if (NROW(breakpoints_current) == 0) {
+      # no note about missing breakpoints - it's already in the header before the interpretation starts
+      next
+    }
+    
+    # veterinary host check
+    host_current <- unique(df_unique[i, "host", drop = TRUE])[1]
+    breakpoints_current$host_match <- breakpoints_current$host == host_current
+    if (breakpoint_type == "animal") {
+      if (any(breakpoints_current$host_match == TRUE, na.rm = TRUE)) {
+        breakpoints_current <- breakpoints_current %pm>%
+          subset(host_match == TRUE)
+      } else {
+        # no breakpoint found for this host, so sort on mostly available guidelines
+        msgs <- c(msgs, paste0("No ", guideline_coerced, " breakpoints for ", font_bold(host_current), " available for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " breakpoints instead."))
+      }
+    }
+ 
     # throw notes for different body sites
     site <- breakpoints_current[1L, "site", drop = FALSE] # this is the one we'll take
     if (is.na(site)) {
@@ -1012,15 +1114,12 @@ as_sir_method <- function(method_short,
       rise_warning <- TRUE
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_coerced)) {
       # both UTI and Non-UTI breakpoints available
-      msgs <- c(msgs, paste0("Breakpoints for UTI ", font_underline("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
+      msgs <- c(msgs, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
       breakpoints_current <- breakpoints_current %pm>%
         pm_filter(uti == FALSE)
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_coerced)) {
       # breakpoints for multiple body sites available
       msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, "."))
-    } else if (nrow(breakpoints_current) == 0) {
-      # # do not note - it's already in the header before the interpretation starts
-      next
     }
     
     # first check if mo is intrinsic resistant
@@ -1081,6 +1180,7 @@ as_sir_method <- function(method_short,
           method = rep(method_coerced, length(rows)),
           breakpoint_S_R = rep(paste0(breakpoints_current[, "breakpoint_S", drop = TRUE], "-", breakpoints_current[, "breakpoint_R", drop = TRUE]), length(rows)),
           guideline = rep(guideline_coerced, length(rows)),
+          host = rep(breakpoints_current[, "host", drop = TRUE], length(rows)),
           ref_table = rep(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
           uti = rep(breakpoints_current[, "uti", drop = TRUE], length(rows)),
           stringsAsFactors = FALSE

R/sir_calc.R

@@ -223,7 +223,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
                         combine_SI = TRUE,
                         confidence_level = 0.95) {
   meet_criteria(type, is_in = c("proportion", "count", "both"), has_length = 1)
-  meet_criteria(data, allow_class = "data.frame", contains_column_class = c("sir", "rsi"))
+  meet_criteria(data, allow_class = "data.frame", contains_column_class = "sir")
   meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
   language <- validate_language(language)
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
@@ -373,5 +373,5 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
 
   rownames(out) <- NULL
   out <- as_original_data_class(out, class(data.bak)) # will remove tibble groups
-  structure(out, class = c("sir_df", "rsi_df", class(out)))
+  structure(out, class = c("sir_df", class(out)))
 }

R/translate.R

@@ -66,17 +66,12 @@
 #' mo_name("Coagulase-negative Staphylococcus (CoNS)")
 #'
 #' # setting another language
-#' set_AMR_locale("Spanish")
+#' set_AMR_locale("Dutch")
 #' ab_name("Ciprofloxacin")
 #' mo_name("Coagulase-negative Staphylococcus (CoNS)")
 #'
 #' # setting yet another language
-#' set_AMR_locale("Greek")
-#' ab_name("Ciprofloxacin")
-#' mo_name("Coagulase-negative Staphylococcus (CoNS)")
-#'
-#' # setting yet another language
-#' set_AMR_locale("Ukrainian")
+#' set_AMR_locale("German")
 #' ab_name("Ciprofloxacin")
 #' mo_name("Coagulase-negative Staphylococcus (CoNS)")
 #'
@@ -266,7 +261,7 @@ translate_into_language <- function(from,
   # a kind of left join to get all results back
   out <- from_unique_translated[match(from.bak, from_unique)]
 
-  if (!identical(from.bak, out) && get_AMR_locale() == lang && message_not_thrown_before("translation", entire_session = TRUE) && interactive()) {
+  if (!identical(from.bak, out) && get_AMR_locale() == lang && is.null(getOption("AMR_locale", default = NULL)) && message_not_thrown_before("translation", entire_session = TRUE) && interactive()) {
     message(word_wrap(
       "Assuming the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym, " language (",
       LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package. See `set_AMR_locale()` to change this or to silence this once-per-session note.",

R/vctrs.R

@@ -34,7 +34,8 @@
 
 # see https://github.com/tidyverse/dplyr/issues/5955 why this is required
 
-# S3: ab_selector
+# S3: ab_selector ----
+# this does not need a .default method since it's used internally only
 vec_ptype2.character.ab_selector <- function(x, y, ...) {
   x
 }
@@ -45,7 +46,8 @@ vec_cast.character.ab_selector <- function(x, to, ...) {
   unclass(x)
 }
 
-# S3: ab_selector_any_all
+# S3: ab_selector_any_all ----
+# this does not need a .default method since it's used internally only
 vec_ptype2.logical.ab_selector_any_all <- function(x, y, ...) {
   x
 }
@@ -56,12 +58,12 @@ vec_cast.logical.ab_selector_any_all <- function(x, to, ...) {
   unclass(x)
 }
 
-# S3: ab
-vec_ptype2.character.ab <- function(x, y, ...) {
+# S3: ab ----
+vec_ptype2.ab.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
-vec_ptype2.ab.character <- function(x, y, ...) {
-  y
+vec_ptype2.ab.ab <- function(x, y, ...) {
+  x
 }
 vec_cast.character.ab <- function(x, to, ...) {
   as.character(x)
@@ -70,12 +72,12 @@ vec_cast.ab.character <- function(x, to, ...) {
   return_after_integrity_check(x, "antimicrobial drug code", as.character(AMR_env$AB_lookup$ab))
 }
 
-# S3: av
-vec_ptype2.character.av <- function(x, y, ...) {
+# S3: av ----
+vec_ptype2.av.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
-vec_ptype2.av.character <- function(x, y, ...) {
-  y
+vec_ptype2.av.av <- function(x, y, ...) {
+  x
 }
 vec_cast.character.av <- function(x, to, ...) {
   as.character(x)
@@ -84,12 +86,12 @@ vec_cast.av.character <- function(x, to, ...) {
   return_after_integrity_check(x, "antiviral drug code", as.character(AMR_env$AV_lookup$av))
 }
 
-# S3: mo
-vec_ptype2.character.mo <- function(x, y, ...) {
+# S3: mo ----
+vec_ptype2.mo.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
-vec_ptype2.mo.character <- function(x, y, ...) {
-  y
+vec_ptype2.mo.mo <- function(x, y, ...) {
+  x
 }
 vec_cast.character.mo <- function(x, to, ...) {
   as.character(x)
@@ -99,12 +101,18 @@ vec_cast.mo.character <- function(x, to, ...) {
   return_after_integrity_check(x, "microorganism code", as.character(AMR_env$MO_lookup$mo))
 }
 
-# S3: disk
-vec_ptype2.integer.disk <- function(x, y, ...) {
+# S3: disk ----
+vec_ptype_full.disk <- function(x, ...) {
+  "disk"
+}
+vec_ptype_abbr.disk <- function(x, ...) {
+  "disk"
+}
+vec_ptype2.disk.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
-vec_ptype2.disk.integer <- function(x, y, ...) {
-  y
+vec_ptype2.disk.disk <- function(x, y, ...) {
+  x
 }
 vec_cast.integer.disk <- function(x, to, ...) {
   unclass(x)
@@ -125,29 +133,56 @@ vec_cast.disk.character <- function(x, to, ...) {
   as.disk(x)
 }
 
-# S3: mic
+# S3: mic ----
+vec_ptype2.mic.default <- function (x, y, ..., x_arg = "", y_arg = "") {
+  # this will make sure that currently implemented MIC levels are returned
+  as.mic(x)
+}
+vec_ptype2.mic.mic <- function(x, y, ...) {
+  # this will make sure that currently implemented MIC levels are returned
+  as.mic(x)
+}
+vec_cast.mic.mic <- function(x, to, ...) {
+  # this will make sure that currently implemented MIC levels are returned
+  as.mic(x)
+}
 vec_cast.character.mic <- function(x, to, ...) {
   as.character(x)
 }
 vec_cast.double.mic <- function(x, to, ...) {
   as.double(x)
 }
+vec_cast.integer.mic <- function(x, to, ...) {
+  as.integer(x)
+}
+vec_cast.factor.mic <- function(x, to, ...) {
+  factor(as.character(x))
+}
 vec_cast.mic.double <- function(x, to, ...) {
   as.mic(x)
 }
 vec_cast.mic.character <- function(x, to, ...) {
   as.mic(x)
 }
+vec_cast.mic.integer <- function(x, to, ...) {
+  as.mic(x)
+}
+vec_cast.mic.factor <- function(x, to, ...) {
+  as.mic(x)
+}
 vec_math.mic <- function(.fn, x, ...) {
   .fn(as.double(x), ...)
 }
+vec_arith.mic <- function(op, x, y, ...) {
+  vctrs::vec_arith(op, as.double(x), as.double(y))
+}
 
-# S3: sir
-vec_ptype2.character.sir <- function(x, y, ...) {
+# S3: sir ----
+vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") {
   x
 }
-vec_ptype2.sir.character <- function(x, y, ...) {
-  y
+vec_ptype2.sir.sir <- function(x, y, ...) {
+  x
 }
 vec_cast.character.sir <- function(x, to, ...) {
   as.character(x)

R/whocc.R

@@ -31,13 +31,13 @@
 #'
 #' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
 #' @section WHOCC:
-#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://www.whocc.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
+#' This package contains **all ~550 antibiotic, antimycotic and antiviral drugs** and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <https://atcddd.fhi.no>) and the Pharmaceuticals Community Register of the European Commission (<https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm>).
 #'
 #' These have become the gold standard for international drug utilisation monitoring and research.
 #'
 #' The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
 #'
-#' **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.** See <https://www.whocc.no/copyright_disclaimer/.>
+#' **NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.** See <https://atcddd.fhi.no/copyright_disclaimer/.>
 
 #' @name WHOCC
 #' @rdname WHOCC

R/zz_deprecated.R

@@ -27,171 +27,14 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-#' Deprecated Functions
-#'
-#' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
-#' @keywords internal
-#' @name AMR-deprecated
-#' @rdname AMR-deprecated
-#' @export
-NA_rsi_ <- set_clean_class(factor(NA_character_, levels = c("S", "I", "R"), ordered = TRUE),
-  new_class = c("rsi", "ordered", "factor")
-)
-#' @rdname AMR-deprecated
-#' @export
-as.rsi <- function(x, ...) {
-  deprecation_warning("as.rsi", "as.sir")
-  UseMethod("as.rsi")
-}
-#' @noRd
-#' @export
-as.rsi.default <- function(...) {
-  as.sir.default(...)
-}
-#' @noRd
-#' @export
-as.rsi.mic <- function(...) {
-  as.sir.mic(...)
-}
-#' @noRd
-#' @export
-as.rsi.disk <- function(...) {
-  as.sir.disk(...)
-}
-#' @noRd
-#' @export
-as.rsi.data.frame <- function(...) {
-  as.sir.data.frame(...)
-}
-
-#' @rdname AMR-deprecated
-#' @export
-facet_rsi <- function(...) {
-  deprecation_warning("facet_rsi", "facet_sir")
-  facet_sir(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-geom_rsi <- function(...) {
-  deprecation_warning("geom_rsi", "geom_sir")
-  geom_sir(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-ggplot_rsi <- function(...) {
-  deprecation_warning("ggplot_rsi", "ggplot_sir")
-  ggplot_sir(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-ggplot_rsi_predict <- function(...) {
-  deprecation_warning("ggplot_rsi_predict", "ggplot_sir_predict")
-  ggplot_sir_predict(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-is.rsi <- function(...) {
-  # REMINDER: change as.sir() to remove the deprecation warning there
-  suppressWarnings(is.sir(...))
-}
-#' @rdname AMR-deprecated
-#' @export
-is.rsi.eligible <- function(...) {
-  deprecation_warning("is.rsi.eligible", "is_sir_eligible")
-  is_sir_eligible(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-labels_rsi_count <- function(...) {
-  deprecation_warning("labels_rsi_count", "labels_sir_count")
-  labels_sir_count(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-n_rsi <- function(...) {
-  deprecation_warning("n_rsi", "n_sir")
-  n_sir(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-random_rsi <- function(...) {
-  deprecation_warning("random_rsi", "random_sir")
-  random_sir(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-rsi_df <- function(...) {
-  deprecation_warning("rsi_df", "sir_df")
-  sir_df(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-rsi_predict <- function(...) {
-  deprecation_warning("rsi_predict", "sir_predict")
-  sir_predict(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-scale_rsi_colours <- function(...) {
-  deprecation_warning("scale_rsi_colours", "scale_sir_colours")
-  scale_sir_colours(...)
-}
-#' @rdname AMR-deprecated
-#' @export
-theme_rsi <- function(...) {
-  deprecation_warning("theme_rsi", "theme_sir")
-  theme_sir(...)
-}
-
-# will be exported using s3_register() in R/zzz.R
-pillar_shaft.rsi <- pillar_shaft.sir
-type_sum.rsi <- function(x, ...) {
-  if (message_not_thrown_before("type_sum.rsi")) {
-    deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir'. Transform your 'rsi' columns to 'sir' with `as.sir()`, e.g.:\n  your_data %>% mutate_if(is.rsi, as.sir)")
-  }
-  "rsi"
-}
-
-#' @method print rsi
-#' @export
-#' @noRd
-print.rsi <- function(x, ...) {
-  deprecation_warning(extra_msg = "The 'rsi' class has been replaced with 'sir' - transform your 'rsi' data with `as.sir()`")
-  cat("Class 'rsi'", font_bold(font_red("[!]\n")))
-  print(as.character(x), quote = FALSE)
-}
-
-#' @noRd
-#' @export
-`[<-.rsi` <- `[<-.sir`
-#' @noRd
-#' @export
-`[[<-.rsi` <- `[[<-.sir`
-#' @noRd
-#' @export
-barplot.rsi <- barplot.sir
-#' @noRd
-#' @export
-c.rsi <- c.sir
-#' @noRd
-#' @export
-droplevels.rsi <- droplevels.sir
-#' @noRd
-#' @export
-plot.rsi <- plot.sir
-#' @noRd
-#' @export
-rep.rsi <- rep.sir
-#' @noRd
-#' @export
-summary.rsi <- summary.sir
-#' @noRd
-#' @export
-unique.rsi <- unique.sir
-
-# WHEN REMOVING RSI, DON'T FORGET TO REMOVE :
-# - THE "rsi_df" CLASS FROM R/sir_calc.R
-# - CODE CONTAINING only_rsi_columns, colours_RSI, include_untested_rsi, prob_RSI
+# #' Deprecated Functions
+# #' 
+# #' These functions are so-called '[Deprecated]'. **They will be removed in a future release.** Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
+# #' @keywords internal
+# #' @name AMR-deprecated
+# #' @rdname AMR-deprecated
+# #' @export
+# NULL
 
 deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE) {
   if (is.null(old)) {

R/zzz.R

@@ -67,6 +67,7 @@ AMR_env$sir_interpretation_history <- data.frame(
   method = character(0),
   breakpoint_S_R = character(0),
   guideline = character(0),
+  host = character(0),
   ref_table = character(0),
   stringsAsFactors = FALSE
 )
@@ -98,16 +99,13 @@ if (pkg_is_available("cli")) {
   s3_register("pillar::pillar_shaft", "av")
   s3_register("pillar::pillar_shaft", "mo")
   s3_register("pillar::pillar_shaft", "sir")
-  s3_register("pillar::pillar_shaft", "rsi") # remove in a later version
   s3_register("pillar::pillar_shaft", "mic")
   s3_register("pillar::pillar_shaft", "disk")
   s3_register("pillar::type_sum", "ab")
   s3_register("pillar::type_sum", "av")
   s3_register("pillar::type_sum", "mo")
   s3_register("pillar::type_sum", "sir")
-  s3_register("pillar::type_sum", "rsi") # remove in a later version
   s3_register("pillar::type_sum", "mic")
-  s3_register("pillar::type_sum", "disk")
   # Support for frequency tables from the cleaner package
   s3_register("cleaner::freq", "mo")
   s3_register("cleaner::freq", "sir")
@@ -132,6 +130,7 @@ if (pkg_is_available("cli")) {
   s3_register("knitr::knit_print", "antibiogram")
   s3_register("knitr::knit_print", "formatted_bug_drug_combinations")
   # Support vctrs package for use in e.g. dplyr verbs
+  # NOTE 2024-02-22 this is the right way - it should be 2 S3 classes in the second argument
   # S3: ab_selector
   s3_register("vctrs::vec_ptype2", "character.ab_selector")
   s3_register("vctrs::vec_ptype2", "ab_selector.character")
@@ -141,23 +140,25 @@ if (pkg_is_available("cli")) {
   s3_register("vctrs::vec_ptype2", "ab_selector_any_all.logical")
   s3_register("vctrs::vec_cast", "logical.ab_selector_any_all")
   # S3: ab
-  s3_register("vctrs::vec_ptype2", "character.ab")
-  s3_register("vctrs::vec_ptype2", "ab.character")
+  s3_register("vctrs::vec_ptype2", "ab.default")
+  s3_register("vctrs::vec_ptype2", "ab.ab")
   s3_register("vctrs::vec_cast", "character.ab")
   s3_register("vctrs::vec_cast", "ab.character")
   # S3: av
-  s3_register("vctrs::vec_ptype2", "character.av")
-  s3_register("vctrs::vec_ptype2", "av.character")
+  s3_register("vctrs::vec_ptype2", "av.default")
+  s3_register("vctrs::vec_ptype2", "av.av")
   s3_register("vctrs::vec_cast", "character.av")
   s3_register("vctrs::vec_cast", "av.character")
   # S3: mo
-  s3_register("vctrs::vec_ptype2", "character.mo")
-  s3_register("vctrs::vec_ptype2", "mo.character")
+  s3_register("vctrs::vec_ptype2", "mo.default")
+  s3_register("vctrs::vec_ptype2", "mo.mo")
   s3_register("vctrs::vec_cast", "character.mo")
   s3_register("vctrs::vec_cast", "mo.character")
   # S3: disk
-  s3_register("vctrs::vec_ptype2", "integer.disk")
-  s3_register("vctrs::vec_ptype2", "disk.integer")
+  s3_register("vctrs::vec_ptype_full", "disk")
+  s3_register("vctrs::vec_ptype_abbr", "disk")
+  s3_register("vctrs::vec_ptype2", "disk.default")
+  s3_register("vctrs::vec_ptype2", "disk.disk")
   s3_register("vctrs::vec_cast", "integer.disk")
   s3_register("vctrs::vec_cast", "disk.integer")
   s3_register("vctrs::vec_cast", "double.disk")
@@ -165,14 +166,22 @@ if (pkg_is_available("cli")) {
   s3_register("vctrs::vec_cast", "character.disk")
   s3_register("vctrs::vec_cast", "disk.character")
   # S3: mic
+  s3_register("vctrs::vec_ptype2", "mic.default")
+  s3_register("vctrs::vec_ptype2", "mic.mic")
   s3_register("vctrs::vec_cast", "character.mic")
   s3_register("vctrs::vec_cast", "double.mic")
+  s3_register("vctrs::vec_cast", "integer.mic")
+  s3_register("vctrs::vec_cast", "factor.mic")
   s3_register("vctrs::vec_cast", "mic.character")
   s3_register("vctrs::vec_cast", "mic.double")
+  s3_register("vctrs::vec_cast", "mic.integer")
+  s3_register("vctrs::vec_cast", "mic.factor")
+  s3_register("vctrs::vec_cast", "mic.mic")
   s3_register("vctrs::vec_math", "mic")
+  s3_register("vctrs::vec_arith", "mic")
   # S3: sir
-  s3_register("vctrs::vec_ptype2", "character.sir")
-  s3_register("vctrs::vec_ptype2", "sir.character")
+  s3_register("vctrs::vec_ptype2", "sir.default")
+  s3_register("vctrs::vec_ptype2", "sir.sir")
   s3_register("vctrs::vec_cast", "character.sir")
   s3_register("vctrs::vec_cast", "sir.character")
 
@@ -189,31 +198,41 @@ if (pkg_is_available("cli")) {
   # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
   AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
   AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
+  
+  AMR_env$host_preferred_order <- names(sort(table(AMR::clinical_breakpoints$host[!AMR::clinical_breakpoints$host %in% AMR::clinical_breakpoints$type]), decreasing = TRUE))
 }
 
 .onAttach <- function(lib, pkg) {
   # if custom ab option is available, load it
   if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
-    packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
-    x <- readRDS_AMR(getOption("AMR_custom_ab"))
-    tryCatch(
-      {
-        suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
-        packageStartupMessage("OK.")
-      },
-      error = function(e) packageStartupMessage("Failed: ", e$message)
-    )
+    if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {
+      packageStartupMessage("The file with custom antimicrobials must be an RDS file. Set the option `AMR_custom_ab` to another path.")
+    } else {
+      packageStartupMessage("Adding custom antimicrobials from '", getOption("AMR_custom_ab"), "'...", appendLF = FALSE)
+      x <- readRDS_AMR(getOption("AMR_custom_ab"))
+      tryCatch(
+        {
+          suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
+          packageStartupMessage("OK.")
+        },
+        error = function(e) packageStartupMessage("Failed: ", e$message)
+      )
+    }
   }
   # if custom mo option is available, load it
   if (!is.null(getOption("AMR_custom_mo")) && file.exists(getOption("AMR_custom_mo", default = ""))) {
-    packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
-    x <- readRDS_AMR(getOption("AMR_custom_mo"))
-    tryCatch(
-      {
-        suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
-        packageStartupMessage("OK.")
-      },
-      error = function(e) packageStartupMessage("Failed: ", e$message)
-    )
+    if (getOption("AMR_custom_mo") %unlike% "[.]rds$") {
+      packageStartupMessage("The file with custom microorganisms must be an RDS file. Set the option `AMR_custom_mo` to another path.")
+    } else {
+      packageStartupMessage("Adding custom microorganisms from '", getOption("AMR_custom_mo"), "'...", appendLF = FALSE)
+      x <- readRDS_AMR(getOption("AMR_custom_mo"))
+      tryCatch(
+        {
+          suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
+          packageStartupMessage("OK.")
+        },
+        error = function(e) packageStartupMessage("Failed: ", e$message)
+      )
+    }
   }
 }

_pkgdown.yml

@@ -35,15 +35,11 @@ template:
   bootswatch: "flatly"
   assets: "pkgdown/logos" # use logos in this folder
   bslib:
+    base_font: {google: "Lato"}
+    heading_font: {google: "Lato"}
     code_font: {google: "Fira Code"}
     # body-text-align: "justify"
     line-height-base: 1.75
-    # the green "success" colour of this bootstrap theme should be the same as the green in our logo
-    success: "#128f76"
-    link-color: "#128f76"
-    light: "#128f76a6" # this is success with 60% alpha
-    # the template "info" is blue - this should be a green fitting our theme
-    info: "#60a799"
     # make top bar a bit wider
     navbar-padding-y: "0.5rem"
   opengraph:
@@ -145,6 +141,12 @@ navbar:
       href: "https://github.com/msberends/AMR"
 
 reference:
+  - title: "Introduction to the package"
+    desc: >
+      Please find the introduction to (and some general information about) our package here.
+    contents:
+    - "`AMR`"
+    
   - title: "Preparing data: microorganisms"
     desc: >
       These functions are meant to get taxonomically valid properties of microorganisms from any input, but
@@ -168,7 +170,7 @@ reference:
     - "`atc_online_property`"
     - "`add_custom_antimicrobials`"
 
-  - title: "Preparing data: antimicrobial resistance"
+  - title: "Preparing data"
     desc: >
       With `as.mic()` and `as.disk()` you can transform your raw input to valid MIC or disk diffusion values.
       Use `as.sir()` for cleaning raw data to let it only contain "R", "I" and "S", or to interpret MIC or disk diffusion values as SIR based on the lastest EUCAST and CLSI guidelines.
@@ -180,7 +182,7 @@ reference:
     - "`eucast_rules`"
     - "`custom_eucast_rules`"
 
-  - title: "Analysing data: antimicrobial resistance"
+  - title: "Analysing data"
     desc: >
       Use these function for the analysis part. You can use `susceptibility()` or `resistance()` on any antibiotic column.
       With `antibiogram()`, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination
@@ -196,14 +198,25 @@ reference:
     - "`key_antimicrobials`"
     - "`mdro`"
     - "`count`"
-    - "`plot`"
-    - "`ggplot_sir`"
     - "`bug_drug_combinations`"
     - "`antibiotic_class_selectors`"
     - "`mean_amr_distance`"
     - "`resistance_predict`"
     - "`guess_ab_col`"
     
+  - title: "Plotting data"
+    desc: >
+      Use these functions for the plotting part. The `scale_*_mic()` functions extend the ggplot2 package to allow plotting of 
+      MIC values, even within a manually set range.
+      If using `plot()` (base R) or `autoplot()` (ggplot2) on MIC values or disk diffusion values, the user can
+      set the interpretation guideline to give the bars the right SIR colours.
+      The `ggplot_sir()` function is a short wrapper for users not much accustomed to ggplot2 yet.
+      The `ggplot_pca()` function is a specific function to plot so-called biplots for PCA (principal component analysis).
+    contents:
+    - "`plot`"
+    - "`ggplot_sir`"
+    - "`ggplot_pca`"
+    
   - title: "Other: AMR-specific options"
     desc: >
       The AMR package is customisable, by providing settings that can be set per user or per team. For
@@ -229,7 +242,6 @@ reference:
       Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
       for more information about how to work with functions in this package.
     contents:
-    - "`AMR`"
     - "`example_isolates`"
     - "`microorganisms`"
     - "`microorganisms.codes`"
@@ -252,7 +264,6 @@ reference:
     - "`age`"
     - "`availability`"
     - "`get_AMR_locale`"
-    - "`ggplot_pca`"
     - "`italicise_taxonomy`"
     - "`join`"
     - "`like`"
@@ -268,10 +279,10 @@ reference:
     - "`kurtosis`"
     - "`skewness`"
 
-  - title: "Other: deprecated functions"
-    desc: >
-      These functions are deprecated, meaning that they will still
-      work but show a warning with every use and will be removed
-      in a future version.
-    contents:
-    - "`AMR-deprecated`"
+  # - title: "Other: deprecated functions"
+  #   desc: >
+  #     These functions are deprecated, meaning that they will still
+  #     work but show a warning with every use and will be removed
+  #     in a future version.
+  #   contents:
+  #   - "`AMR-deprecated`"

cran-comments.md

@@ -1,7 +1,9 @@
-The email address of the maintainer has changed - not the person.
+**On the 15th of October, 2023, we received an email from Prof Ripley about an issue in UTF-8 strings in our documentation. This version contains a fix to this issue.**
+
+Previous comments:
 
 As with all previous >20 releases, some CHECKs might return a NOTE for *just* hitting the installation size limit, though its size has been brought down to a minimum in collaboration with CRAN maintainers previously.
 
-We consider this a high-impact package: it was published in the Journal of Statistical Software (2022), is including in a CRAN Task View (Epidemiology), and is according to download stats used in almost all countries in the world. If there is anything to note, please let us know up-front without directly archiving the current version. That said, we continually unit test our package extensively and have no reason to assume that anything is wrong.
+We consider this a high-impact package: it was published in the Journal of Statistical Software (2022), is included in a CRAN Task View (Epidemiology), and is according to download stats used in almost all countries in the world. If there is anything to note, please let us know up-front without directly archiving the current version. That said, we continually unit test our package extensively and have no reason to assume that anything is wrong.
 
 Thanks for maintaining and hosting CRAN! It's empowering R and its use enormously!

data-raw/AMR new logo.txt

@@ -0,0 +1,3 @@
+green grass #a7dbc3
+green bacteria #128F76
+blue sky #a8d5ef

data-raw/AMR_vet.qmd

@@ -0,0 +1,71 @@
+---
+title: "AMR Goes Vet"
+author: "Jason, Matthew, Javier, Matthijs"
+date: "2024-02-20"
+format: 
+  html: 
+    embed-resources: true
+---
+
+## Import WHONET data set
+
+```{r, message=FALSE, warning=FALSE}
+library(dplyr)
+library(readr)
+library(tidyr)
+library(janitor)
+
+# WHONET version of 16th Feb 2024
+whonet_breakpoints <- read_tsv("WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
+                               show_col_types = FALSE, guess_max = Inf) %>%
+  filter(GUIDELINES %in% c("CLSI", "EUCAST"))
+
+dim(whonet_breakpoints)
+```
+
+# EDA of Animal Breakpoints
+
+```{r}
+whonet_breakpoints |>
+  filter(BREAKPOINT_TYPE != "Human")
+whonet_breakpoints |>
+  filter(BREAKPOINT_TYPE != "Human") |>
+  count(BREAKPOINT_TYPE)
+whonet_breakpoints |>
+  filter(BREAKPOINT_TYPE == "Animal")
+```
+
+### Count of all animal breakpoints
+
+```{r}
+whonet_breakpoints |>
+  filter(BREAKPOINT_TYPE == "Animal") |>
+  count(YEAR, HOST, REFERENCE_TABLE = gsub("VET[0-9]+ ", "", REFERENCE_TABLE)) |>
+  pivot_wider(names_from = YEAR, values_from = n, values_fill = list(n = 0)) |>
+  arrange(HOST, REFERENCE_TABLE) |> 
+  adorn_totals(name = "TOTAL")
+```
+
+### Cats only
+
+```{r}
+whonet_breakpoints |>
+  filter(HOST == "Cats", YEAR >= 2021) |> 
+  select(GUIDELINES, YEAR, TEST_METHOD, ORGANISM_CODE, R, S) |> 
+  mutate(MO_NAME = AMR::mo_shortname(ORGANISM_CODE), .before = R) |> 
+  as.data.frame()
+```
+
+### Site of infection in cats (2023)
+
+```{r}
+whonet_breakpoints |>
+  filter(HOST == "Cats", YEAR == 2023) |> 
+  mutate(MO = AMR::mo_shortname(ORGANISM_CODE),
+         AB = AMR::ab_name(WHONET_ABX_CODE),
+         SITE_OF_INFECTION = substr(SITE_OF_INFECTION, 1, 25)) |> 
+  arrange(MO, AB) |> 
+  select(MO, AB, SITE_OF_INFECTION) |> 
+  as.data.frame()
+```
+

data-raw/_pre_commit_hook.R

@@ -157,20 +157,21 @@ MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Stre
 MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
 MO_PREVALENT_GENERA <- c(
   "Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
-  "Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
-  "Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Cladophialophora",
+  "Anisakis", "Anopheles", "Apophysomyces", "Arthroderma", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
+  "Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Chrysosporium", "Cladophialophora",
   "Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex",
   "Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Echinostoma", "Entamoeba", "Enterobius",
-  "Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Giardia", "Haloarcula", "Halobacterium",
+  "Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Geotrichum", "Giardia", "Haloarcula", "Halobacterium",
   "Halococcus", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces",
-  "Hysterothylacium", "Leishmania", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
-  "Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
-  "Oidiodendron", "Opisthorchis", "Pediculus", "Penicillium", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
+  "Hysterothylacium", "Kloeckera", "Kodamaea", "Leishmania", "Lichtheimia", "Lodderomyces",
+  "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
+  "Microsporum", "Millerozyma", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
+  "Oidiodendron", "Opisthorchis", "Paecilomyces", "Pediculus", "Penicillium", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
   "Pityrosporum", "Pneumocystis", "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus",
-  "Rhodotorula", "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
-  "Sporobolomyces", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Trichinella",
+  "Rhodotorula", "Saccharomyces", "Saprochaete", "Sarcoptes", "Scedosporium", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
+  "Sporobolomyces", "Sporotrichum", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Trichinella",
   "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris",
-  "Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Wuchereria"
+  "Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Verticillium", "Wuchereria"
 )
 
 # antibiotic groups

data-raw/ab.md5

@@ -1 +1 @@
-8bf97fd5f1d8d82486902d05916ebca0
+85e31c828b6f1795c8cb18b568f15c3e

data-raw/antibiotics.txt

@@ -3,256 +3,256 @@
 "ACM"	6450012	"Acetylmidecamycin"	"Macrolides/lincosamides"	"NA"			""	""					""
 "ASP"	49787020	"Acetylspiramycin"	"Macrolides/lincosamides"	"NA"			""	"acetylspiramycin,foromacidin b,spiramycin ii"					""
 "ALS"	8954	"Aldesulfone sodium"	"Other antibacterials"	"J04BA03"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"adesulfone sodium,aldapsone,aldesulfona sodica,aldesulfone,aldesulfone sodique,aldesulfone sodium,aldesulphone sodium,diamidin,diasone,diasone sodium,diazon,novotrone,sodium aldesulphone,sodium sulfoxone,sulfoxone sodium"	0.33	"g"			""
-"AMK"	37768	"Amikacin"	"Aminoglycosides"	"D06AX12,J01GB06,S01AA21"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"ak,ami,amik,amk,an"	"amicacin,amikacillin,amikacin,amikacin base,amikacin dihydrate,amikacin free base,amikacin sulfate,amikacina,amikacine,amikacinum,amikavet,amikin,amiklin,amikozit,amukin,arikace,arikayce liposomal,briclin,kaminax,lukadin,mikavir,pierami,potentox"			1	"g"	"13546-7,15098-7,17798-0,31097-9,31098-7,31099-5,3319-1,3320-9,3321-7,35669-1,50802-8,50803-6,56628-1,59378-0,80972-3"
+"AMK"	37768	"Amikacin"	"Aminoglycosides"	"D06AX12,J01GB06,S01AA21"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"ak,ami,amik,amk,an"	"amicacin,amikacillin,amikacin,amikacin base,amikacin dihydrate,amikacin free base,amikacin sulfate,amikacina,amikacine,amikacinum,amikavet,amikin,amiklin,amikozit,amukin,arikace,arikayce liposomal,briclin,kaminax,lukadin,mikavir,pierami,potentox"			1	"g"	"101493-5,11-7,12-5,13-3,13546-7,14-1,15098-7,17798-0,18860-7,20373-7,23624-0,25174-4,25175-1,25176-9,25177-7,25178-5,25179-3,31097-9,31098-7,31099-5,3319-1,3320-9,3321-7,35669-1,42642-9,48169-7,50802-8,50803-6,56628-1,59378-0,60564-2,60565-9,6975-7,80972-3,89484-0"
 "AKF"		"Amikacin/fosfomycin"	"Aminoglycosides"	"NA"			""	""					""
-"AMX"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"J01CA04"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"ac,amox,amx"	"actimoxi,amoclen,amolin,amopen,amopenixin,amoxibiotic,amoxicaps,amoxicilina,amoxicillin,amoxicillin hydrate,amoxicilline,amoxicillinum,amoxiden,amoxil,amoxivet,amoxy,amoxycillin,amoxyke,anemolin,aspenil,atoksilin,biomox,bristamox,cemoxin,clamoxyl,damoxy,delacillin,demoksil,dispermox,efpenix,flemoxin,hiconcil,histocillin,hydroxyampicillin,ibiamox,imacillin,lamoxy,largopen,metafarma capsules,metifarma capsules,moksilin,moxacin,moxatag,ospamox,pamoxicillin,piramox,promoxil,remoxil,robamox,sawamox pm,tolodina,topramoxin,unicillin,utimox,vetramox"	1.5	"g"	3	"g"	"16365-9,25274-2,3344-9,80133-2"
+"AMX"	33613	"Amoxicillin"	"Beta-lactams/penicillins"	"J01CA04"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"ac,amox,amx"	"actimoxi,amoclen,amolin,amopen,amopenixin,amoxibiotic,amoxicaps,amoxicilina,amoxicillin,amoxicillin hydrate,amoxicilline,amoxicillinum,amoxiden,amoxil,amoxivet,amoxy,amoxycillin,amoxyke,anemolin,aspenil,atoksilin,biomox,bristamox,cemoxin,clamoxyl,damoxy,delacillin,demoksil,dispermox,efpenix,flemoxin,hiconcil,histocillin,hydroxyampicillin,ibiamox,imacillin,lamoxy,largopen,metafarma capsules,metifarma capsules,moksilin,moxacin,moxatag,ospamox,pamoxicillin,piramox,promoxil,remoxil,robamox,sawamox pm,tolodina,topramoxin,unicillin,utimox,vetramox"	1.5	"g"	3	"g"	"101498-4,15-8,16-6,16365-9,17-4,18-2,18861-5,18862-3,19-0,20-8,21-6,22-4,25274-2,25310-4,3344-9,55614-2,55615-9,55616-7,6976-5,6977-3,80133-2"
 "AMC"	23665637	"Amoxicillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR02"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/c,amcl,aml,aug,xl"	"amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,augmentan,augmentin,augmentin xr,augmentine,auspilic,clamentin,clamobit,clavamox,clavinex,clavoxilin plus,clavulin,clavumox,coamoxiclav,eumetinex,kmoxilin,spectramox,spektramox,synulox,viaclav,xiclav"	1.5	"g"	3	"g"	""
-"AXS"	465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
-"AMB"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"A01AB04,A07AA07,G01AA03,J02AA01"	"Antimycotics for systemic use"	"Antibiotics"	"amf,amfb,amph"	"abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon"	40	"mg"	35	"mg"	"16370-9,3353-0,3354-8,40707-2,40757-7,49859-2"
+"AXS"	465441	"Amoxicillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					"55614-2,55615-9,55616-7"
+"AMB"	5280965	"Amphotericin B"	"Antifungals/antimycotics"	"A01AB04,A07AA07,G01AA03,J02AA01"	"Antimycotics for systemic use"	"Antibiotics"	"amf,amfb,amph"	"abelcet,abelecet,ambisome,amfotericina b,amphocin,amphomoronal,amphortericin b,amphotec,amphotericin,amphotericin b,amphotericine b,amphotericinum b,amphozone,anfotericine b,fungilin,fungisome,fungisone,fungizone,halizon"	40	"mg"	210	"mg"	"16370-9,18863-1,23-2,24-0,25-7,26-5,3353-0,3354-8,40707-2,40757-7,49859-2,6978-1"
 "AMH"		"Amphotericin B-high"	"Aminoglycosides"	"NA"			"amfo b high,amhl,ampho b high,amphotericin high"	""					""
-"AMP"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"J01CA01,S01AA19"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"am,amp,ampi"	"acillin,adobacillin,amblosin,amcill,amfipen,amfipen v,amipenix s,ampichel,ampicil,ampicilina,ampicillin,ampicillin a,ampicillin acid,ampicillin anhydrate,ampicillin anhydrous,ampicillin base,ampicillin hydrate,ampicillin sodium,ampicillina,ampicilline,ampicillinum,ampicin,ampifarm,ampikel,ampimed,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,anhydrous ampicillin,austrapen,binotal,bonapicillin,britacil,campicillin,copharcilin,delcillin,deripen,divercillin,doktacillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,olin kid,omnipen,orbicilina,pen a oral,pen ampil,penbristol,penbritin,penbritin paediatric,penbritin syrup,penbrock,penicline,penimic,pensyn,pentrex,pentrexl,pentrexyl,pentritin,pfizerpen a,polycillin,polyflex,ponecil,princillin,principen,qidamp,racenacillin,redicilin,rosampline,roscillin,semicillin,semicillin r,servicillin,sumipanto,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,viccillin s,vidocillin,wypicil"	2	"g"	6	"g"	"21066-6,3355-5,33562-0,33919-2,43883-8,43884-6,87604-5"
-"SAM"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/s,ab,ams,amsu,apsu,sam"	"sulacillin"			6	"g"	""
-"AMR"	73341	"Amprolium"	"Other antibacterials"	"NA"			""	"amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid"					""
-"ANI"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"J02AX06"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid"	"anidulafungin,anidulafungina,anidulafungine,anidulafunginum,ecalta,eraxis"			0.1	"g"	"58420-1"
+"AMP"	6249	"Ampicillin"	"Beta-lactams/penicillins"	"J01CA01,S01AA19"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"am,amp,ampi"	"acillin,adobacillin,amblosin,amcill,amfipen,amfipen v,amipenix s,ampichel,ampicil,ampicilina,ampicillin,ampicillin a,ampicillin acid,ampicillin anhydrate,ampicillin anhydrous,ampicillin base,ampicillin hydrate,ampicillin sodium,ampicillina,ampicilline,ampicillinum,ampicin,ampifarm,ampikel,ampimed,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,anhydrous ampicillin,austrapen,binotal,bonapicillin,britacil,campicillin,copharcilin,delcillin,deripen,divercillin,doktacillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,olin kid,omnipen,orbicilina,pen a oral,pen ampil,penbristol,penbritin,penbritin paediatric,penbritin syrup,penbrock,penicline,penimic,pensyn,pentrex,pentrexl,pentrexyl,pentritin,pfizerpen a,polycillin,polyflex,ponecil,princillin,principen,qidamp,racenacillin,redicilin,rosampline,roscillin,semicillin,semicillin r,servicillin,sumipanto,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,viccillin s,vidocillin,wypicil"	2	"g"	6	"g"	"101477-8,101478-6,18864-9,18865-6,20374-5,21066-6,23618-2,27-3,28-1,29-9,30-7,31-5,32-3,33-1,3355-5,33562-0,33919-2,34-9,43883-8,43884-6,6979-9,6980-7,87604-5"
+"SAM"	119561	"Ampicillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR01"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"a/s,ab,ams,amsu,apsu,sam"	"sulacillin"			6	"g"	"101478-6,18865-6,20374-5,23618-2,31-5,32-3,33-1,34-9,6980-7"
+"AMR"	73341	"Amprolium"	"Other antibacterials"	"QP51BX02"			""	"amprocidum,amprol,amprolio,amprolium,amprolium chloride,amprovine,thiacoccid"					""
+"ANI"	166548	"Anidulafungin"	"Antifungals/antimycotics"	"J02AX06"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"anid"	"anidulafungin,anidulafungina,anidulafungine,anidulafunginum,ecalta,eraxis"			0.1	"g"	"55343-8,57095-2,58420-1,77162-6"
 "APL"	6602341	"Apalcillin"	"Beta-lactams/penicillins"	"NA"			""	"apalcilina,apalcillin,apalcilline,apalcillinum"					""
-"APR"	3081545	"Apramycin"	"Aminoglycosides"	"NA"			""	"ambylan,apralan,apramicina,apramycin,apramycine,apramycinum,nebramycin ii"					""
-"ARB"	68682	"Arbekacin"	"Aminoglycosides"	"J01GB12"			""	"arbekacin,arbekacina,arbekacine,arbekacini sulfas,arbekacinum,habekacin,haberacin"			0.2	"g"	""
+"APR"	3081545	"Apramycin"	"Aminoglycosides"	"QA07AA92,QJ01GB90,QJ51GB90"			""	"ambylan,apralan,apramicina,apramycin,apramycine,apramycinum,nebramycin ii"					"23659-6,73652-0,73653-8"
+"ARB"	68682	"Arbekacin"	"Aminoglycosides"	"J01GB12"			""	"arbekacin,arbekacina,arbekacine,arbekacini sulfas,arbekacinum,habekacin,haberacin"			0.2	"g"	"32373-3,53818-1,54173-0"
 "APX"	71961	"Aspoxicillin"	"Beta-lactams/penicillins"	"J01CA19"			""	"aspoxicilina,aspoxicillan,aspoxicillin,aspoxicilline,aspoxicillinum"			4	"g"	""
 "AST"	5284517	"Astromicin"	"Aminoglycosides"	"NA"			""	"astromicin,astromicin a,astromicina,astromicine,astromicinum,fortimicin,fortimicin a"					""
 "AVB"	9835049	"Avibactam"	"Beta-lactams/penicillins"	"NA"			""	"avibactam,avibactam free acid,avibactamfreeacid"					""
-"AVI"	71674	"Avilamycin"	"Other antibacterials"	"NA"			""	"avilamycin,avilamycina,avilamycine,avilamycinum,surmax"					""
+"AVI"	71674	"Avilamycin"	"Other antibacterials"	"QA07AA95"			""	"avilamycin,avilamycina,avilamycine,avilamycinum,surmax"					"35754-1,35755-8,35756-6,55619-1"
 "AVO"	16131159	"Avoparcin"	"Glycopeptides"	"NA"			""	"avoparcin,avoparcina,avoparcine,avoparcinum,avotan"					""
 "AZD"	15574941	"Azidocillin"	"Beta-lactams/penicillins"	"J01CE04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"azidocilina,azidocillin,azidocillina,azidocilline,azidocillinum"	1.5	"g"			""
-"AZM"	447043	"Azithromycin"	"Macrolides/lincosamides"	"J01FA10,S01AA26"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"az,azi,azit,azm"	"aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,azythromycin,durasite,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zithrax,zithromac,zithromax,zithromax iv,zithromycin,zitrim,zitromax,zitrotek,zmax sr,zythromax"	0.3	"g"	0.5	"g"	"16420-2,25233-8"
+"AZM"	447043	"Azithromycin"	"Macrolides/lincosamides"	"J01FA10,S01AA26"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"az,azi,azit,azm"	"aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,azythromycin,durasite,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zithrax,zithromac,zithromax,zithromax iv,zithromycin,zitrim,zitromax,zitrotek,zmax sr,zythromax"	0.3	"g"	0.5	"g"	"100043-9,16420-2,16421-0,18866-4,23612-5,25233-8,35-6,36-4,37-2,38-0,6981-5,89480-8"
 "AFC"		"Azithromycin/fluconazole/secnidazole"	"Other antibacterials"	"J01RA07"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"AZL"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"J01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"az,azl,azlo"	"azlocilina,azlocillin,azlocilline,azlocillinum"			12	"g"	""
-"ATM"	5742832	"Aztreonam"	"Beta-lactams/penicillins"	"J01DF01"	"Other beta-lactam antibacterials"	"Monobactams"	"at,atm,azm,azt,aztr"	"azactam,azetreonam,azonam,azthreonam,aztreon,aztreonam,nebactam,primbactam"			4	"g"	"16423-6,25234-6,3369-6"
+"AZL"	6479523	"Azlocillin"	"Beta-lactams/penicillins"	"J01CA09"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"az,azl,azlo"	"azlocilina,azlocillin,azlocilline,azlocillinum"			12	"g"	"16422-8,18867-2,3368-8,39-8,40-6,41-4,41661-0,42-2"
+"ATM"	5742832	"Aztreonam"	"Beta-lactams/penicillins"	"J01DF01"	"Other beta-lactam antibacterials"	"Monobactams"	"at,atm,azm,azt,aztr"	"azactam,azetreonam,azonam,azthreonam,aztreon,aztreonam,nebactam,primbactam"			4	"g"	"101497-6,16423-6,18868-0,25234-6,3369-6,41662-8,41663-6,41664-4,41727-9,43-0,44-8,45-5,46-3,6982-3"
 "AZA"		"Aztreonam/avibactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
 "ANC"		"Aztreonam/nacubactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
-"BAM"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"J01CA06"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"bacampicilina,bacampicillin,bacampicilline,bacampicillinum,penglobe"	1.2	"g"			""
-"BAC"	78358334	"Bacitracin"	"Other antibacterials"	"R02AB04,J01XX10"			"baci"	"fortracin,md bacitracin"					""
-"BDQ"	5388906	"Bedaquiline"	"Other antibacterials"	"J04AK05"			""	"bedaquiline,sirturo"	86	"mg"			"80637-2"
+"BAM"	441397	"Bacampicillin"	"Beta-lactams/penicillins"	"J01CA06"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"bacampicilina,bacampicillin,bacampicilline,bacampicillinum,penglobe"	1.2	"g"			"18869-8,47-1,48-9,49-7,50-5,55620-9"
+"BAC"	78358334	"Bacitracin"	"Other antibacterials"	"D06AX05,J01XX10,R02AB04,S01AA32"			"baci"	"fortracin,md bacitracin"					"10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
+"BDQ"	5388906	"Bedaquiline"	"Other antibacterials"	"J04AK05"			""	"bedaquiline,sirturo"	86	"mg"			"80637-2,88703-4,88704-2,94274-8,96107-8"
 "BEK"	439318	"Bekanamycin"	"Aminoglycosides"	"J01GB13"			""	"aminodeoxykanamycin,becanamicina,bekanamycin,bekanamycine,bekanamycinum,kanamycin b,klebcil,nebramycin v"			0.6	"g"	""
 "BNB"		"Benzathine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE08"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"beacillin,cepacilina,extencilline,lentopenil,penidural,tardocillin"			3.6	"g"	""
 "BNP"	64725	"Benzathine phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE10"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"bicillin v,biphecillin"	2	"g"			""
 "PEN"	5904	"Benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE01,S01AA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"bepe,pen,peni,peni g,penicillin,penicillin g,pg"	"abbocillin,ayercillin,bencilpenicilina,benzopenicillin,benzyl penicillin,benzylpenicillin,benzylpenicillin g,benzylpenicilline,benzylpenicillinum,bicillin,cillora,cilloral,cilopen,compocillin g,cosmopen,dropcillin,free penicillin g,free penicillin ii,galofak,gelacillin,liquacillin,megacillin,pencillin g,penicillin,penicilling,pentids,permapen,pfizerpen,pfizerpen g,pharmacillin,pradupen,specilline g,ursopen"			3.6	"g"	""
-"BES"	10178705	"Besifloxacin"	"Quinolones"	"S01AE08"			""	"besifloxacin,besivance"					""
-"BIA"	71339	"Biapenem"	"Carbapenems"	"J01DH05"			""	"biapenem,biapenern,bipenem,omegacin"			1.2	"g"	""
+"BES"	10178705	"Besifloxacin"	"Quinolones"	"S01AE08"			""	"besifloxacin,besivance"					"73606-6,73628-0,73651-2"
+"BIA"	71339	"Biapenem"	"Carbapenems"	"J01DH05"			""	"biapenem,biapenern,bipenem,omegacin"			1.2	"g"	"41665-1,41666-9,41667-7,41728-7"
 "BCZ"	65807	"Bicyclomycin"	"Other antibacterials"	"NA"			"bicozamycin"	"aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum,bicyclomycin"					""
 "BDP"	68760	"Brodimoprim"	"Trimethoprims"	"J01EA02"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	""	"brodimoprim,brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim"	0.2	"g"			""
 "BUT"	47472	"Butoconazole"	"Antifungals/antimycotics"	"G01AF15"			""	"butaconazole,butoconazol,butoconazole,butoconazolum,compositenstarke,dahlin,femstat,gynofort,polyfructosanum"					""
 "CDZ"	44242317	"Cadazolid"	"Oxazolidinones"	"NA"			""	"cadazolid"					""
 "CLA"		"Calcium aminosalicylate"	"Antimycobacterials"	"J04AA03"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	""	15	"g"			""
-"CAP"	135565060	"Capreomycin"	"Antimycobacterials"	"J04AB30"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"capr"	""			1	"g"	""
-"CRB"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"J01CA03"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bar,carb,cb"	"anabactyl,carbenicilina,carbenicillin,carbenicillina,carbenicilline,carbenicillinum,geopen,pyopen"			12	"g"	"3434-8"
+"CAP"	135565060	"Capreomycin"	"Antimycobacterials"	"J04AB30"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"capr"	""			1	"g"	"16545-6,18872-2,23607-5,25210-6,25211-4,25212-2,42643-7,48170-5,55-4,55623-3,56-2,57-0,58-8,61355-4,89483-2"
+"CRB"	20824	"Carbenicillin"	"Beta-lactams/penicillins"	"J01CA03"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"bar,carb,cb"	"anabactyl,carbenicilina,carbenicillin,carbenicillina,carbenicilline,carbenicillinum,geopen,pyopen"			12	"g"	"18873-0,3434-8,41668-5,59-6,60-4,61-2,62-0"
 "CRN"	93184	"Carindacillin"	"Beta-lactams/penicillins"	"J01CA05"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"carindacilina,carindacillin,carindacilline,carindacillinum"	4	"g"			""
-"CAR"	6540466	"Carumonam"	"Other antibacterials"	"J01DF02"			""	"carumonam,carumonamum"			2	"g"	""
-"CAS"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"J02AX04"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp"	"cancidas,capsofungin,caspofungin"			50	"mg"	"58419-3"
-"CAC"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"J01DB10"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"cefacetril,cefacetrile,cefacetrilo,cefacetrilum,celospor,celtol,cephacetrile,cristacef,vetrimast"					""
-"CEC"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"J01DC04"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"ccl,cec,cf,cfac,cfc,cfcl,cfr,fac"	"alenfral,alfacet,ceclor,ceclor cd,cefaclor,cefaclor anhydrous,cefaclor impurity c,cefaclor monohydrate,cefaclorimpurityc,cefacloro,cefaclorum,cefeaclor,cephaclor,dystaclor mr,keflor,kefral,panoral,raniclor"	1	"g"			"16564-7,21149-0"
-"CFR"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"J01DB05"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfdx,cfr,fad"	"anhydrous cefadroxil,cefadrops,cefadroxil,cefadroxil anhydrous,cefadroxilo,cefadroxilum,cefradroxil,cephadroxil,duracef,duricef,sumacef,ultracef"	2	"g"			"16565-4"
+"CAR"	6540466	"Carumonam"	"Other antibacterials"	"J01DF02"			""	"carumonam,carumonamum"			2	"g"	"51694-8"
+"CAS"	2826718	"Caspofungin"	"Antifungals/antimycotics"	"J02AX04"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"casp"	"cancidas,capsofungin,caspofungin"			50	"mg"	"32378-2,54175-5,54176-3,54185-4,58419-3"
+"CAC"	91562	"Cefacetrile"	"Cephalosporins (1st gen.)"	"J01DB10"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"cefacetril,cefacetrile,cefacetrilo,cefacetrilum,celospor,celtol,cephacetrile,cristacef,vetrimast"					"55624-1,55625-8,55626-6,55627-4"
+"CEC"	51039	"Cefaclor"	"Cephalosporins (2nd gen.)"	"J01DC04"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"ccl,cec,cf,cfac,cfc,cfcl,cfr,fac"	"alenfral,alfacet,ceclor,ceclor cd,cefaclor,cefaclor anhydrous,cefaclor impurity c,cefaclor monohydrate,cefaclorimpurityc,cefacloro,cefaclorum,cefeaclor,cephaclor,dystaclor mr,keflor,kefral,panoral,raniclor"	1	"g"			"16564-7,18874-8,21149-0,6986-4,83-6,84-4,85-1,86-9"
+"CFR"	47965	"Cefadroxil"	"Cephalosporins (1st gen.)"	"J01DB05"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfdx,cfr,fad"	"anhydrous cefadroxil,cefadrops,cefadroxil,cefadroxil anhydrous,cefadroxilo,cefadroxilum,cefradroxil,cephadroxil,duracef,duricef,sumacef,ultracef"	2	"g"			"16565-4,18875-5,55628-2,63-8,64-6,65-3,66-1"
 "LEX"	27447	"Cefalexin"	"Cephalosporins (1st gen.)"	"J01DB01"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cflx"	"alcephin,alexin,alsporin,amplex,anhydrous cefalexin,anhydrous cephalexin,biocef,carnosporin,cefablan,cefadal,cefadin,cefadina,cefaleksin,cefalessina,cefalexin,cefalexin anhydrous,cefalexina,cefalexine,cefalexinum,cefalin,cefaloto,cefaseptin,ceffanex,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexin,cephalexin anhydrous,cephalexine,cephalexinum,cephanasten,cephaxin,cephin,ceporex,ceporex forte,ceporexin,ceporexine,cerexin,cerexins,cophalexin,durantel,durantel ds,erocetin,factagard,felexin,ibilex,ibrexin,inphalex,kefalospes,keflet,keflex,kefolan,keforal,keftab,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,lonflex,lopilexin,madlexin,mamalexin,mamlexin,medoxine,neokef,neolexina,novolexin,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine disperdose,pectril,pyassan,roceph,roceph distab,sanaxin,sartosona,sencephalin,sepexin,servispor,sialexin,sinthecillin,sporicef,sporidex,syncle,synecl,tepaxin,tokiolexin,uphalexin,voxxim,winlex,zozarine"	2	"g"			""
 "RID"	5773	"Cefaloridine"	"Cephalosporins (1st gen.)"	"J01DB02"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cefa"	"aliporina,ampligram,cefaloridin,cefaloridina,cefaloridine,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,loridine,sasperin,sefacin,verolgin,vioviantine"			3	"g"	""
 "CEP"	6024	"Cefalotin"	"Cephalosporins (1st gen.)"	"J01DB03"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfal,cflt"	"cefalothin,cefalotin,cefalotina,cefalotina fabra,cefalotine,cefalotinum,cemastin,cephalothinum,cephalotin,cephalotin acid,coaxin,keflin,seffin"			4	"g"	""
-"MAN"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"J01DC03"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfam,cfmn"	"cefadole,cefamandol,cefamandole,cefamandolum,cephadole,cephamandole,kefamandol,kefdole,mancef"			6	"g"	"3441-3"
+"MAN"	456255	"Cefamandole"	"Cephalosporins (2nd gen.)"	"J01DC03"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfam,cfmn"	"cefadole,cefamandol,cefamandole,cefamandolum,cephadole,cephamandole,kefamandol,kefdole,mancef"			6	"g"	"18876-3,3441-3,41669-3,55634-0,55635-7,55636-5,55637-3,67-9,68-7,69-5,70-3"
 "HAP"	30699	"Cefapirin"	"Cephalosporins (1st gen.)"	"J01DB08"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"ambrocef,cefadyl,cefapilin,cefapirin,cefapirina,cefapirine,cefapirinum,cefaprin,cefaprin sodium,cefatrex,cefatrexyl,cephapirine,metricure"			4	"g"	""
-"CTZ"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"J01DB07"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"bricef,cefatrix,cefatrizine,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,trizina"	1	"g"			""
+"CTZ"	6410758	"Cefatrizine"	"Cephalosporins (1st gen.)"	"J01DB07"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"bricef,cefatrix,cefatrizine,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,trizina"	1	"g"			"18877-1,55639-9,71-1,72-9,73-7,74-5"
 "CZD"	71736	"Cefazedone"	"Cephalosporins (1st gen.)"	"J01DB06"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"cefazedon,cefazedona,cefazedone,cefazedone acid,cefazedonum,refosporen,refosporene,refosporin"			3	"g"	""
-"CZO"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"J01DB04"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfz,cfzl,cz,czol,faz,kz"	"atirin,cefamezin,cefamezine,cefazina,cefazolin,cefazolin acid,cefazolina,cefazoline,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,kefzol,liviclina,totacef"			3	"g"	"16566-2,25235-3,3442-1,3443-9,80962-4"
+"CZO"	33255	"Cefazolin"	"Cephalosporins (1st gen.)"	"J01DB04"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfz,cfzl,cz,czol,faz,kz"	"atirin,cefamezin,cefamezine,cefazina,cefazolin,cefazolin acid,cefazolina,cefazoline,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,kefzol,liviclina,totacef"			3	"g"	"16566-2,18878-9,25235-3,3442-1,3443-9,41670-1,75-2,76-0,77-8,78-6,80962-4,85422-4"
 "CFB"	127527	"Cefbuperazone"	"Other antibacterials"	"J01DC13"			""	"cefbuperazona,cefbuperazone,cefbuperazonum,cefbuperzaone,cerbuperazone,tomiporan"			2	"g"	""
-"CCP"	6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"	"J01DD17"			""	"cefcamate,cefcapene"	0.45	"g"			""
+"CCP"	6436055	"Cefcapene"	"Cephalosporins (3rd gen.)"	"J01DD17"			""	"cefcamate,cefcapene"	0.45	"g"			"100044-7,76143-7"
 "CCX"	5282438	"Cefcapene pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefcamate pivoxil,cefcapene piroxil"					""
-"CDR"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"J01DD15"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cd,cdn,cdr,cfd,din"	"cefdinir,cefdinir anhydrous,cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef"	0.6	"g"			""
-"DIT"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"J01DD16"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn"	"cefditoren"	0.4	"g"			""
+"CDR"	6915944	"Cefdinir"	"Cephalosporins (3rd gen.)"	"J01DD15"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cd,cdn,cdr,cfd,din"	"cefdinir,cefdinir anhydrous,cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef"	0.6	"g"			"23636-4,23637-2,35757-4,35758-2"
+"DIT"	9870843	"Cefditoren"	"Cephalosporins (3rd gen.)"	"J01DD16"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cdn"	"cefditoren"	0.4	"g"			"35759-0,35760-8,35761-6,35762-4"
 "DIX"	6437877	"Cefditoren pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefditoren,cefditoren pi voxil,cefditoren pivoxil,cefditorin,cefditorin pivoxil,meiact,spectracef"					""
-"FEP"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"J01DE01"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cfep,cfpi,cpe,cpm,fep,pm,xpm"	"axepim,cefepima,cefepime,cefepimum,cepimax,cepimex,maxcef,maxipime"			4	"g"	"38363-8"
+"FEP"	5479537	"Cefepime"	"Cephalosporins (4th gen.)"	"J01DE01"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cfep,cfpi,cpe,cpm,fep,pm,xpm"	"axepim,cefepima,cefepime,cefepimum,cepimax,cepimex,maxcef,maxipime"			4	"g"	"101502-3,18879-7,31142-3,31143-1,35763-2,38363-8,42350-9,42351-7,42353-3,50631-1,58412-8,6643-1,6644-9,6645-7,6646-5,6987-2,8272-7,8273-5"
 "CFA"		"Cefepime/amikacin"	"Other antibacterials"	"J01RA06"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "CPC"	9567559	"Cefepime/clavulanic acid"	"Cephalosporins (4th gen.)"	"NA"			"cicl,xpml"	""					""
 "FNC"		"Cefepime/nacubactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
 "FPT"	9567558	"Cefepime/tazobactam"	"Cephalosporins (4th gen.)"	"NA"			""	""					""
 "FPZ"		"Cefepime/zidebactam"	"Other antibacterials"	"NA"			""	""					""
-"CAT"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"J01DD10"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cefetamet,cefetametum,cepime o,deacetoxycefotaxime"	1	"g"			""
+"CAT"	5487888	"Cefetamet"	"Cephalosporins (3rd gen.)"	"J01DD10"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cefetamet,cefetametum,cepime o,deacetoxycefotaxime"	1	"g"			"32377-4,35764-0,35765-7,55640-7"
 "CPI"	5486182	"Cefetamet pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefetamet pivoxyl,globocef"					""
 "CCL"	71719688	"Cefetecol"	"Cephalosporins (4th gen.)"	"NA"			"cefcatacol"	"cefetecol,cefetecol anhydrous"					""
 "CZL"	193956	"Cefetrizole"	"Cephalosporins (unclassified gen.)"	"NA"			""	"cefetrizole,cefetrizolum"					""
-"FDC"	77843966	"Cefiderocol"	"Other antibacterials"	"J01DI04"			""	"cefiderocol"					""
-"CFM"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"J01DD08"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfe,cfix,cfxm,dcfm,fix,ix"	"anhydrous cefixime,cefixim,cefixima,cefixime,cefixime anhydrous,cefixime hydrate,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oroken,suprax,tricef,unixime"	0.4	"g"			"16567-0,25236-1"
+"FDC"	77843966	"Cefiderocol"	"Other antibacterials"	"J01DI04"			""	"cefiderocol"			6	"g"	"95767-0,99280-0,99503-5"
+"CFM"	5362065	"Cefixime"	"Cephalosporins (3rd gen.)"	"J01DD08"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfe,cfix,cfxm,dcfm,fix,ix"	"anhydrous cefixime,cefixim,cefixima,cefixime,cefixime anhydrous,cefixime hydrate,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oroken,suprax,tricef,unixime"	0.4	"g"			"16567-0,18880-5,25236-1,35766-5,79-4,80-2,81-0,82-8"
 "CEO"		"Cefixime/ornidazole"	"Other antibacterials"	"J01RA15"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"CMX"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"J01DD05"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"bestron,cefmax,cefmenoxima,cefmenoxime,cefmenoximum"			2	"g"	""
-"CMZ"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"J01DC09"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefmetazole,cefmetazolesodium,cefmetazolo,cefmetazolum"			4	"g"	""
-"CNX"	71141	"Cefminox"	"Other antibacterials"	"J01DC12"			""	"cefminox,cefminoxum"			4	"g"	""
-"DIZ"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"J01DD09"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cefodizima,cefodizime,cefodizime acid,cefodizime disodium,cefodizimum,cefodizme,diezime,modivid,neucef,timecef"			2	"g"	""
-"CID"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"J01DC06"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefonicid,cefonicido,cefonicidum,monocef"			1	"g"	"25237-9,3444-7"
-"CFP"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"J01DD12"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfp,cfpz,cp,cpz,fop,per"	"bioperazone,cefobid,cefoperazine,cefoperazon,cefoperazone,cefoperazone acid,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef"			4	"g"	"3445-4"
-"CSL"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"J01DD62"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	""			4	"g"	""
-"CND"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"J01DC11"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"ceforanide,ceforanido,ceforanidum,precef,radacef"			4	"g"	""
+"CMX"	9570757	"Cefmenoxime"	"Cephalosporins (3rd gen.)"	"J01DD05,S01AA31,S02AA18"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"bestron,cefmax,cefmenoxima,cefmenoxime,cefmenoximum"			2	"g"	"32375-8,54174-8,54203-5,55641-5"
+"CMZ"	42008	"Cefmetazole"	"Cephalosporins (2nd gen.)"	"J01DC09"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefmetazole,cefmetazolesodium,cefmetazolo,cefmetazolum"			4	"g"	"11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
+"CNX"	71141	"Cefminox"	"Other antibacterials"	"J01DC12"			""	"cefminox,cefminoxum"			4	"g"	"54908-9"
+"DIZ"	5361871	"Cefodizime"	"Cephalosporins (3rd gen.)"	"J01DD09"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cefodizima,cefodizime,cefodizime acid,cefodizime disodium,cefodizimum,cefodizme,diezime,modivid,neucef,timecef"			2	"g"	"18882-1,6988-0,91-9,92-7,93-5,94-3"
+"CID"	43594	"Cefonicid"	"Cephalosporins (2nd gen.)"	"J01DC06"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefonicid,cefonicido,cefonicidum,monocef"			1	"g"	"18883-9,25237-9,3444-7,55642-3,95-0,96-8,97-6,98-4"
+"CFP"	44187	"Cefoperazone"	"Cephalosporins (3rd gen.)"	"J01DD12"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfp,cfpz,cp,cpz,fop,per"	"bioperazone,cefobid,cefoperazine,cefoperazon,cefoperazone,cefoperazone acid,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef"			4	"g"	"100-8,101-6,102-4,18884-7,3445-4,35767-3,35768-1,54166-4,54167-2,54168-0,99-2"
+"CSL"		"Cefoperazone/sulbactam"	"Cephalosporins (3rd gen.)"	"J01DD62"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	""			4	"g"	"35768-1,54166-4,54167-2,54168-0"
+"CND"	43507	"Ceforanide"	"Cephalosporins (2nd gen.)"	"J01DC11"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"ceforanide,ceforanido,ceforanidum,precef,radacef"			4	"g"	"103-2,104-0,105-7,106-5,18885-4,55643-1"
 "CSE"	9830519	"Cefoselis"	"Cephalosporins (4th gen.)"	"NA"			""	"cefoselis,cefoselis sulfate,wincef,winsef"					""
-"CTX"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"J01DD01"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfot,cft,cftx,ct,ctx,fot,tax,xct"	"cefotaxim,cefotaxim hikma,cefotaxima,cefotaxima acid,cefotaxime,cefotaxime acid,cefotaximum,cephotaxime,claforan,omnatax"			4	"g"	"25238-7,3446-2,80961-6"
+"CTX"	5742673	"Cefotaxime"	"Cephalosporins (3rd gen.)"	"J01DD01"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfot,cft,cftx,ct,ctx,fot,tax,xct"	"cefotaxim,cefotaxim hikma,cefotaxima,cefotaxima acid,cefotaxime,cefotaxime acid,cefotaximum,cephotaxime,claforan,omnatax"			4	"g"	"101479-4,101480-2,107-3,108-1,109-9,110-7,18886-2,25238-7,31138-1,31139-9,3446-2,35769-9,35770-7,35771-5,41671-9,50632-9,52128-6,54191-2,54192-0,54193-8,55189-5,55644-9,6989-8,80961-6"
 "CTC"	9575353	"Cefotaxime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"NA,J01DD51"			"cxcl,xctl"	""					""
-"CTS"	9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"	"NA"			""	""					""
-"CTT"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"J01DC05"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cftt,cn,cte,ctn,ctt,tans"	"apacef,cefotan,cefotetan,cefotetan acid,cefotetan free acid,cefotetanum"			4	"g"	"25239-5,3447-0"
-"CTF"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"J01DC07"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefotiam,cefotiam?,cefotiamum,ceradolan,ceradon,haloapor"	1.2	"g"	4	"g"	""
-"CHE"	125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefotiam cilexetil,pansporin t"					""
-"FOV"	9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefovecin"					""
-"FOX"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"J01DC01"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfox,cfx,cfxt,cx,fox,fx"	"cefoxitin,cefoxitina,cefoxitine,cefoxitinum,cefoxotin,cenomycin,cephoxitin,mefoxin,mefoxitin,rephoxitin"			6	"g"	"25240-3,3448-8"
+"CTS"	9574753	"Cefotaxime/sulbactam"	"Cephalosporins (3rd gen.)"	"NA"			""	""					"54191-2,54192-0,54193-8,55644-9"
+"CTT"	53025	"Cefotetan"	"Cephalosporins (2nd gen.)"	"J01DC05"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cftt,cn,cte,ctn,ctt,tans"	"apacef,cefotan,cefotetan,cefotetan acid,cefotetan free acid,cefotetanum"			4	"g"	"111-5,112-3,113-1,114-9,18887-0,25239-5,3447-0,41672-7,41673-5,41674-3,41729-5,6990-6"
+"CTF"	43708	"Cefotiam"	"Cephalosporins (2nd gen.)"	"J01DC07"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	""	"cefotiam,cefotiam?,cefotiamum,ceradolan,ceradon,haloapor"	1.2	"g"	4	"g"	"32374-1,35772-3,35773-1,55645-6,55737-1,55738-9,55739-7,55740-5"
+"CHE"	125846	"Cefotiam hexetil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefotiam cilexetil,pansporin t"					"55737-1,55738-9,55739-7,55740-5"
+"FOV"	9578573	"Cefovecin"	"Cephalosporins (3rd gen.)"	"QJ01DD91"			""	"cefovecin"					"76147-8,87792-8"
+"FOX"	441199	"Cefoxitin"	"Cephalosporins (2nd gen.)"	"J01DC01"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfox,cfx,cfxt,cx,fox,fx"	"cefoxitin,cefoxitina,cefoxitine,cefoxitinum,cefoxotin,cenomycin,cephoxitin,mefoxin,mefoxitin,rephoxitin"			6	"g"	"101492-7,115-6,116-4,117-2,118-0,18888-8,25220-5,25240-3,25366-6,3448-8,41675-0,41676-8,41677-6,41730-3,6991-4"
 "FOX1"		"Cefoxitin screening"	"Cephalosporins (2nd gen.)"	"NA"			"cfsc"	""					""
-"ZOP"	9571080	"Cefozopran"	"Cephalosporins (4th gen.)"	"J01DE03"			""	"cefozopran"			4	"g"	""
+"ZOP"	9571080	"Cefozopran"	"Cephalosporins (4th gen.)"	"J01DE03"			""	"cefozopran"			4	"g"	"100045-4,53820-7"
 "CFZ"	68597	"Cefpimizole"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefpimizol,cefpimizole,cefpimizole sodium,cefpimizolum"					""
 "CPM"	636405	"Cefpiramide"	"Cephalosporins (3rd gen.)"	"J01DD11"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	"cefpiramide,cefpiramide acid,cefpiramido,cefpiramidum"			2	"g"	""
-"CPO"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"J01DE02"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cfpr"	"broact,cefpiroma,cefpirome,cefpiromum,cefrom,cerfpirome,keiten"			4	"g"	""
-"CPD"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"J01DD13"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfpd,cfpo,cpd,pod,px"	"cefpodoxim acid,cefpodoxima,cefpodoxime,cefpodoxime acid,cefpodoximum,epoxim"	0.4	"g"			"25241-1"
+"CPO"	5479539	"Cefpirome"	"Cephalosporins (4th gen.)"	"J01DE02"	"Other beta-lactam antibacterials"	"Fourth-generation cephalosporins"	"cfpr"	"broact,cefpiroma,cefpirome,cefpiromum,cefrom,cerfpirome,keiten"			4	"g"	"18889-6,6647-3,6648-1,6649-9,6650-6,6992-2,8274-3,8275-0,8276-8"
+"CPD"	6335986	"Cefpodoxime"	"Cephalosporins (3rd gen.)"	"J01DD13"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfpd,cfpo,cpd,pod,px"	"cefpodoxim acid,cefpodoxima,cefpodoxime,cefpodoxime acid,cefpodoximum,epoxim"	0.4	"g"			"119-8,120-6,121-4,122-2,18890-4,25241-1,41678-4,41679-2,41680-0,41731-1,6993-0,90849-1"
 "CPX"	6526396	"Cefpodoxime proxetil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefodox,cefoprox,cefpodoxime proxetil,cepodem,orelox,orelox paed,otreon,podomexef,simplicef,vantin"					""
 "CDC"		"Cefpodoxime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"NA"			"cecl"	""					""
-"CPR"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"J01DC10"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cpr,cpz,fp"	"arzimol,brisoral,cefprozil,cefprozil anhydrous,cefprozil hydrate,cefprozilo,cefprozilum,cefzil,cronocef,procef,serozil"	1	"g"			""
-"CEQ"	5464355	"Cefquinome"	"Cephalosporins (4th gen.)"	"NA"			""	"cefquinoma,cefquinome,cefquinomum,cobactan"					""
+"CPR"	5281006	"Cefprozil"	"Cephalosporins (2nd gen.)"	"J01DC10"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cpr,cpz,fp"	"arzimol,brisoral,cefprozil,cefprozil anhydrous,cefprozil hydrate,cefprozilo,cefprozilum,cefzil,cronocef,procef,serozil"	1	"g"			"123-0,124-8,125-5,126-3,18891-2,6994-8"
+"CEQ"	5464355	"Cefquinome"	"Cephalosporins (4th gen.)"	"QG51AA07,QJ01DE90,QJ51DE90"			""	"cefquinoma,cefquinome,cefquinomum,cobactan"					"100046-2,76150-2"
 "CRD"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"J01DB11"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"cefroxadin,cefroxadine,cefroxadino,cefroxadinum,oraspor"	2.1	"g"			""
-"CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"J01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfsl,cfsu"	"cefonomil,cefsulodin,cefsulodine,cefsulodino,cefsulodinum"			4	"g"	"131-3,25242-9"
+"CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"J01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfsl,cfsu"	"cefonomil,cefsulodin,cefsulodine,cefsulodino,cefsulodinum"			4	"g"	"127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
 "CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"	"NA"			""	"cefsulmid,cefsumide,cefsumido,cefsumidum"					""
-"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02"			"cfro"	"ceftaroline fosamil,teflaro,zinforo"			1.2	"g"	""
-"CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			""	""					""
-"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,cfta,cftz,taz,tz,xtz"	"ceftazidim,ceftazidima,ceftazidime,ceftazidimum,ceptaz,fortaz,fortum,pentacef,tazicef,tazidime"			4	"g"	"21151-6,3449-6,80960-8"
-"CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"NA"			"cfav"	"avycaz,zavicefta"					""
+"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02"			"cfro"	"ceftaroline fosamil,teflaro,zinforo"			1.2	"g"	"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
+"CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			""	""					"73604-1,73626-4,73649-6"
+"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,cfta,cftz,taz,tz,xtz"	"ceftazidim,ceftazidima,ceftazidime,ceftazidimum,ceptaz,fortaz,fortum,pentacef,tazicef,tazidime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
+"CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"NA"			"cfav"	"avycaz,zavicefta"					"101483-6,73603-3,73625-6,73648-8,87734-0"
 "CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"czcl,xtzl"	""			6	"g"	""
-"CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18"			""	"cefteram,cefterame,cefteramum,ceftetrame"	0.4	"g"			""
+"CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18"			""	"cefteram,cefterame,cefteramum,ceftetrame"	0.4	"g"			"100047-0,76144-5"
 "CPL"	5362114	"Cefteram pivoxil"	"Cephalosporins (3rd gen.)"	"NA"			""	"cefteram pivoxil,cefterampivoxil,tomiron"					""
 "CTL"	65755	"Ceftezole"	"Cephalosporins (1st gen.)"	"J01DB12"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	""	"ceftezol,ceftezole,ceftezolo,ceftezolum,demethylcefazolin"			3	"g"	""
-"CTB"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"J01DD14"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cb,cfbu,ctb,tib"	"ceftem,ceftibuten,ceftibuten dihydrate,ceftibuten hydrate,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,cephem,ceprifran,isocef,keimax"	0.4	"g"			""
-"TIO"	6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"	"NA"			""	"ceftiofur,ceftiofurum,excede,excenel,naxcel"					""
-"CZX"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"J01DD07"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfzx,ctz,cz,czx,tiz,zox"	"cefizox,ceftisomin,ceftix,ceftizoxima,ceftizoxime,ceftizoximum,epocelin,eposerin"			4	"g"	"25243-7,3450-4"
+"CTB"	5282242	"Ceftibuten"	"Cephalosporins (3rd gen.)"	"J01DD14"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cb,cfbu,ctb,tib"	"ceftem,ceftibuten,ceftibuten dihydrate,ceftibuten hydrate,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,cephem,ceprifran,isocef,keimax"	0.4	"g"			"35777-2,35778-0,35779-8,6996-3"
+"TIO"	6328657	"Ceftiofur"	"Cephalosporins (3rd gen.)"	"QJ01DD90,QJ51DD90"			""	"ceftiofur,ceftiofurum,excede,excenel,naxcel"					"23709-9,35780-6,35781-4,55652-2"
+"CZX"	6533629	"Ceftizoxime"	"Cephalosporins (3rd gen.)"	"J01DD07"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cfzx,ctz,cz,czx,tiz,zox"	"cefizox,ceftisomin,ceftix,ceftizoxima,ceftizoxime,ceftizoximum,epocelin,eposerin"			4	"g"	"136-2,137-0,138-8,139-6,18894-6,20378-6,23622-4,25243-7,3450-4,6997-1"
 "CZP"	9578661	"Ceftizoxime alapivoxil"	"Cephalosporins (3rd gen.)"	"NA"			""	""					""
-"BPR"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"	"NA"			""	"ceftobiprole"					""
+"BPR"	135413542	"Ceftobiprole"	"Cephalosporins (5th gen.)"	"NA"			""	"ceftobiprole"					"43269-0,43270-8,43271-6,43272-4,85052-9"
 "CFM1"	135413544	"Ceftobiprole medocaril"	"Cephalosporins (5th gen.)"	"J01DI01"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	""			1.5	"g"	""
-"CZT"	86291594	"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"	"J01DI54"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"CEI"	"zerbaxa"			3	"g"	""
-"CRO"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"J01DD04"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"axo,cax,cftr,cro,ctr,frx,tx"	"biotrakson,cefatriaxone,cefatriaxone hydrate,ceftriaxon,ceftriaxona,ceftriaxone,ceftriaxone sodium,ceftriaxonum,ceftriazone,cephtriaxone,longacef,rocefin,rocephalin,rocephin,rocephine,rophex"			2	"g"	"25244-5,3451-2,80957-4"
+"CZT"	86291594	"Ceftolozane/tazobactam"	"Cephalosporins (5th gen.)"	"J01DI54"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	"cei"	"zerbaxa"			3	"g"	"101484-4,73602-5,73624-9,73647-0,87735-7"
+"CRO"	5479530	"Ceftriaxone"	"Cephalosporins (3rd gen.)"	"J01DD04"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"axo,cax,cftr,cro,ctr,frx,tx"	"biotrakson,cefatriaxone,cefatriaxone hydrate,ceftriaxon,ceftriaxona,ceftriaxone,ceftriaxone sodium,ceftriaxonum,ceftriazone,cephtriaxone,longacef,rocefin,rocephalin,rocephin,rocephine,rophex"			2	"g"	"101485-1,140-4,141-2,142-0,143-8,18895-3,25244-5,25367-4,31140-7,31141-5,3451-2,41681-8,41682-6,41683-4,41732-9,50633-7,55190-3,6998-9,80957-4"
 "CEB"		"Ceftriaxone/beta-lactamase inhibitor"	"Cephalosporins (3rd gen.)"	"J01DD63"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	""	""			2	"g"	""
-"CXM"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"J01DC02,S01AA27"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfrx,cfur,cfx,crm,cxm,fur,rox,xm"	"biofuroksym,cefuril,cefuroxim,cefuroxima,cefuroxime,cefuroxime acid,cefuroximine,cefuroximo,cefuroximum,cephuroxime,kefurox,sharox,zinacef,zinacef danmark"	0.5	"g"	3	"g"	"25245-2,3452-0,80608-3,80617-4"
+"CXM"	5479529	"Cefuroxime"	"Cephalosporins (2nd gen.)"	"J01DC02,S01AA27"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"cfrx,cfur,cfx,crm,cxm,fur,rox,xm"	"biofuroksym,cefuril,cefuroxim,cefuroxima,cefuroxime,cefuroxime acid,cefuroximine,cefuroximo,cefuroximum,cephuroxime,kefurox,sharox,zinacef,zinacef danmark"	0.5	"g"	3	"g"	"101503-1,144-6,145-3,146-1,147-9,18896-1,20460-2,25245-2,3452-0,35782-2,35783-0,51724-3,51774-8,55653-0,55654-8,6999-7,74699-0,80608-3,80617-4"
 "CXA"	6321416	"Cefuroxime axetil"	"Cephalosporins (2nd gen.)"	"NA"			"cfax"	"altacef,bioracef,cefaks,cefazine,ceftin,cefurax,cefuroximaxetil,cefuroxime,cefuroxime axetil,celocid,cepazine,cethixim,cetoxil,coliofossim,elobact,forcef,furoxime,kalcef,maxitil,medoxm,nivador,novador,novocef,oraxim,zinnat"					""
 "CFM2"		"Cefuroxime/metronidazole"	"Other antibacterials"	"J01RA03"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "ZON"	6336505	"Cefuzonam"	"Other antibacterials"	"NA"			""	"cefuzonam,cefuzonam sodium,cefuzoname,cefuzonamum"					""
-"CED"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"J01DB09"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfra,cfrd"	"anspor,cefradin,cefradina,cefradine,cefradine hydrate,cefradinum,cekodin,cephradin,cephradine,cephradine anhydrous,cephradine hydrate,eskacef,infexin,megace f,megacef,sefril,velocef,velosef"	2	"g"	2	"g"	""
+"CED"	38103	"Cephradine"	"Cephalosporins (1st gen.)"	"J01DB09"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"cfra,cfrd"	"anspor,cefradin,cefradina,cefradine,cefradine hydrate,cefradinum,cekodin,cephradin,cephradine,cephradine anhydrous,cephradine hydrate,eskacef,infexin,megace f,megacef,sefril,velocef,velosef"	2	"g"	2	"g"	"168-5,169-3,170-1,171-9,18902-7,55646-4"
 "CTO"	71402	"Cetocycline"	"Tetracyclines"	"NA"			""	"cetocycline,cetocyline,cetotetrine,chelocardin"					""
-"CHL"	5959	"Chloramphenicol"	"Amphenicols"	"D06AX02,D10AF03,G01AA05,J01BA01,S01AA01,S02AA01,S03AA08"	"Amphenicols"	"Amphenicols"	"c,chl,chlo,cl"	"alficetyn,ambofen,amphenicol,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,ch loramex,chemiceticol,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicol,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlormycetin r,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocid s,chlorocide,chlorocidin c,chlorocidin c tetran,chlorocin,chlorocol,chlorofair,chloroject l,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chloroptic s.o.p,chloroptic s.o.p.,chlorovules,chlorsig,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramical,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,cloromissan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextromycetin,doctamicina,duphenicol,econochlor,embacetin,emetren,enicol,enteromycetin,erbaplast,ertilen,f armicetina,farmicetina,fenicol,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,interomycetine,intramycetin,intramyctin,isicetin,ismicetina,isophenicol,isopto fenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,klorocid s,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromicetina,loromisan,loromisin,mastiphen,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,myscel,normimycin v,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,quemicetina,rivomycin,romphenil,ronfenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,sintomicetine r,sno phenicol,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,vice ton,viceton"	3	"g"	3	"g"	"15101-9,16603-3,16604-1,25247-8,29214-4,29346-4,29347-2,3455-3"
-"CTE"	54675777	"Chlortetracycline"	"Tetracyclines"	"A01AB21,D06AA02,J01AA03,S01AA02"	"Tetracyclines"	"Tetracyclines"	""	"acronize,aueromycin,aureocina,aureomycin,aureomykoin,biomitsin,biomycin,biomycin a,chlormax,chlorotetracycline,chlortetracycline,chlortetracyclinum,chrysomykine,clortetraciclina,duomycin,flamycin,uromycin"	1	"g"			"87600-3"
+"CHL"	5959	"Chloramphenicol"	"Amphenicols"	"D06AX02,D10AF03,G01AA05,J01BA01,S01AA01,S02AA01,S03AA08"	"Amphenicols"	"Amphenicols"	"c,chl,chlo,cl"	"alficetyn,ambofen,amphenicol,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,ch loramex,chemiceticol,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicol,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlormycetin r,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocid s,chlorocide,chlorocidin c,chlorocidin c tetran,chlorocin,chlorocol,chlorofair,chloroject l,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chloroptic s.o.p,chloroptic s.o.p.,chlorovules,chlorsig,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramical,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,cloromissan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextromycetin,doctamicina,duphenicol,econochlor,embacetin,emetren,enicol,enteromycetin,erbaplast,ertilen,f armicetina,farmicetina,fenicol,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,interomycetine,intramycetin,intramyctin,isicetin,ismicetina,isophenicol,isopto fenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,klorocid s,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromicetina,loromisan,loromisin,mastiphen,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,myscel,normimycin v,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,quemicetina,rivomycin,romphenil,ronfenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,sintomicetine r,sno phenicol,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,vice ton,viceton"	3	"g"	3	"g"	"15101-9,16603-3,16604-1,172-7,173-5,174-3,175-0,18903-5,25247-8,29214-4,29346-4,29347-2,3455-3,7001-1"
+"CTE"	54675777	"Chlortetracycline"	"Tetracyclines"	"A01AB21,D06AA02,J01AA03,S01AA02"	"Tetracyclines"	"Tetracyclines"	""	"acronize,aueromycin,aureocina,aureomycin,aureomykoin,biomitsin,biomycin,biomycin a,chlormax,chlorotetracycline,chlortetracycline,chlortetracyclinum,chrysomykine,clortetraciclina,duomycin,flamycin,uromycin"	1	"g"			"176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
 "CIC"	19003	"Ciclacillin"	"Beta-lactams/penicillins"	"NA"			""	"bastcillin,calthor,ciclacilina,ciclacillin,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital"					""
 "CIX"	47472	"Ciclopirox"	"Antifungals/antimycotics"	"D01AE14,G01AX12"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"butaconazole,butoconazol,butoconazole,butoconazolum,ciclodan,ciclopirox,ciclopirox gel,ciclopirox olamin,ciclopiroxum,compositenstarke,dahlin,femstat,gynofort,loprox,loprox cream,loprox gel,penlac,polyfructosanum,stieprox"					""
-"CIN"	2762	"Cinoxacin"	"Quinolones"	"J01MB06"	"Quinolone antibacterials"	"Other quinolones"	"cino,cnox"	"azolinic acid,cinobac,cinobactin,cinoxacin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm"	1	"g"			""
-"CIP"	2764	"Ciprofloxacin"	"Quinolones"	"J01MA02,S01AE03,S02AA15,S03AA07"	"Quinolone antibacterials"	"Fluoroquinolones"	"ci,cip,cipr,cp"	"alcon cilox,auripro,bacquinor,baflox,baycip,bernoflox,cetraxal,ciflox,cifloxin,ciloxan,ciplus,ciprecu,ciprine,ciprinol,cipro i.v.,cipro iv,cipro xl,cipro xr,ciprobay,ciprobay uro,ciprocinol,ciprodar,ciproflox,ciprofloxacin,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprogis,ciprolin,ciprolon,cipromycin,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citopcin,corsacin,cyprobay,fimoflox,flociprin,ipiflox,italnik,linhaliq,otiprio,probiox,proflaxin,quinolid,quintor,rancif,roxytal,septicide,sophixin ofteno,spitacin,superocin,velmonit,velomonit,zumaflox"	1	"g"	0.8	"g"	"14031-9,14032-7,14058-2,14059-0,25248-6,34636-1,3484-3"
+"CIN"	2762	"Cinoxacin"	"Quinolones"	"J01MB06"	"Quinolone antibacterials"	"Other quinolones"	"cino,cnox"	"azolinic acid,cinobac,cinobactin,cinoxacin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm"	1	"g"			"180-0,181-8,182-6,183-4,18905-0,55656-3"
+"CIP"	2764	"Ciprofloxacin"	"Quinolones"	"J01MA02,S01AE03,S02AA15,S03AA07"	"Quinolone antibacterials"	"Fluoroquinolones"	"ci,cip,cipr,cp"	"alcon cilox,auripro,bacquinor,baflox,baycip,bernoflox,cetraxal,ciflox,cifloxin,ciloxan,ciplus,ciprecu,ciprine,ciprinol,cipro i.v.,cipro iv,cipro xl,cipro xr,ciprobay,ciprobay uro,ciprocinol,ciprodar,ciproflox,ciprofloxacin,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprogis,ciprolin,ciprolon,cipromycin,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citopcin,corsacin,cyprobay,fimoflox,flociprin,ipiflox,italnik,linhaliq,otiprio,probiox,proflaxin,quinolid,quintor,rancif,roxytal,septicide,sophixin ofteno,spitacin,superocin,velmonit,velomonit,zumaflox"	1	"g"	0.8	"g"	"101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
 "CIM"		"Ciprofloxacin/metronidazole"	"Other antibacterials"	"J01RA10"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "CIO"		"Ciprofloxacin/ornidazole"	"Other antibacterials"	"J01RA12"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "CIT"		"Ciprofloxacin/tinidazole"	"Other antibacterials"	"J01RA11"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"CLR"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"J01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"ch,cla,clar,clm,clr"	"abbotic,astromen,biaxin,biaxin filmtab,biaxin hp,biaxin xl,biaxin xl filmtab,bicrolid,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycin,clarithromycine,clarithromycinum,claritromicina,clathromycin,crixan,cyllid,cyllind,fromilid,heliclar,klabax,klacid,klaciped,klaricid,klaricid h.p,klaricid h.p.,klaricid pediatric,klaricid xl,klarid,klarin,kofron,mabicrol,macladin,maclar,prevpac,veclam,vikrol,zeclar"	0.5	"g"	1	"g"	"16619-9,25253-6,34638-7,80559-8"
+"CLR"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"J01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"ch,cla,clar,clm,clr"	"abbotic,astromen,biaxin,biaxin filmtab,biaxin hp,biaxin xl,biaxin xl filmtab,bicrolid,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycin,clarithromycine,clarithromycinum,claritromicina,clathromycin,crixan,cyllid,cyllind,fromilid,heliclar,klabax,klacid,klaciped,klaricid,klaricid h.p,klaricid h.p.,klaricid pediatric,klaricid xl,klarid,klarin,kofron,mabicrol,macladin,maclar,prevpac,veclam,vikrol,zeclar"	0.5	"g"	1	"g"	"100048-8,16619-9,16620-7,188-3,189-1,18907-6,190-9,191-7,20375-2,23619-0,25190-0,25191-8,25192-6,25253-6,34638-7,43987-7,43990-1,43991-9,7003-7,80559-8,89485-7"
 "CLA1"	5280980	"Clavulanic acid"	"Other antibacterials"	"NA"			""	"acide clavulanique,acido clavulanico,acidum clavulanicum,clavulanate,clavulanate acid,clavulanate lithium,clavulanateacid,clavulanic acid,clavulansaeure,clavulansaure,clavulinic acid,clavulox,serdaxin,sodium clavulanate"					""
-"CLX"	60063	"Clinafloxacin"	"Quinolones"	"NA"			""	"clinafloxacin"					""
-"CLI"	446598	"Clindamycin"	"Macrolides/lincosamides"	"D10AF01,G01AA10,J01FF01"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"cc,cd,cli,clin,cm,da"	"antirobe,chlolincocin,clindaderm,clindamicina,clindamycin,clindamycine,clindamycinum,clinimycin,dalacin c,dalacine,klimicin,sobelin"	1.2	"g"	1.8	"g"	"16621-5,16622-3,25249-4,3486-8"
-"CLF"	2794	"Clofazimine"	"Antimycobacterials"	"J04BA01"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"chlofazimine,clofazimin,clofazimina,clofazimine,clofaziminum,colfazimine,lampren,lamprene,riminophenazine"	0.1	"g"			""
+"CLX"	60063	"Clinafloxacin"	"Quinolones"	"NA"			""	"clinafloxacin"					"32376-6,33284-1,35785-5,35786-3,7004-5"
+"CLI"	446598	"Clindamycin"	"Macrolides/lincosamides"	"D10AF01,G01AA10,J01FF01"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"cc,cd,cli,clin,cm,da"	"antirobe,chlolincocin,clindaderm,clindamicina,clindamycin,clindamycine,clindamycinum,clinimycin,dalacin c,dalacine,klimicin,sobelin"	1.2	"g"	1.8	"g"	"16621-5,16622-3,18908-4,192-5,193-3,194-1,195-8,25249-4,3486-8,42720-3,55657-1,55658-9,55659-7,55660-5,61188-9,7005-2"
+"CLF"	2794	"Clofazimine"	"Antimycobacterials"	"J04BA01"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"chlofazimine,clofazimin,clofazimina,clofazimine,clofaziminum,colfazimine,lampren,lamprene,riminophenazine"	0.1	"g"			"16623-1,20376-0,23620-8,23627-3,43986-9,43988-5,43989-3,55661-3,55662-1,96108-6"
 "CLF1"	2799	"Clofoctol"	"Other antibacterials"	"J01XX03"	"Other antibacterials"	"Other antibacterials"	""	"clofoctol,clofoctolo,clofoctolum,gramplus,octofene"					""
 "CLM"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"J01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"chlomethocillin,clometacillin,clometocilina,clometocillin,clometocilline,clometocillinum,rixapen"	1	"g"			""
 "CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11"	"Tetracyclines"	"Tetracyclines"	""	"chlormethylencycline,clomociclina,clomocyclin,clomocycline,clomocyclinum,megaclor"	1	"g"			""
-"CTR"	2812	"Clotrimazole"	"Antifungals/antimycotics"	"A01AB18,D01AC01,G01AF02"			"clot"	"canesten,canesten cream,canesten solution,canestene,canestine,canifug,chlotrimazole,cimitidine,clomatin,clotrimaderm,clotrimaderm cream,clotrimazol,clotrimazole,clotrimazolum,cutistad,desamix f,diphenylmethane,empecid,esparol,fem care,femcare,gyne lotrimin,jidesheng,kanesten,klotrimazole,lotrimax,lotrimin,lotrimin af,lotrimin af cream,lotrimin af lotion,lotrimin af solution,lotrimin cream,lotrimin lotion,lotrimin solution,monobaycuten,mycelax,mycelex,mycelex cream,mycelex g,mycelex otc,mycelex solution,mycelex troches,mycelex twin pack,myclo cream,myclo solution,myclo spray solution,mycofug,mycosporin,mykosporin,nalbix,otomax,pedisafe,rimazole,stiemazol,tibatin,trimysten,trivagizole,veltrim"					""
-"CLO"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"J01CF02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox"	"chloroxacillin,clossacillina,cloxacilina,cloxacillin,cloxacillin sodium,cloxacilline,cloxacillinna,cloxacillinum,cloxapen,methocillin s,orbenin,syntarpen,tegopen"	2	"g"	2	"g"	"16628-0,25250-2"
-"COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,cs,cst,ct"	"belcomycine,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colobreathe,colomycin,coly-mycin,polymyxin e,polymyxin e. sulfate,promixin,totazina"	9	"MU"	9	"MU"	"16645-4,29493-4"
+"CTR"	2812	"Clotrimazole"	"Antifungals/antimycotics"	"A01AB18,D01AC01,G01AF02"			"clot"	"canesten,canesten cream,canesten solution,canestene,canestine,canifug,chlotrimazole,cimitidine,clomatin,clotrimaderm,clotrimaderm cream,clotrimazol,clotrimazole,clotrimazolum,cutistad,desamix f,diphenylmethane,empecid,esparol,fem care,femcare,gyne lotrimin,jidesheng,kanesten,klotrimazole,lotrimax,lotrimin,lotrimin af,lotrimin af cream,lotrimin af lotion,lotrimin af solution,lotrimin cream,lotrimin lotion,lotrimin solution,monobaycuten,mycelax,mycelex,mycelex cream,mycelex g,mycelex otc,mycelex solution,mycelex troches,mycelex twin pack,myclo cream,myclo solution,myclo spray solution,mycofug,mycosporin,mykosporin,nalbix,otomax,pedisafe,rimazole,stiemazol,tibatin,trimysten,trivagizole,veltrim"					"10653-4,10654-2,18909-2,54177-1,55663-9"
+"CLO"	6098	"Cloxacillin"	"Beta-lactams/penicillins"	"J01CF02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox"	"chloroxacillin,clossacillina,cloxacilina,cloxacillin,cloxacillin sodium,cloxacilline,cloxacillinna,cloxacillinum,cloxapen,methocillin s,orbenin,syntarpen,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
+"COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,cs,cst,ct"	"belcomycine,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colobreathe,colomycin,coly-mycin,polymyxin e,polymyxin e. sulfate,promixin,totazina"	9	"MU"	9	"MU"	"16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
 "COP"		"Colistin/polysorbate"	"Other antibacterials"	"NA"			""	""					""
-"CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl"	"cicloserina,closerin,closina,cyclorin,cycloserin,cycloserine,cycloserinum,farmiserina,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,tisomycin,wasserina"	0.75	"g"			"16702-3,25251-0,3519-6"
-"DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb"	"dalbavancin,dalvance"			1.5	"g"	""
-"DAN"	71335	"Danofloxacin"	"Quinolones"	"NA"			""	"advocin,danofloxacin,danofloxacine,danofloxacino,danofloxacinum"					""
-"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"aczone,araldite ht,atrisone,avlosulfon,avlosulfone,avlosulphone,avsulfor,bis sulfone,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsone,dapsonum,di sulfone,diaphenyl sulfone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,dimitone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dubronaz,dumitone,eporal,metabolite c,novophone,protogen,servidapson,slphadione,sulfadione,sulfona,sulfone ucb,sulfonyldianiline,sulphadione,sulphonyldianiline,sumicure s,tarimyl,udolac"	50	"mg"			"9747-7"
-"DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum"			0.28	"g"	""
-"DFX"	487101	"Delafloxacin"	"Quinolones"	"J01MA23"			""	"baxdela,delafloxacin,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	""
-"DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"delamanid,deltyba"	0.2	"g"			""
-"DEM"	54680690	"Demeclocycline"	"Tetracyclines"	"D06AA01,J01AA01"	"Tetracyclines"	"Tetracyclines"	""	"bioterciclin,clortetrin,declomycin,deganol,demeclociclina,demeclocycline,demeclocyclinum,demeclor,demetraclin,diuciclin,elkamicina,ledermycin,mexocine,novotriclina,perciclina,sumaclina"	0.6	"g"			"10982-7,29494-2"
-"DKB"	470999	"Dibekacin"	"Aminoglycosides"	"J01GB09"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"debecacin,dibekacin,dibekacin sulfate,dibekacina,dibekacine,dibekacinum,dideoxykanamycin b,kappati,orbicin,panamicin"			0.14	"g"	""
-"DIC"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"J01CF01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"dicl"	"dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillin,dicloxacillin sodium,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,dycill,dynapen,maclicine,nm|| dicloxacillin,pathocil"	2	"g"	2	"g"	"10984-3,16769-2,25252-8"
-"DIF"	56206	"Difloxacin"	"Quinolones"	"NA"			""	"dicural,difloxacin,pulsaflox"					""
-"DIR"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"J01FA13"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"dirithromycin,dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin"	0.5	"g"			""
-"DOR"	73303	"Doripenem"	"Carbapenems"	"J01DH04"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"doribax,doripenem,doripenem hydrate,finibax"			1.5	"g"	""
-"DOX"	54671203	"Doxycycline"	"Tetracyclines"	"A01AB22,J01AA02"	"Tetracyclines"	"Tetracyclines"	"dox,doxy"	"atridox,azudoxat,deoxymykoin,dossiciclina,doxcycline anhydrous,doxiciclina,doxirobe,doxitard,doxivetin,doxycen,doxychel,doxycin,doxycyclin,doxycycline,doxycycline calcium,doxycycline hyclate,doxycyclinum,doxylin,doxysol,doxytec,doxytetracycline,hydramycin,investin,jenacyclin,liviatin,monodox,oracea,periostat,ronaxan,spanor,supracyclin,vibramycin,vibramycin novum,vibramycine,vibravenos,zenavod"	0.1	"g"	0.1	"g"	"10986-8,21250-6,26902-7"
-"ECO"	3198	"Econazole"	"Antifungals/antimycotics"	"D01AC03,G01AF05"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"econazol,econazole,econazolum,ecostatin,ecostatin cream,palavale,pevaryl,spectazole,spectazole cream"					""
-"ENX"	3229	"Enoxacin"	"Quinolones"	"J01MA04"	"Quinolone antibacterials"	"Fluoroquinolones"	"enox"	"almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacin,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex"	0.8	"g"			"16816-1,3590-7"
-"ENR"	71188	"Enrofloxacin"	"Quinolones"	"NA"			""	"baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum,enroxil"					""
-"ENV"	135565326	"Enviomycin"	"Antimycobacterials"	"J04AB06"			"tuberactinomycin"	"enviomicina,enviomycin,enviomycina,enviomycinum,tuberactin"					""
+"CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl"	"cicloserina,closerin,closina,cyclorin,cycloserin,cycloserine,cycloserinum,farmiserina,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,tisomycin,wasserina"	0.75	"g"			"16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
+"DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb"	"dalbavancin,dalvance"			1.5	"g"	"41688-3,41689-1,41690-9,41734-5"
+"DAN"	71335	"Danofloxacin"	"Quinolones"	"QJ01MA92"			""	"advocin,danofloxacin,danofloxacine,danofloxacino,danofloxacinum"					"73601-7,73623-1,73646-2"
+"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	""	"aczone,araldite ht,atrisone,avlosulfon,avlosulfone,avlosulphone,avsulfor,bis sulfone,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsone,dapsonum,di sulfone,diaphenyl sulfone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,dimitone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dubronaz,dumitone,eporal,metabolite c,novophone,protogen,servidapson,slphadione,sulfadione,sulfona,sulfone ucb,sulfonyldianiline,sulphadione,sulphonyldianiline,sumicure s,tarimyl,udolac"	50	"mg"			"51698-9,9747-7"
+"DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum"			0.28	"g"	"35787-1,35788-9,35789-7,41691-7"
+"DFX"	487101	"Delafloxacin"	"Quinolones"	"J01MA23"			""	"baxdela,delafloxacin,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	"88885-9,90447-4,93790-4"
+"DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"delamanid,deltyba"	0.2	"g"			"93851-4,96109-4"
+"DEM"	54680690	"Demeclocycline"	"Tetracyclines"	"D06AA01,J01AA01"	"Tetracyclines"	"Tetracyclines"	""	"bioterciclin,clortetrin,declomycin,deganol,demeclociclina,demeclocycline,demeclocyclinum,demeclor,demetraclin,diuciclin,elkamicina,ledermycin,mexocine,novotriclina,perciclina,sumaclina"	0.6	"g"			"10982-7,18915-9,216-2,217-0,218-8,219-6,29494-2,7006-0"
+"DKB"	470999	"Dibekacin"	"Aminoglycosides"	"J01GB09,S01AA29"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"debecacin,dibekacin,dibekacin sulfate,dibekacina,dibekacine,dibekacinum,dideoxykanamycin b,kappati,orbicin,panamicin"			0.14	"g"	"55669-6,55670-4,55671-2,55672-0"
+"DIC"	18381	"Dicloxacillin"	"Beta-lactams/penicillins"	"J01CF01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"dicl"	"dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillin,dicloxacillin sodium,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,dycill,dynapen,maclicine,nm|| dicloxacillin,pathocil"	2	"g"	2	"g"	"10984-3,16769-2,18916-7,220-4,221-2,222-0,223-8,25252-8,32380-8,55668-8"
+"DIF"	56206	"Difloxacin"	"Quinolones"	"QJ01MA94"			""	"dicural,difloxacin,pulsaflox"					"35790-5,35791-3,35792-1"
+"DIR"	6473883	"Dirithromycin"	"Macrolides/lincosamides"	"J01FA13"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"dirithromycin,dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin"	0.5	"g"			"35793-9,35794-7,35795-4,7007-8"
+"DOR"	73303	"Doripenem"	"Carbapenems"	"J01DH04"	"Other beta-lactam antibacterials"	"Carbapenems"	"dori"	"doribax,doripenem,doripenem hydrate,finibax"			1.5	"g"	"56031-8,58711-3,60535-2,72893-1"
+"DOX"	54671203	"Doxycycline"	"Tetracyclines"	"A01AB22,J01AA02"	"Tetracyclines"	"Tetracyclines"	"dox,doxy"	"atridox,azudoxat,deoxymykoin,dossiciclina,doxcycline anhydrous,doxiciclina,doxirobe,doxitard,doxivetin,doxycen,doxychel,doxycin,doxycyclin,doxycycline,doxycycline calcium,doxycycline hyclate,doxycyclinum,doxylin,doxysol,doxytec,doxytetracycline,hydramycin,investin,jenacyclin,liviatin,monodox,oracea,periostat,ronaxan,spanor,supracyclin,vibramycin,vibramycin novum,vibramycine,vibravenos,zenavod"	0.1	"g"	0.1	"g"	"10986-8,18917-5,20379-4,21250-6,224-6,225-3,226-1,227-9,23623-2,25223-9,26902-7,7008-6"
+"ECO"	3198	"Econazole"	"Antifungals/antimycotics"	"D01AC03,G01AF05"	"Antifungals for topical use"	"Imidazole and triazole derivatives"	"econ"	"econazol,econazole,econazolum,ecostatin,ecostatin cream,palavale,pevaryl,spectazole,spectazole cream"					"25595-0,25637-0,54178-9,55673-8"
+"ENX"	3229	"Enoxacin"	"Quinolones"	"J01MA04"	"Quinolone antibacterials"	"Fluoroquinolones"	"enox"	"almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,enoxacin,enoxacina,enoxacine,enoxacino,enoxacinum,enoxen,enoxin,enoxor,flumark,penetrex"	0.8	"g"			"16816-1,18918-3,228-7,229-5,230-3,231-1,3590-7,41692-5"
+"ENR"	71188	"Enrofloxacin"	"Quinolones"	"QJ01MA90"			""	"baytril,enrofloxacin,enrofloxacine,enrofloxacino,enrofloxacinum,enroxil"					"23712-3,35796-2,35797-0,35798-8"
+"ENV"	135565326	"Enviomycin"	"Antimycobacterials"	"J04AB06"			"tuberactinomycin"	"enviomicina,enviomycin,enviomycina,enviomycinum,tuberactin"			1	"g"	""
 "EPE"		"Eperozolid"	"Other antibacterials"	"NA"			""	""					""
 "EPC"	71392	"Epicillin"	"Beta-lactams/penicillins"	"J01CA07"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"dexacillin,dihydroampicillin,epicilina,epicillin,epicilline,epicillinum"	2	"g"	2	"g"	""
 "EPP"	68916	"Epiroprim"	"Other antibacterials"	"NA"			""	"epiroprim,epiroprima,epiroprime,epiroprimum"					""
-"ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"eravacycline,xerava"					""
-"ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,etp"	"ertapenem,invanz"			1	"g"	""
-"ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"D10AF02,J01FA01,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,eryt"	"abboticin,abomacetin,acneryne,acnesol,akne cordes losung,aknederm ery gel,aknemycin,austrias,benzamycin,bristamycin,derimer,deripil,dotycin,dumotrycin,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,eryc sprinkles,erycen,erycette,erycin,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erypar,erysafe,erytab,erythrocin,erythrocin stearate,erythroderm,erythrogran,erythroguent,erythromid,erythromycin,erythromycin a,erythromycin base,erythromycin lactate,erythromycine,erythromycines,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,ilotycin gluceptate,ilotycin t.s.,inderm,inderm gel,indermretcin,latotryd,lederpax,mephamycin,mercina,oftamolets,paediathrocin,pantoderm,pantodrin,pantomicina,pce dispertab,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,romycin,sansac,skid gel e,staticin,stiemicyn,stiemycin,theramycin z,tiloryth,tiprocin,torlamicina,udima ery gel,wyamycin s"	2	"g"	1	"g"	"12298-6,16829-4,25275-9,3597-2"
-"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha"	"aethambutolum,diambutol,ebutol,etambutol,etambutolo,etapiam,ethambutol,ethambutolum,myambutol,mycobutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"25404-5,3607-9"
+"ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"eravacycline,xerava"			0.14	"g"	"100049-6,85423-2,93767-2"
+"ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,etp"	"ertapenem,invanz"			1	"g"	"101486-9,35799-6,35800-2,35801-0,35802-8"
+"ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"D10AF02,J01FA01,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,eryt"	"abboticin,abomacetin,acneryne,acnesol,akne cordes losung,aknederm ery gel,aknemycin,austrias,benzamycin,bristamycin,derimer,deripil,dotycin,dumotrycin,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,eryc sprinkles,erycen,erycette,erycin,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erypar,erysafe,erytab,erythrocin,erythrocin stearate,erythroderm,erythrogran,erythroguent,erythromid,erythromycin,erythromycin a,erythromycin base,erythromycin lactate,erythromycine,erythromycines,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,ilotycin gluceptate,ilotycin t.s.,inderm,inderm gel,indermretcin,latotryd,lederpax,mephamycin,mercina,oftamolets,paediathrocin,pantoderm,pantodrin,pantomicina,pce dispertab,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,romycin,sansac,skid gel e,staticin,stiemicyn,stiemycin,theramycin z,tiloryth,tiprocin,torlamicina,udima ery gel,wyamycin s"	2	"g"	1	"g"	"100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
+"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha"	"aethambutolum,diambutol,ebutol,etambutol,etambutolo,etapiam,ethambutol,ethambutolum,myambutol,mycobutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
 "ETI"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"J04AM03"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"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"	"NA"			""	"amprol plus,ethopabat,ethopabate,ethyl pabate"					""
+"ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi"	"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"			"16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
+"ETO"	6034	"Ethopabate"	"Other antibacterials"	"QP51AX17"			""	"amprol plus,ethopabat,ethopabate,ethyl pabate"					""
 "EXE"		"Exebacase"		"NA"			""	""					""
-"FAR"	65894	"Faropenem"	"Other antibacterials"	"J01DI03"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	"faropenem,faropenem sodium,fropenem,fropenum sodium"	0.75	"g"			""
-"FDX"	10034073	"Fidaxomicin"	"Other antibacterials"	"A07AA12"			""	"dificid,dificlir,difimicin,fidaxomicin,lipiarmicin,lipiarmycin,lipiarrmycin,tiacumicin b"	0.4	"g"			""
-"FIN"	11567473	"Finafloxacin"	"Quinolones"	"NA"			""	"finafloxacin"					""
+"FAR"	65894	"Faropenem"	"Other antibacterials"	"J01DI03"	"Other beta-lactam antibacterials"	"Other cephalosporins and penems"	""	"faropenem,faropenem sodium,fropenem,fropenum sodium"	0.75	"g"			"73600-9,73622-3,73645-4"
+"FDX"	10034073	"Fidaxomicin"	"Other antibacterials"	"A07AA12"			""	"dificid,dificlir,difimicin,fidaxomicin,lipiarmicin,lipiarmycin,lipiarrmycin,tiacumicin b"	0.4	"g"			"73599-3,73621-5,73644-7"
+"FIN"	11567473	"Finafloxacin"	"Quinolones"	"NA"			""	"finafloxacin"					"73598-5,73620-7,73643-9"
 "FLA"	46783781	"Flavomycin"	"Other antibacterials"	"NA"			""	"flavophospholipol,moenomycin complex"					""
-"FLE"	3357	"Fleroxacin"	"Quinolones"	"J01MA08"	"Quinolone antibacterials"	"Fluoroquinolones"	"fler"	"fleroxacin,fleroxacine,fleroxacino,fleroxacinum,fleroxicin,megalocin,megalone,megalosin,quinodis"	0.4	"g"	0.4	"g"	""
-"FLO"	65864	"Flomoxef"	"Other antibacterials"	"J01DC14"			""	"flomoxef,flomoxefo,flomoxefum"			2	"g"	""
-"FLR"	114811	"Florfenicol"	"Other antibacterials"	"NA"			""	"aquafen,florfenicol,nuflor,nuflor gold"					"87599-7"
+"FLE"	3357	"Fleroxacin"	"Quinolones"	"J01MA08"	"Quinolone antibacterials"	"Fluoroquinolones"	"fler"	"fleroxacin,fleroxacine,fleroxacino,fleroxacinum,fleroxicin,megalocin,megalone,megalosin,quinodis"	0.4	"g"	0.4	"g"	"25411-0,32372-5,35806-9,7012-8"
+"FLO"	65864	"Flomoxef"	"Other antibacterials"	"J01DC14"			""	"flomoxef,flomoxefo,flomoxefum"			2	"g"	"100052-0,53822-3"
+"FLR"	114811	"Florfenicol"	"Other antibacterials"	"QJ01BA90,QJ51BA90"			""	"aquafen,florfenicol,nuflor,nuflor gold"					"23740-4,35807-7,35808-5,87599-7"
 "FLC"	21319	"Flucloxacillin"	"Beta-lactams/penicillins"	"J01CF05"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,flux"	"culpen,floxacillin,floxacillin sodium,floxapen,floxapen sodium salt,fluclox,flucloxacilina,flucloxacillin,flucloxacilline,flucloxacillinum,fluorochloroxacillin,staphylex"	2	"g"	2	"g"	""
-"FLU"	3365	"Fluconazole"	"Antifungals/antimycotics"	"D01AC15,J02AC01"	"Antimycotics for systemic use"	"Triazole derivatives"	"fluc,fluz,flz"	"alflucoz,alfumet,alkanazole,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazol,fluconazole,fluconazole capsules,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,flusol,fluzon,fluzone,forcan,fuconal,fungata,loitin,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zoltec"	0.2	"g"	0.2	"g"	"10987-6,16870-8,25255-1,80530-9"
-"FCT"	3366	"Flucytosine"	"Antifungals/antimycotics"	"D01AE21,J02AX01"	"Antifungals for topical use"	"Other antifungals for topical use"	"5flc,fcu,fluo,fluy"	"alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucystine,flucytosin,flucytosine,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine"					""
-"FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07"	"Quinolone antibacterials"	"Other quinolones"	""	"apurone,fantacin,flumequine,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl"	1.2	"g"			""
+"FLU"	3365	"Fluconazole"	"Antifungals/antimycotics"	"D01AC15,J02AC01"	"Antimycotics for systemic use"	"Triazole derivatives"	"fluc,fluz,flz"	"alflucoz,alfumet,alkanazole,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazol,fluconazole,fluconazole capsules,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,flusol,fluzon,fluzone,forcan,fuconal,fungata,loitin,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zoltec"	0.2	"g"	0.2	"g"	"10987-6,16870-8,18924-1,248-5,249-3,250-1,251-9,25255-1,7013-6,80530-9"
+"FCT"	3366	"Flucytosine"	"Antifungals/antimycotics"	"D01AE21,J02AX01"	"Antifungals for topical use"	"Other antifungals for topical use"	"5flc,fcu,fluo,fluy"	"alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucystine,flucytosin,flucytosine,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine"	10	"g"	10	"g"	""
+"FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07"	"Quinolone antibacterials"	"Other quinolones"	""	"apurone,fantacin,flumequine,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl"	1.2	"g"			"55675-3,55676-1,55677-9,55678-7"
 "FLR1"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"J01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"flurithromicina,flurithromycime,flurithromycin,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic"	0.75	"g"			""
 "FFL"	214356	"Fosfluconazole"	"Antifungals/antimycotics"	"NA"			""	"fosfluconazole,phosfluconazole,procif,prodif"					""
-"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf"	"calcium fosfomycin,fosfocina,fosfomicin,fosfomicina,fosfomycin,fosfomycin sodium,fosfomycine,fosfomycinum,fosfonomycin,infectophos,monuril,monurol,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	""
+"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf"	"calcium fosfomycin,fosfocina,fosfomicin,fosfomicina,fosfomycin,fosfomycin sodium,fosfomycine,fosfomycinum,fosfonomycin,infectophos,monuril,monurol,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
 "FMD"	572	"Fosmidomycin"	"Other antibacterials"	"NA"			""	"fosmidomycin,fosmidomycina,fosmidomycine,fosmidomycinum"					""
-"FRM"	8378	"Framycetin"	"Aminoglycosides"	"D09AA01,R01AX08,S01AA07"			"fram"	"actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v"					""
+"FRM"	8378	"Framycetin"	"Aminoglycosides"	"D09AA01,R01AX08,S01AA07"			"fram"	"actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v"					"18926-6,257-6,258-4,259-2,260-0,55679-5"
 "FUR"	6870646	"Furazidin"	"Other antibacterials"	"J01XE03"	"Other antibacterials"	"Nitrofuran derivatives"	""	"akritoin,furagin,furaginum,furamag,furazidin,furazidine"	0.3	"g"			""
-"FRZ"	5323714	"Furazolidone"	"Other antibacterials"	"G01AX06"			""	"bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furaxon,furaxone,furazol,furazolidine,furazolidon,furazolidona,furazolidone,furazolidonum,furazolum,furazon,furidon,furovag,furox aerosol powder,furoxal,furoxane,furoxon,furoxone,furoxone liquid,furoxone swine mix,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn"					""
+"FRZ"	5323714	"Furazolidone"	"Other antibacterials"	"G01AX06"			""	"bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furaxon,furaxone,furazol,furazolidine,furazolidon,furazolidona,furazolidone,furazolidonum,furazolum,furazon,furidon,furovag,furox aerosol powder,furoxal,furoxane,furoxon,furoxone,furoxone liquid,furoxone swine mix,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn"					"69574-2,87794-4"
 "FUS"	3000226	"Fusidic acid"	"Other antibacterials"	"D06AX01,D09AA02,J01XC01,S01AA13"	"Other antibacterials"	"Steroid antibacterials"	"fa,fusi"	"acide fusidique,acido fusidico,acidum fusidicum,flucidin,fucidate,fucidate sodium,fucidic acid,fucidin,fucidin acid,fucithalmic,fusidate,fusidate acid,fusidic acid,fusidicacid,fusidine,fusidinic acid,ramycin,taksta"	1.5	"g"	1.5	"g"	""
-"GAM"	59364992	"Gamithromycin"	"Macrolides/lincosamides"	"NA"			""	"gamithromycin"					""
-"GRN"	124093	"Garenoxacin"	"Quinolones"	"J01MA19"			""	"ganefloxacin,garenfloxacin,garenoxacin"	0.4	"g"			""
-"GAT"	5379	"Gatifloxacin"	"Quinolones"	"J01MA16,S01AE06"	"Quinolone antibacterials"	"Fluoroquinolones"	"gati"	"gatiflo,gatifloxacin,gatifloxacin hydrate,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,tequin,tequin and zymar,zymaxid"	0.4	"g"	0.4	"g"	""
-"GEM"	9571107	"Gemifloxacin"	"Quinolones"	"J01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"factiv,factive,gemifioxacin,gemifloxacin,gemifloxacine,gemifloxacino,gemifloxacinum"	0.32	"g"			""
-"GEN"	3467	"Gentamicin"	"Aminoglycosides"	"D06AX07,J01GB03,S01AA11,S02AA14,S03AA06"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"cn,gen,gent,gm"	"apogen,centicin,cidomycin,garamycin,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"	"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"	"NA"			"gehi,gehl,genta high,gentamicin high"	""					""
+"GAM"	59364992	"Gamithromycin"	"Macrolides/lincosamides"	"QJ01FA95"			""	"gamithromycin"					"100054-6,88376-9,88378-5"
+"GRN"	124093	"Garenoxacin"	"Quinolones"	"J01MA19"			""	"ganefloxacin,garenfloxacin,garenoxacin"	0.4	"g"			"35811-9,35812-7,35813-5"
+"GAT"	5379	"Gatifloxacin"	"Quinolones"	"J01MA16,S01AE06"	"Quinolone antibacterials"	"Fluoroquinolones"	"gati"	"gatiflo,gatifloxacin,gatifloxacin hydrate,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,tequin,tequin and zymar,zymaxid"	0.4	"g"	0.4	"g"	"31036-7,31038-3,31040-9,31042-5,41494-6"
+"GEM"	9571107	"Gemifloxacin"	"Quinolones"	"J01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"factiv,factive,gemifioxacin,gemifloxacin,gemifloxacine,gemifloxacino,gemifloxacinum"	0.32	"g"	0.2	"g"	"35814-3,35815-0,35816-8,41697-4"
+"GEN"	3467	"Gentamicin"	"Aminoglycosides"	"D06AX07,J01GB03,S01AA11,S02AA14,S03AA06"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"cn,gen,gent,gm"	"apogen,centicin,cidomycin,garamycin,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"	"101494-3,13561-6,13562-4,15106-8,18928-2,18929-0,22746-2,22747-0,266-7,267-5,268-3,269-1,31091-2,31092-0,31093-8,35668-3,35817-6,3663-2,3664-0,3665-7,39082-3,47109-4,50630-3,59379-8,7016-9,7017-7,7018-5,80971-5,88111-0,89481-6"
+"GEH"		"Gentamicin-high"	"Aminoglycosides"	"NA"			"gehi,gehl,genta high,gentamicin high"	""					"18929-0,35817-6,7017-7,7018-5"
 "GEP"	25101874	"Gepotidacin"	"Other antibacterials"	"NA"			""	"gepotidacin"					""
-"GRX"	72474	"Grepafloxacin"	"Quinolones"	"J01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"grep"	"grepafloxacin"	0.4	"g"			""
-"GRI"	441140	"Griseofulvin"	"Antifungals/antimycotics"	"D01AA08,D01BA01"			""	"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,griseoflulvin,griseofulvin,griseofulvin forte,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisovin fp,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spirofulvin,sporostatin xan,xuanjing"	0.5	"g"			"12402-4"
+"GRX"	72474	"Grepafloxacin"	"Quinolones"	"J01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"grep"	"grepafloxacin"	0.4	"g"			"21316-5,23638-0,23639-8,35818-4"
+"GRI"	441140	"Griseofulvin"	"Antifungals/antimycotics"	"D01AA08,D01BA01"			""	"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,griseoflulvin,griseofulvin,griseofulvin forte,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisovin fp,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spirofulvin,sporostatin xan,xuanjing"	0.5	"g"			"12402-4,54200-1,54201-9,54202-7"
 "HAB"	175989	"Habekacin"	"Aminoglycosides"	"NA"			""	"arbekacin sulfate,arbekacin sulphate,habekacin,habekacin sulfate,habekacin xsulfate,habekacinxsulfate"					""
 "HCH"	11979956	"Hachimycin"	"Antifungals/antimycotics"	"D01AA03,G01AA06,J02AA02"	"Antimycotics for systemic use"	"Antibiotics"	""	"cabimicina,hachimicina,hachimycin,hachimycine,hachimycinum,trichomycinum,trichonat"					""
-"HET"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"J01CA18"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"etacillina,hetacilina,hetacillin,hetacillin acid,hetacilline,hetacillinum,phenazacillin,versapen"	2	"g"			""
+"HET"	443387	"Hetacillin"	"Beta-lactams/penicillins"	"J01CA18"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"etacillina,hetacilina,hetacillin,hetacillin acid,hetacilline,hetacillinum,phenazacillin,versapen"	2	"g"			"18931-6,274-1,275-8,276-6,277-4"
 "HYG"	56928061	"Hygromycin"	"Aminoglycosides"	"NA"			""	"antihelmycin,hydromycin b,hygrovetine"					""
-"IBX"		"Ibrexafungerp"	"Antifungals"	"NA"			""	"ibrexafungerp"					""
-"ICL"	213043	"Iclaprim"	"Other antibacterials"	"J01EA03"			""	"iclaprim,mersarex"					""
-"IPM"	104838	"Imipenem"	"Carbapenems"	"J01DH51"	"Other beta-lactam antibacterials"	"Carbapenems"	"imci,imi,imip,imp"	"imipemide,imipenem,imipenem anhydrous,imipenem hydrate,imipenem/cilastatin,imipenemum,imipenen,primaxin,recarbrio .,tienamycin"			2	"g"	"17010-0,25257-7,27331-8,3688-9"
-"IPE"		"Imipenem/EDTA"	"Carbapenems"	"NA"			""	""					""
-"IMR"		"Imipenem/relebactam"	"Carbapenems"	"NA,J01DH56"			""	""					""
-"ISV"	6918485	"Isavuconazole"	"Antifungals/antimycotics"	"J02AC05"			"isav"	"isavuconazole"	0.2	"g"	0.2	"g"	""
-"ISE"	3037209	"Isepamicin"	"Aminoglycosides"	"J01GB11"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"isepacin,isepalline,isepamicin,isepamicina,isepamicine,isepamicinsulphate,isepamicinum"			0.4	"g"	""
-"ISO"	3760	"Isoconazole"	"Antifungals/antimycotics"	"D01AC05,G01AF07"	"Antimycotics for topic use"	"Triazole derivatives"	""	"isoconazol,isoconazole,isoconazolum,travogen"					""
-"INH"	3767	"Isoniazid"	"Antimycobacterials"	"J04AC01"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh"	"abdizide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azt + isoniazid,azuren,bacillin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hid rasonil,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydrazid,hydrazide,hyozid,i.a.i.,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazid,isoniazid sa,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,lanizid,mayambutol,mybasan,neoteben,neoxin,neumandin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nydrazid,nyscozid,pelazid,percin,phthisen,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide"	0.3	"g"	0.3	"g"	"25451-6,26756-7,3697-0,40371-7"
+"IBX"		"Ibrexafungerp"	"Antifungals"	"J02AX07"			""	"ibrexafungerp"					""
+"ICL"	213043	"Iclaprim"	"Other antibacterials"	"J01EA03"			""	"iclaprim,mersarex"					"73597-7,73619-9,73642-1"
+"IPM"	104838	"Imipenem"	"Carbapenems"	"J01DH51"	"Other beta-lactam antibacterials"	"Carbapenems"	"imci,imi,imip,imp"	"imipemide,imipenem,imipenem anhydrous,imipenem hydrate,imipenem/cilastatin,imipenemum,imipenen,primaxin,recarbrio .,tienamycin"			2	"g"	"101487-7,17010-0,18932-4,18933-2,23613-3,25221-3,25257-7,27331-8,278-2,279-0,280-8,281-6,282-4,283-2,284-0,285-7,35819-2,3688-9,54170-6,54171-4,54172-2,7019-3,85424-0,93232-7,96372-8"
+"IPE"		"Imipenem/EDTA"	"Carbapenems"	"NA"			""	""					"35819-2,54170-6,54171-4,54172-2"
+"IMR"		"Imipenem/relebactam"	"Carbapenems"	"NA,J01DH56"			""	""			2	"g"	"85424-0,93232-7,96372-8"
+"ISV"	6918485	"Isavuconazole"	"Antifungals/antimycotics"	"J02AC05"			"isav"	"isavuconazole"	0.2	"g"	0.2	"g"	"85381-2,88887-5"
+"ISE"	3037209	"Isepamicin"	"Aminoglycosides"	"J01GB11"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"isepacin,isepalline,isepamicin,isepamicina,isepamicine,isepamicinsulphate,isepamicinum"			0.4	"g"	"32381-6,35820-0,35821-8,55680-3"
+"ISO"	3760	"Isoconazole"	"Antifungals/antimycotics"	"D01AC05,G01AF07"	"Antimycotics for topic use"	"Triazole derivatives"	""	"isoconazol,isoconazole,isoconazolum,travogen"					"55681-1,55682-9,55683-7,55684-5"
+"INH"	3767	"Isoniazid"	"Antimycobacterials"	"J04AC01"	"Drugs for treatment of tuberculosis"	"Hydrazides"	"inh"	"abdizide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azt + isoniazid,azuren,bacillin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hid rasonil,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydrazid,hydrazide,hyozid,i.a.i.,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,isoniazid,isoniazid sa,isoniazida,isoniazide,isoniazidum,isonicazide,isonicid,isonico,isonicotan,isonicotil,isonicotinhydrazid,isonicotinohydrazide,isonide,isonidrin,isonikazid,isonilex,isonin,isonindon,isonirit,isoniton,isonizida,isonizide,isotamine,isotebe,isotebezid,isotinyl,isozid,isozide,isozyd,laniazid,laniozid,lanizid,mayambutol,mybasan,neoteben,neoxin,neumandin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nydrazid,nyscozid,pelazid,percin,phthisen,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,unicocyde,unicozyde,vazadrine,vederon,zidafimia,zinadon,zonazide"	0.3	"g"	0.3	"g"	"18934-0,20383-6,23947-5,25217-1,25218-9,25219-7,25451-6,26756-7,286-5,287-3,288-1,289-9,29315-9,3697-0,40371-7,42649-4,42650-2,42651-0,45215-1,48171-3,48172-1,55685-2,7020-1,89488-1"
 "IST"		"Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine"	"Antimycobacterials"	"J04AM08"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"ITR"	3793	"Itraconazole"	"Antifungals/antimycotics"	"J02AC02"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra"	"intraconazole,itraconazol,itraconazole,itraconazolo,itraconazolum,itraconzaole,itrazole,itrizole,oriconazole,sporanox"	0.2	"g"	0.2	"g"	"10989-2,12392-7,25258-5,27081-9,32184-4,32185-1,80531-7"
-"JOS"	5282165	"Josamycin"	"Macrolides/lincosamides"	"J01FA07"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"jomybel,josacine,josamicina,josamycin,josamycine,josamycinum"	2	"g"			""
-"KAN"	6032	"Kanamycin"	"Aminoglycosides"	"A07AA08,J01GB04,S01AA24"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"hlk,k,kan,kana,km"	"kanamicina,kanamycin,kanamycin a,kanamycin base,kanamycin sulfate,kanamycina,kanamycine,kanamycins,kanamycinum,kantrex,kenamycin a,klebcil,liposomal kanamycin"	3	"g"	1	"g"	"23889-9,3698-8,3699-6,3700-2,47395-9"
-"KAH"		"Kanamycin-high"	"Aminoglycosides"	"NA"			"k_h,kahl"	""					""
+"ITR"	3793	"Itraconazole"	"Antifungals/antimycotics"	"J02AC02"	"Antimycotics for systemic use"	"Triazole derivatives"	"itra"	"intraconazole,itraconazol,itraconazole,itraconazolo,itraconazolum,itraconzaole,itrazole,itrizole,oriconazole,sporanox"	0.2	"g"	0.2	"g"	"10989-2,12392-7,25258-5,25452-4,27081-9,32184-4,32185-1,32603-3,54179-7,7021-9,80531-7"
+"JOS"	5282165	"Josamycin"	"Macrolides/lincosamides"	"J01FA07"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"jomybel,josacine,josamicina,josamycin,josamycine,josamycinum"	2	"g"			"25597-6,25702-2,41698-2,41699-0"
+"KAN"	6032	"Kanamycin"	"Aminoglycosides"	"A07AA08,J01GB04,S01AA24"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"hlk,k,kan,kana,km"	"kanamicina,kanamycin,kanamycin a,kanamycin base,kanamycin sulfate,kanamycina,kanamycine,kanamycins,kanamycinum,kantrex,kenamycin a,klebcil,liposomal kanamycin"	3	"g"	1	"g"	"18935-7,18936-5,23609-1,23889-9,25182-7,25213-0,25214-8,290-7,291-5,292-3,293-1,3698-8,3699-6,3700-2,42652-8,47395-9,49080-5,7022-7,7023-5,7024-3,88002-1,88705-9,89482-4"
+"KAH"		"Kanamycin-high"	"Aminoglycosides"	"NA"			"k_h,kahl"	""					"18936-5,7023-5,7024-3"
 "KAC"		"Kanamycin/cephalexin"	"Aminoglycosides"	"NA"			""	""					""
-"KET"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"D01AC08,G01AF11,H02CA03,J02AB02"	"Antimycotics for systemic use"	"Imidazole derivatives"	"keto,ktc"	"extina,fungarest,fungoral,ketocanazole,ketoconazol,ketoconazole,ketoconazolum,ketoderm,nizoral,xolegel"	0.6	"g"			"10990-0,12393-5,25259-3,60091-6,60092-4"
-"KIT"		"Kitasamycin"	"Macrolides/lincosamides"	"NA"			"leucomycin"	"jomybel,josacine,josamicina,josamycin,josamycine,josamycinum"					""
-"LAS"	5360807	"Lasalocid"	"Other antibacterials"	"NA"			""	"avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum"					"87598-9"
+"KET"	456201	"Ketoconazole"	"Antifungals/antimycotics"	"D01AC08,G01AF11,H02CA03,J02AB02"	"Antimycotics for systemic use"	"Imidazole derivatives"	"keto,ktc"	"extina,fungarest,fungoral,ketocanazole,ketoconazol,ketoconazole,ketoconazolum,ketoderm,nizoral,xolegel"	0.6	"g"			"10990-0,12393-5,18937-3,25259-3,294-9,295-6,296-4,297-2,60091-6,60092-4,7025-0"
+"KIT"		"Kitasamycin"	"Macrolides/lincosamides"	"QJ01FA93"			"leucomycin"	"jomybel,josacine,josamicina,josamycin,josamycine,josamycinum"					""
+"LAS"	5360807	"Lasalocid"	"Other antibacterials"	"QP51BB02"			""	"avatec,lasalocid,lasalocid a,lasalocide,lasalocide a,lasalocido,lasalocidum"					"87598-9"
 "LSC"	71528768	"Lascufloxacin"	"Quinolones"	"J01MA25"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"lascufloxacin"	75	"mg"			""
 "LTM"	47499	"Latamoxef"	"Cephalosporins (3rd gen.)"	"J01DD06"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"mox,moxa,moxalactam"	"disodium moxalactam,festamoxin,lamoxactam,latamoxef,latamoxefum,moxalactamsupplement,shiomarin"			4	"g"	""
-"LMU"	25185057	"Lefamulin"	"Other antibacterials"	"J01XX12"			""	"lefamulin,xenleta"					""
+"LMU"	25185057	"Lefamulin"	"Other antibacterials"	"J01XX12"			""	"lefamulin,xenleta"					"85425-7,99281-8"
 "LEN"	65646	"Lenampicillin"	"Beta-lactams/penicillins"	"NA"			""	"lenampicilina,lenampicillin,lenampicillin hcl,lenampicilline,lenampicillinum"					""
-"LVX"	149096	"Levofloxacin"	"Quinolones"	"J01MA12,S01AE05"	"Quinolone antibacterials"	"Fluoroquinolones"	"le,lev,levo,lvx"	"aeroquin,anhydrous ofloxacin,cravit,cravit hydrate,cravit iv,cravit ophthalmic,elequine,floxacin,floxel,fluoroquinolone,iquix hydrate,leroxacin,lesacin,levaquin,levaquin hydrate,levo floxacin,levofiexacin,levofloxacin,levofloxacin hydrate,levofloxacine,levofloxacino,levofloxacinum,levokacin,levoxacin,mosardal,nofaxin,ofloxcacin,oftaquix,quinsair,quixin,reskuin,tavanic,unibiotic,venaxan,volequin"	0.5	"g"	0.5	"g"	"21368-6,30532-6,30533-4"
+"LVX"	149096	"Levofloxacin"	"Quinolones"	"J01MA12,S01AE05"	"Quinolone antibacterials"	"Fluoroquinolones"	"le,lev,levo,lvx"	"aeroquin,anhydrous ofloxacin,cravit,cravit hydrate,cravit iv,cravit ophthalmic,elequine,floxacin,floxel,fluoroquinolone,iquix hydrate,leroxacin,lesacin,levaquin,levaquin hydrate,levo floxacin,levofiexacin,levofloxacin,levofloxacin hydrate,levofloxacine,levofloxacino,levofloxacinum,levokacin,levoxacin,mosardal,nofaxin,ofloxcacin,oftaquix,quinsair,quixin,reskuin,tavanic,unibiotic,venaxan,volequin"	0.5	"g"	0.5	"g"	"101501-5,20396-8,20629-2,21367-8,21368-6,30532-6,30533-4,48173-9,53716-7,7026-8,76040-5,76041-3,76042-1"
 "LEO"		"Levofloxacin/ornidazole"	"Other antibacterials"	"J01RA05"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "LND"	9850038	"Levonadifloxacin"	"Quinolones"	"J01MA24"			""	"levonadifloxacin"					""
 "LSP"		"Linco-spectin"	"Other antibacterials"	"NA"			"lincomycin/spectinomycin"	""					""
-"LIN"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"J01FF02"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc"	"bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincolcina,lincolnensin,lincomicina,lincomycin,lincomycin a,lincomycine,lincomycinum,lincorex"	1.8	"g"	1.8	"g"	"87597-1"
-"LNZ"	441401	"Linezolid"	"Oxazolidinones"	"J01XX08"	"Other antibacterials"	"Other antibacterials"	"line,lnz,lz,lzd"	"linezlid,linezoid,linezolid,linezolide,linezolidum,zivoxid,zyvoxa,zyvoxam,zyvoxid"	1.2	"g"	1.2	"g"	"34202-2,80609-1"
+"LIN"	3000540	"Lincomycin"	"Macrolides/lincosamides"	"J01FF02"	"Macrolides, lincosamides and streptogramins"	"Lincosamides"	"linc"	"bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincolcina,lincolnensin,lincomicina,lincomycin,lincomycin a,lincomycine,lincomycinum,lincorex"	1.8	"g"	1.8	"g"	"18938-1,298-0,299-8,300-4,301-2,41700-6,87597-1"
+"LNZ"	441401	"Linezolid"	"Oxazolidinones"	"J01XX08"	"Other antibacterials"	"Other antibacterials"	"line,lnz,lz,lzd"	"linezlid,linezoid,linezolid,linezolide,linezolidum,zivoxid,zyvoxa,zyvoxam,zyvoxid"	1.2	"g"	1.2	"g"	"29254-0,29255-7,29258-1,33332-8,34202-2,41500-0,80609-1,88706-7,96111-0"
 "LFE"		"Linoprist-flopristin"	"Other antibacterials"	"NA"			""	""					""
-"LOM"	3948	"Lomefloxacin"	"Quinolones"	"J01MA07,S01AE04"	"Quinolone antibacterials"	"Fluoroquinolones"	"lmf,lom,lome"	"lomefloxacin,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin"	0.4	"g"			""
-"LOR"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"J01DC08"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"lora"	"anhydrous loracarbef,lorabid,loracabef,loracarbef,loracarbefum,lorbef,loribid"	0.6	"g"			""
-"LYM"	54707177	"Lymecycline"	"Tetracyclines"	"J01AA04"	"Tetracyclines"	"Tetracyclines"	""	"biovetin,chlortetracyclin,ciclisin,ciclolysal,ciclolysine,infaciclina,limeciclina,lisinbiotic,lymecyclin,lymecycline,lymecyclinum,mucomycin,ntetracycline,tetralisal,tetralysal,vebicyclysal"	0.6	"g"	0.6	"g"	""
+"LOM"	3948	"Lomefloxacin"	"Quinolones"	"J01MA07,S01AE04"	"Quinolone antibacterials"	"Fluoroquinolones"	"lmf,lom,lome"	"lomefloxacin,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin"	0.4	"g"			"18939-9,302-0,303-8,304-6,305-3,41701-4"
+"LOR"	5284585	"Loracarbef"	"Cephalosporins (2nd gen.)"	"J01DC08"	"Other beta-lactam antibacterials"	"Second-generation cephalosporins"	"lora"	"anhydrous loracarbef,lorabid,loracabef,loracarbef,loracarbefum,lorbef,loribid"	0.6	"g"			"18940-7,306-1,307-9,308-7,309-5,7027-6"
+"LYM"	54707177	"Lymecycline"	"Tetracyclines"	"J01AA04"	"Tetracyclines"	"Tetracyclines"	""	"biovetin,chlortetracyclin,ciclisin,ciclolysal,ciclolysine,infaciclina,limeciclina,lisinbiotic,lymecyclin,lymecycline,lymecyclinum,mucomycin,ntetracycline,tetralisal,tetralysal,vebicyclysal"	0.6	"g"	0.6	"g"	"18941-5,310-3,311-1,312-9,313-7"
 "MNA"	1292	"Mandelic acid"	"Other antibacterials"	"B05CA06,J01XX06"	"Other antibacterials"	"Other antibacterials"	""	"acido mandelico,almond acid,ammonium mandelate,amygdalic acid,benzoglycolic acid,hydroxyacetic acid,kyselina mandlova,mandelic acid,paramandelic acid,phenylglycolic acid,uromaline"	12	"g"			""
 "MGX"		"Manogepix"	"Antifungals"	"NA"			""	"manogepix"					""
-"MAR"	60651	"Marbofloxacin"	"Quinolones"	"NA"			""	"marbocyl,marbofloxacin,marbofloxacine,marbofloxacino,marbofloxacinum,zeniquin"					""
+"MAR"	60651	"Marbofloxacin"	"Quinolones"	"QJ01MA93"			""	"marbocyl,marbofloxacin,marbofloxacine,marbofloxacino,marbofloxacinum,zeniquin"					"73596-9,73618-1,73641-3"
 "MEC"	36273	"Mecillinam"	"Beta-lactams/penicillins"	"J01CA11"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"amdinocillin"	"amdinocillin,coactin,hexacillin,mecilinamo,mecillinam,mecillinamum,micillinam,penicillin hx,selexidin"			1.2	"g"	""
 "MEL"	71306732	"Meleumycin"	"Macrolides/lincosamides"	"NA"			""	""					""
-"MEM"	441130	"Meropenem"	"Carbapenems"	"J01DH02"	"Other beta-lactam antibacterials"	"Carbapenems"	"mem,mer,mero,mp,mrp"	"meronem,meropen,meropenem,meropenem anhydrous,meropenem hydrate,meropenem trihydrate,meropenemum,merrem,merrem i.v.,merrem iv"			3	"g"	"41406-0"
+"MEM"	441130	"Meropenem"	"Carbapenems"	"J01DH02"	"Other beta-lactam antibacterials"	"Carbapenems"	"mem,mer,mero,mp,mrp"	"meronem,meropen,meropenem,meropenem anhydrous,meropenem hydrate,meropenem trihydrate,meropenemum,merrem,merrem i.v.,merrem iv"			3	"g"	"101222-8,101488-5,101489-3,18943-1,41406-0,6651-4,6652-2,6653-0,6654-8,7029-2,85426-5,85427-3,88892-5,90980-4"
 "MNC"		"Meropenem/nacubactam"	"Carbapenems"	"NA"			""	""					""
-"MEV"		"Meropenem/vaborbactam"	"Carbapenems"	"J01DH52"	"Other beta-lactam antibacterials"	"Carbapenems"	""	"carbavance,vabomere"			3	"g"	""
+"MEV"		"Meropenem/vaborbactam"	"Carbapenems"	"J01DH52"	"Other beta-lactam antibacterials"	"Carbapenems"	""	"carbavance,vabomere"			3	"g"	"101222-8,101489-3,85427-3,88892-5,90980-4"
 "MES"	176886	"Mesulfamide"	"Other antibacterials"	"NA"			""	"mesulfamide,mesulfamido,mesulfamidum"					""
 "MTC"	54675785	"Metacycline"	"Tetracyclines"	"J01AA05"	"Tetracyclines"	"Tetracyclines"	""	"bialatan,metaciclina,metacycline,metacyclinum,methacycline,methacycline base,methacyclinum,methylenecycline,physiomycine,rondomycin"	0.6	"g"			""
 "MTM"	6713928	"Metampicillin"	"Beta-lactams/penicillins"	"J01CA14"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"blomopen,bonopen,celinmicina,elatocilline,fedacilina kapseln,filorex,italcina kapseln,magnipen,metabacter ampullen,metambac,metampicilina,metampicillin,metampicillin sodium,metampicillina,metampicilline,metampicillinum,methampicillin,metiskia ampullen,micinovo,micinovo ampullen,pangocilin,probiotic,rastomycin k,relyothenate,ruticina,rutizina,rutizina ampullen,sedomycin,suvipen,suvipen ampullen,tampilen ampullen,teonicon trofen,viderpen,viderpin,vioplex"	1.5	"g"	1.5	"g"	""
@@ -260,63 +260,63 @@
 "MET"	6087	"Meticillin"	"Beta-lactams/penicillins"	"J01CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"meti"	"dimocillin,metacillin,methcilline,methicillin,methicillinum,methycillin,meticilina,meticillin,meticillina,meticilline,meticillinum,staphcillin"			4	"g"	""
 "MTP"	68590	"Metioprim"	"Other antibacterials"	"NA"			""	"methioprim,metioprim,metioprima,metioprime,metioprimum"					""
 "MXT"	3047729	"Metioxate"	"Quinolones"	"NA"			""	"metioxate,metioxato,metioxatum"					""
-"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01"	"Other antibacterials"	"Imidazole derivatives"	"metr,mnz"	"acromona,anagiardil,arilin,atrivyl,danizol,deflamon,donnan,efloran,elyzol,entizol,flagemona,flagesol,flagil,flagyl,flagyl er,flagyl i.v.,flagyl i.v. rtu,flazol,flegyl,florazole,fossyol,giatricol,ginefla vir,gineflavir,helidac,mepagyl,meronidal,methronidazole,metric,metro cream,metro gel,metro i.v,metro i.v.,metro iv,metrocream,metrodzhil,metrogel,metrogyl,metrolag,metrolotion,metrolyl,metromidol,metronidaz,metronidazol,metronidazole,metronidazole usp,metronidazolo,metronidazolum,metrotop,metrozine,metryl,mexibol,mexibol 'silanes',monagyl,monasin,nidagel,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosased,sanatrichom,satric,takimetol,trichazol,trichex,tricho cordes,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,tricowas b,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8"
-"MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mz"	"mezlin,mezlocilina,mezlocillin,mezlocillin acid,mezlocillin sodium,mezlocilline,mezlocillinum,multocillin"			6	"g"	"3820-8"
-"MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
-"MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica"	"micafungin,mycamine"			0.1	"g"	"58418-5"
-"MCZ"	4189	"Miconazole"	"Antifungals/antimycotics"	"A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,S02AA13"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"aflorix,albistat,andergin,brentan,conofite,dactarin,daktarin,daktarin iv,florid,lotrimin af,micantin,miconasil nitrate,miconazol,miconazole,miconazole base,miconazolo,miconazolum,micozole,minostate,monista,monistat,monistat iv,oravig,vusion,zimybase,zimycan"	0.2	"g"	1	"g"	"17278-3"
+"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01"	"Other antibacterials"	"Imidazole derivatives"	"metr,mnz"	"acromona,anagiardil,arilin,atrivyl,danizol,deflamon,donnan,efloran,elyzol,entizol,flagemona,flagesol,flagil,flagyl,flagyl er,flagyl i.v.,flagyl i.v. rtu,flazol,flegyl,florazole,fossyol,giatricol,ginefla vir,gineflavir,helidac,mepagyl,meronidal,methronidazole,metric,metro cream,metro gel,metro i.v,metro i.v.,metro iv,metrocream,metrodzhil,metrogel,metrogyl,metrolag,metrolotion,metrolyl,metromidol,metronidaz,metronidazol,metronidazole,metronidazole usp,metronidazolo,metronidazolum,metrotop,metrozine,metryl,mexibol,mexibol 'silanes',monagyl,monasin,nidagel,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosased,sanatrichom,satric,takimetol,trichazol,trichex,tricho cordes,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,tricowas b,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
+"MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mz"	"mezlin,mezlocilina,mezlocillin,mezlocillin acid,mezlocillin sodium,mezlocilline,mezlocillinum,multocillin"			6	"g"	"18947-2,330-1,331-9,332-7,333-5,3820-8,41702-2,54194-6,54195-3,54196-1"
+"MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					"54194-6,54195-3,54196-1"
+"MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica"	"micafungin,mycamine"			0.1	"g"	"53812-4,58418-5,65340-2,85048-7"
+"MCZ"	4189	"Miconazole"	"Antifungals/antimycotics"	"A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,S02AA13"	"Antimycotics for systemic use"	"Imidazole derivatives"	"mico"	"aflorix,albistat,andergin,brentan,conofite,dactarin,daktarin,daktarin iv,florid,lotrimin af,micantin,miconasil nitrate,miconazol,miconazole,miconazole base,miconazolo,miconazolum,micozole,minostate,monista,monistat,monistat iv,oravig,vusion,zimybase,zimycan"	0.2	"g"	1	"g"	"17278-3,25607-3,25722-0,54180-5,55686-0"
 "MCR"	3037206	"Micronomicin"	"Aminoglycosides"	"S01AA22"			""	"gentamicin c,micromicin,micromycin,micronomicin,micronomicina,micronomicine,micronomicinum,sagamicin,santemycin"					""
 "MID"	5282169	"Midecamycin"	"Macrolides/lincosamides"	"J01FA03"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"aboren,espinomycin a,macropen,madecacine,medemycin,midecamicina,midecamycin,midecamycin a,midecamycine,midecamycinum,midecin,momicine,mydecamycin,myoxam,normicina,rubimycin,turimycin p"	1.2	"g"	1	"g"	""
 "MIL"	37614	"Miloxacin"	"Quinolones"	"NA"			""	"miloxacin,miloxacine,miloxacino,miloxacinum"					""
-"MNO"	54675783	"Minocycline"	"Tetracyclines"	"A01AB23,D10AF07,J01AA08"	"Tetracyclines"	"Tetracyclines"	"mc,mh,mi,min,mino,mn,mno"	"akamin,aknemin,borymycin,dynacin,klinomycin,minociclina,minocin,minocline,minocyclin,minocycline,minocyclinum,minocyn,minoderm,minomycin,sebomin,solodyn,vectrin"	1	"mg"	0.2	"g"	"34606-4,3822-4,49757-8"
-"MCM"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"J01FA11"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"acecamycin,macroral,midecamycin acetate,miocamen,miocamycin,miocamycine,miokamycin,myocamicin,ponsinomycin"	1.2	"g"			""
+"MNO"	54675783	"Minocycline"	"Tetracyclines"	"A01AB23,D10AF07,J01AA08"	"Tetracyclines"	"Tetracyclines"	"mc,mh,mi,min,mino,mn,mno"	"akamin,aknemin,borymycin,dynacin,klinomycin,minociclina,minocin,minocline,minocyclin,minocycline,minocyclinum,minocyn,minoderm,minomycin,sebomin,solodyn,vectrin"	1	"mg"	0.2	"g"	"18948-0,25225-4,334-3,335-0,336-8,337-6,34606-4,3822-4,49757-8,55156-4,7032-6"
+"MCM"	5282188	"Miocamycin"	"Macrolides/lincosamides"	"J01FA11"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"acecamycin,macroral,midecamycin acetate,miocamen,miocamycin,miocamycine,miokamycin,myocamicin,ponsinomycin"	1.2	"g"			"18949-8,338-4,339-2,340-0,341-8,55687-8"
 "MON"	23667299	"Monensin sodium"	"Other antibacterials"	"NA"			""	"monensin sodium,sodium monensin"					""
 "MRN"	70374	"Morinamide"	"Antimycobacterials"	"J04AK04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"morfazinamide,morfazinammide,morfgazinamide,morinamida,morinamide,morinamide hcl,morinamidum,morphazinamid,morphazinamide,piazofolina,piazolin,piazolina"					""
-"MFX"	152946	"Moxifloxacin"	"Quinolones"	"J01MA14,S01AE07"	"Quinolone antibacterials"	"Fluoroquinolones"	"mox,moxi,mxf"	"actira,avelox,avelox i.v.,avelox iv,avolex,izilox,moxeza,moxifloxacin,moxifloxacine,moxivig,vigamox,zimoxin"	0.4	"g"	0.4	"g"	"43751-7,45223-5,80540-8"
-"MUP"	446596	"Mupirocin"	"Other antibacterials"	"D06AX09,R01AX06"			"mup,mupi"	"bactoderm,bactroban,bactroban nasal,bactroban ointment,centany,mupirocin,mupirocina,mupirocine,mupirocinum,plasimine,pseudomonic acid,pseudomonic acid a,turixin"					""
+"MFX"	152946	"Moxifloxacin"	"Quinolones"	"J01MA14,S01AE07"	"Quinolone antibacterials"	"Fluoroquinolones"	"mox,moxi,mxf"	"actira,avelox,avelox i.v.,avelox iv,avolex,izilox,moxeza,moxifloxacin,moxifloxacine,moxivig,vigamox,zimoxin"	0.4	"g"	0.4	"g"	"31037-5,31039-1,31041-7,31043-3,41502-6,43751-7,45223-5,76043-9,76044-7,76045-4,80540-8,88707-5,93497-6,96112-8"
+"MUP"	446596	"Mupirocin"	"Other antibacterials"	"D06AX09,R01AX06"			"mup,mupi"	"bactoderm,bactroban,bactroban nasal,bactroban ointment,centany,mupirocin,mupirocina,mupirocine,mupirocinum,plasimine,pseudomonic acid,pseudomonic acid a,turixin"					"20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
 "NAC"	73386748	"Nacubactam"	"Beta-lactams/penicillins"	"NA"			""	"nacubactam"					""
 "NAD"	4410	"Nadifloxacin"	"Quinolones"	"D10AF05"			""	"acuatim,nadifloxacin,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin"					""
-"NAF"	8982	"Nafcillin"	"Beta-lactams/penicillins"	"J01CF06"			""	"nafcilina,nafcillin,nafcillin sodium,nafcilline,nafcillinum,nallpen,naphcillin,unipen"			3	"g"	"10993-4,25232-0"
+"NAF"	8982	"Nafcillin"	"Beta-lactams/penicillins"	"J01CF06"			""	"nafcilina,nafcillin,nafcillin sodium,nafcilline,nafcillinum,nallpen,naphcillin,unipen"			3	"g"	"10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
 "ZWK"	117587595	"Nafithromycin"	"Macrolides/lincosamides"	"NA"			""	"nafithromycin"					""
 "NAL"	4421	"Nalidixic acid"	"Quinolones"	"J01MB02"	"Quinolone antibacterials"	"Other quinolones"	"na,nal,nali"	"acide nalidixico,acide nalidixique,acido nalidissico,acido nalidixico,acidum nalidixicum,betaxina,dixiben,dixinal,eucisten,eucistin,innoxalomn,innoxalon,jicsron,kusnarin,naldixic acid,nalidic acid,nalidicron,nalidixan,nalidixane,nalidixate,nalidixate sodium,nalidixic,nalidixic acid,nalidixicacid,nalidixin,nalidixinic acid,nalidixinsaure,nalitucsan,nalurin,narigix,naxuril,neggram,negram,nevigramon,nicelate,nogram,poleon,sicmylon,specifen,specifin,unaserus,uralgin,uriben,uriclar,urisal,urodixin,uroman,uroneg,uronidix,uropan,wintomylon,wintron"	4	"g"			""
-"NAR"	65452	"Narasin"	"Other antibacterials"	"NA"			""	"monteban,narasin,narasin a,narasine,narasino,narasinum,narasul"					"87570-8"
+"NAR"	65452	"Narasin"	"Other antibacterials"	"QP51BB04"			""	"monteban,narasin,narasin a,narasine,narasino,narasinum,narasul"					"87570-8"
 "NEM"	11993740	"Nemonoxacin"	"Quinolones"	"J01MB08"	"Quinolone antibacterials"	"Other quinolones"	""	"nemonoxacin"					""
-"NEO"	8378	"Neomycin"	"Aminoglycosides"	"A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,R02AB01,S01AA03,S02AA07,S03AA01"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom"	"actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v"	5	"g"			"10995-9,25262-7"
-"NET"	441306	"Netilmicin"	"Aminoglycosides"	"J01GB07,S01AA23"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti"	"netillin,netilmicin,netilmicin sulfate,netilmicina,netilmicine,netilmicinum,netilyn,netira,nettacin,vectacin"	0.35	"g"	0.35	"g"	"25263-5,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8"
+"NEO"	8378	"Neomycin"	"Aminoglycosides"	"A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,R02AB01,S01AA03,S02AA07,S03AA01"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom"	"actilin,actiline,antibiotique,bycomycin,dekamycin iii,endomixin,enterfram,fradiomycin,fradiomycin b,fradiomycinum,framicetina,framidal,framycetin,framycetin sulfate,framycetine,framycetinum,framycin,framygen,francetin,fraquinol,jernadex,myacine,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycin,neomycin b,neomycin b sulfate,neomycin solution,neomycin sulfate,neomycin sulphate,neomycinb,neomycine,neomycinum,nivemycin,pimavecort,soframycin,soframycine,tuttomycin,vonamycin,vonamycin powder v"	5	"g"	1	"g"	"10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
+"NET"	441306	"Netilmicin"	"Aminoglycosides"	"J01GB07,S01AA23"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti"	"netillin,netilmicin,netilmicin sulfate,netilmicina,netilmicine,netilmicinum,netilyn,netira,nettacin,vectacin"	0.35	"g"	0.35	"g"	"18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
 "NIC"	9507	"Nicarbazin"	"Other antibacterials"	"NA"			""	"nicarb,nicarbasin,nicarbazin,nicarbazine,nicoxin,nicrazin,nicrazine,nirazin"					""
 "NIF"	71946	"Nifuroquine"	"Quinolones"	"NA"			""	"abimasten,nifuroquina,nifuroquine,nifuroquinum,quinaldofur"					""
 "NFR"	9571062	"Nifurtoinol"	"Other antibacterials"	"J01XE02"	"Other antibacterials"	"Nitrofuran derivatives"	""	"levantin,nifurtoinol,nifurtoinolo,nifurtoinolum,urfadin,urfadine,urfadyn"	0.16	"g"			""
-"NTZ"	41684	"Nitazoxanide"	"Other antibacterials"	"P01AX11"			""	"adrovet,alinia,azt + nitazoxanide,colufase,cryptaz,dexidex,heliton,kidonax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanide,nitazoxanidum,nitrazoxanide,omniparax,pacovanton,paramix,taenitaz"	1	"g"			""
-"NIT"	6604200	"Nitrofurantoin"	"Other antibacterials"	"J01XE01"	"Other antibacterials"	"Nitrofuran derivatives"	"f,f/m,fd,ft,ni,nit,nitr"	"alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fua med,fuamed,furabid,furachel,furadantin,furadantin retard,furadantina mc,furadantine,furadantine mc,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furadoxyl,furalan,furaloid,furantoin,furantoina,furatoin,furedan,furina,furobactina,furodantin,furophen t,gerofuran,io>>uss>>a<<ixoo,ituran,ivadantin,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantion,nitrofurantoin,nitrofurantoin macro,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,parfuran,phenurin,piyeloseptyl,siraliden,trantoin,uerineks,urantoin,urizept,urodin,urofuran,urofurin,urolisa,urolong,uvamin,welfurin,zoofurin"	0.2	"g"			"3860-4"
-"NIZ"	5447130	"Nitrofurazone"	"Other antibacterials"	"NA"			""	"acutol,aldomycin,alfucin,amifur,babrocid,becafurazone,biofuracina,biofurea,chemofuran,chixin,cocafurin,coxistat,dermofural,dymazone,dynazone,eldezol,fedacin,flavazone,fracine,furacilin,furacilinum,furacillin,furacin,furacine,furacinetten,furacoccid,furacort,furacycline,furaderm,furagent,furalcyn,furaldon,furalone,furametral,furaplast,furaseptyl,furaskin,furatsilin,furaziline,furazin,furazina,furazol w,furazone,furazyme,furesol,furfurin,furosem,fuvacillin,hemofuran,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nfz mix,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazone,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,sanfuran,vabrocid,vadrocid,yatrocin"					""
-"NTR"	19910	"Nitroxoline"	"Quinolones"	"J01XX07"	"Other antibacterials"	"Other antibacterials"	""	"galinok,isinok,nibiol,nicene forte,nitroxlina,nitroxolin,nitroxolina,nitroxoline,nitroxolinum,notroxoline,noxibiol"	1	"g"			""
-"NOR"	4539	"Norfloxacin"	"Quinolones"	"J01MA06,S01AE02"	"Quinolone antibacterials"	"Fluoroquinolones"	"nor,norf,nx,nxn"	"baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,norfloxacin,norfloxacine,norfloxacino,norfloxacinum,norocin,noroxin,noroxine,norxacin,sebercim,uroxacin,utinor,zoroxin"	0.8	"g"			"3867-9"
+"NTZ"	41684	"Nitazoxanide"	"Other antibacterials"	"P01AX11"			""	"adrovet,alinia,azt + nitazoxanide,colufase,cryptaz,dexidex,heliton,kidonax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanide,nitazoxanidum,nitrazoxanide,omniparax,pacovanton,paramix,taenitaz"	1	"g"			"73595-1,73617-3,73640-5"
+"NIT"	6604200	"Nitrofurantoin"	"Other antibacterials"	"J01XE01"	"Other antibacterials"	"Nitrofuran derivatives"	"f,f/m,fd,ft,ni,nit,nitr"	"alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fua med,fuamed,furabid,furachel,furadantin,furadantin retard,furadantina mc,furadantine,furadantine mc,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furadoxyl,furalan,furaloid,furantoin,furantoina,furatoin,furedan,furina,furobactina,furodantin,furophen t,gerofuran,io>>uss>>a<<ixoo,ituran,ivadantin,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantion,nitrofurantoin,nitrofurantoin macro,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,parfuran,phenurin,piyeloseptyl,siraliden,trantoin,uerineks,urantoin,urizept,urodin,urofuran,urofurin,urolisa,urolong,uvamin,welfurin,zoofurin"	0.2	"g"			"18955-5,362-4,363-2,364-0,365-7,3860-4,7036-7"
+"NIZ"	5447130	"Nitrofurazone"	"Other antibacterials"	"NA"			""	"acutol,aldomycin,alfucin,amifur,babrocid,becafurazone,biofuracina,biofurea,chemofuran,chixin,cocafurin,coxistat,dermofural,dymazone,dynazone,eldezol,fedacin,flavazone,fracine,furacilin,furacilinum,furacillin,furacin,furacine,furacinetten,furacoccid,furacort,furacycline,furaderm,furagent,furalcyn,furaldon,furalone,furametral,furaplast,furaseptyl,furaskin,furatsilin,furaziline,furazin,furazina,furazol w,furazone,furazyme,furesol,furfurin,furosem,fuvacillin,hemofuran,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nfz mix,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazone,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,sanfuran,vabrocid,vadrocid,yatrocin"					"20388-5,87793-6"
+"NTR"	19910	"Nitroxoline"	"Quinolones"	"J01XX07"	"Other antibacterials"	"Other antibacterials"	""	"galinok,isinok,nibiol,nicene forte,nitroxlina,nitroxolin,nitroxolina,nitroxoline,nitroxolinum,notroxoline,noxibiol"	1	"g"			"25608-1,25723-8,32382-4,54181-3,55688-6"
+"NOR"	4539	"Norfloxacin"	"Quinolones"	"J01MA06,S01AE02"	"Quinolone antibacterials"	"Fluoroquinolones"	"nor,norf,nx,nxn"	"baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,norfloxacin,norfloxacine,norfloxacino,norfloxacinum,norocin,noroxin,noroxine,norxacin,sebercim,uroxacin,utinor,zoroxin"	0.8	"g"			"18956-3,366-5,367-3,368-1,369-9,3867-9,41504-2,7037-5"
 "NME"		"Norfloxacin/metronidazole"	"Other antibacterials"	"J01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "NTI"		"Norfloxacin/tinidazole"	"Other antibacterials"	"J01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "NVA"	10419027	"Norvancomycin"	"Glycopeptides"	"NA"			""	"norvancomycin"					""
-"NOV"	54675769	"Novobiocin"	"Other antibacterials"	"NA"			"novo"	"albamix,albamycin,cardelmycin,cathocin,cathomycin,crystallinic acid,inamycin,novobiocin,novobiocina,novobiocine,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin"					"17378-1"
-"NYS"	6433272	"Nystatin"	"Antifungals/antimycotics"	"A07AA02,D01AA01,G01AA01"			"nyst"	"biofanal,candex lotion,comycin,diastatin,herniocid,moronal,myconystatin,mycostatin,mycostatin pastilles,mykinac,mykostatyna,nilstat,nistatin,nistatina,nyamyc,nyotran,nyotrantrade mark,nystaform,nystan,nystatin,nystatin a,nystatin g,nystatin hydrate,nystatin lf,nystatine,nystatinum,nystatyna,nystavescent,nystex,nystop,stamycin,terrastatin,zydin e"	1.5	"MU"			""
-"OFX"	4583	"Ofloxacin"	"Quinolones"	"J01MA01,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofx"	"bactocin,danoflox,dextrofloxacin,effexin,exocin,exocine,flobacin,flodemex,flotavid,flovid,floxal,floxil,floxin,floxin otic,floxstat,fugacin,inoflox,kinflocin,kinoxacin,levofloxacin hcl,liflox,loxinter,marfloxacin,medofloxine,mergexin,monoflocet,novecin,nufafloqo,occidal,ocuflox,oflocee,oflocet,oflocin,oflodal,oflodex,oflodura,ofloxacin,ofloxacin otic,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxin,onexacin,operan,orocin,otonil,oxaldin,pharflox,praxin,puiritol,qinolon,quinolon,quotavil,sinflo,tabrin,taravid,tariflox,tarivid,telbit,tructum,uro tarivid,viotisone,visiren,zanocin"	0.4	"g"	0.4	"g"	"25264-3,3877-8"
+"NOV"	54675769	"Novobiocin"	"Other antibacterials"	"QJ01XX95"			"novo"	"albamix,albamycin,cardelmycin,cathocin,cathomycin,crystallinic acid,inamycin,novobiocin,novobiocina,novobiocine,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
+"NYS"	6433272	"Nystatin"	"Antifungals/antimycotics"	"A07AA02,D01AA01,G01AA01"			"nyst"	"biofanal,candex lotion,comycin,diastatin,herniocid,moronal,myconystatin,mycostatin,mycostatin pastilles,mykinac,mykostatyna,nilstat,nistatin,nistatina,nyamyc,nyotran,nyotrantrade mark,nystaform,nystan,nystatin,nystatin a,nystatin g,nystatin hydrate,nystatin lf,nystatine,nystatinum,nystatyna,nystavescent,nystex,nystop,stamycin,terrastatin,zydin e"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
+"OFX"	4583	"Ofloxacin"	"Quinolones"	"J01MA01,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofx"	"bactocin,danoflox,dextrofloxacin,effexin,exocin,exocine,flobacin,flodemex,flotavid,flovid,floxal,floxil,floxin,floxin otic,floxstat,fugacin,inoflox,kinflocin,kinoxacin,levofloxacin hcl,liflox,loxinter,marfloxacin,medofloxine,mergexin,monoflocet,novecin,nufafloqo,occidal,ocuflox,oflocee,oflocet,oflocin,oflodal,oflodex,oflodura,ofloxacin,ofloxacin otic,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxin,onexacin,operan,orocin,otonil,oxaldin,pharflox,praxin,puiritol,qinolon,quinolon,quotavil,sinflo,tabrin,taravid,tariflox,tarivid,telbit,tructum,uro tarivid,viotisone,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
 "OOR"		"Ofloxacin/ornidazole"	"Other antibacterials"	"J01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
-"OLE"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"J01FA05"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"amimycin,landomycin,matromycin,oleandomicina,oleandomycin,oleandomycin a,oleandomycine,oleandomycinum,romicil"	1	"g"			""
-"OMC"	54697325	"Omadacycline"	"Tetracyclines"	"J01AA15"			""	"amadacycline,omadacycline"	0.3	"g"	0.1	"g"	""
-"OPT"	87880	"Optochin"	"Other antibacterials"	"NA"			""	"numoquin,optochin,optoquine"					""
-"ORB"	60605	"Orbifloxacin"	"Quinolones"	"NA"			""	"orbifloxacin"					""
-"ORI"	16136912	"Oritavancin"	"Glycopeptides"	"J01XA05"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit"	"kimyrsa,oritavancin"					""
-"ORS"		"Ormetroprim/sulfamethoxazole"	"Other antibacterials"	"NA"			""	""					""
-"ORN"	28061	"Ornidazole"	"Other antibacterials"	"G01AF06,J01XD03,P01AB03"	"Other antibacterials"	"Imidazole derivatives"	""	"madelen,ornidal,ornidazol,ornidazole,ornidazolum,tiberal"	1.5	"g"	1	"g"	""
-"OTE"	77050711	"Oteseconazole"	"Antifungals/antimycotics"	"J02AC06"	"Antimycotics for systemic use"	"Triazole derivatives"	""	"oteseconazole"					""
-"OXA"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"J01CF04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"ox,oxa,oxac,oxal,oxs"	"bactocill,ossacillina,oxacilina,oxacillin,oxacillin sodium,oxacilline,oxacillinum,oxazocillin,oxazocilline,prostaphlin,prostaphlyn,sodium oxacillin"	2	"g"	2	"g"	"25265-0,3882-8"
+"OLE"	72493	"Oleandomycin"	"Macrolides/lincosamides"	"J01FA05"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"amimycin,landomycin,matromycin,oleandomicina,oleandomycin,oleandomycin a,oleandomycine,oleandomycinum,romicil"	1	"g"			"18960-5,378-0,379-8,380-6,381-4,55690-2"
+"OMC"	54697325	"Omadacycline"	"Tetracyclines"	"J01AA15"			""	"amadacycline,omadacycline"	0.3	"g"	0.1	"g"	"73594-4,73616-5,73639-7"
+"OPT"	87880	"Optochin"	"Other antibacterials"	"NA"			""	"numoquin,optochin,optoquine"					"100055-3,73665-2"
+"ORB"	60605	"Orbifloxacin"	"Quinolones"	"QJ01MA95"			""	"orbifloxacin"					"35825-9,35826-7,35827-5"
+"ORI"	16136912	"Oritavancin"	"Glycopeptides"	"J01XA05"	"Other antibacterials"	"Glycopeptide antibacterials"	"orit"	"kimyrsa,oritavancin"					"41707-1,41708-9,41709-7,41736-0"
+"ORS"		"Ormetroprim/sulfamethoxazole"	"Other antibacterials"	"NA"			""	""					"73593-6,73615-7,73638-9"
+"ORN"	28061	"Ornidazole"	"Other antibacterials"	"G01AF06,J01XD03,P01AB03"	"Other antibacterials"	"Imidazole derivatives"	""	"madelen,ornidal,ornidazol,ornidazole,ornidazolum,tiberal"	1.5	"g"	1	"g"	"55691-0,55692-8,55693-6,55694-4"
+"OTE"	77050711	"Oteseconazole"	"Antifungals/antimycotics"	"J02AC06"	"Antimycotics for systemic use"	"Triazole derivatives"	""	"oteseconazole"	21	"mg"			""
+"OXA"	6196	"Oxacillin"	"Beta-lactams/penicillins"	"J01CF04"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"ox,oxa,oxac,oxal,oxs"	"bactocill,ossacillina,oxacilina,oxacillin,oxacillin sodium,oxacilline,oxacillinum,oxazocillin,oxazocilline,prostaphlin,prostaphlyn,sodium oxacillin"	2	"g"	2	"g"	"18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
 "OXO"	4628	"Oxolinic acid"	"Quinolones"	"J01MB05"	"Quinolone antibacterials"	"Other quinolones"	""	"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"			""
-"OXY"	54675779	"Oxytetracycline"	"Tetracyclines"	"D06AA03,G01AA07,J01AA06,S01AA04"	"Tetracyclines"	"Tetracyclines"	""	"adamycin,berkmycen,biostat,biostat pa,bisolvomycin,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,terramycine,tetran,unimycin,ursocyclin,ursocycline,vendarcin"	1	"g"	1	"g"	"17396-3,25266-8,87595-5"
+"OXY"	54675779	"Oxytetracycline"	"Tetracyclines"	"A01AB25,D06AA03,G01AA07,J01AA06,S01AA04"	"Tetracyclines"	"Tetracyclines"	""	"adamycin,berkmycen,biostat,biostat pa,bisolvomycin,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,terramycine,tetran,unimycin,ursocyclin,ursocycline,vendarcin"	1	"g"	1	"g"	"17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
 "OZN"		"Ozenoxacin"		"D06AX14"			""	"ozadub,ozenoxacin,ozenoxacin cream"					""
 "PAS"	4649	"P-aminosalicylic acid"	"Antimycobacterials"	"NA"			""	"aminopar,aminosalicylic,aminosalicylic acid,aminosalyl,aminox,apacil,deapasil,entepas,ferrosan,gabbropas,granupas,helipidyl,hellipidyl,neopasalate,osacyl,pamacyl,pamisyl,paramycin,parasal,parasalicil,parasalindon,pasalon,pasara,pascorbic,pasdium,paser granules,paskalium,pasmed,pasnodia,pasolac,propasa,rezipas,teebacin"					""
-"PAN"	72015	"Panipenem"	"Carbapenems"	"NA,J01DH55"			""	"panipenem,panipenem/betamipron,panipenemum,penipanem"					""
-"PAR"	165580	"Paromomycin"	"Other antibacterials"	"A07AA06"			""	"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"			""
+"PAN"	72015	"Panipenem"	"Carbapenems"	"NA,J01DH55"			""	"panipenem,panipenem/betamipron,panipenemum,penipanem"			2	"g"	"100056-1,53823-1"
+"PAR"	165580	"Paromomycin"	"Other antibacterials"	"A07AA06"			""	"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"			"51719-3,53824-9,55700-9,55701-7,55702-5"
 "PAZ"	65957	"Pazufloxacin"	"Quinolones"	"J01MA18"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"pazufloxacin,pazufloxacine,pazufloxacino,pazufloxacinum"			1	"g"	""
-"PEF"	51081	"Pefloxacin"	"Quinolones"	"J01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl"	"abactal,labocton,pefloxacin,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,perfloxacin,silver pefloxacin"	0.8	"g"	0.8	"g"	"3906-5"
+"PEF"	51081	"Pefloxacin"	"Quinolones"	"J01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl"	"abactal,labocton,pefloxacin,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,perfloxacin,silver pefloxacin"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
 "PNM"	10250769	"Penamecillin"	"Beta-lactams/penicillins"	"J01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"hydroxymethyl,penamecilina,penamecillin,penamecillina,penamecilline,penamecillinum"	1.05	"g"			""
-"PNO"		"Penicillin/novobiocin"	"Beta-lactams/penicillins"	"NA"			""	""					""
+"PNO"		"Penicillin/novobiocin"	"Beta-lactams/penicillins"	"NA"			""	""					"35872-1,35873-9,35874-7"
 "PSU"		"Penicillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
 "PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10"	"Tetracyclines"	"Tetracyclines"	""	"criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicycline,penimepicyclinum"					""
 "PIM"	65453	"Pentisomicin"	"Aminoglycosides"	"NA"			""	"pentisomicin,pentisomicina,pentisomicine,pentisomicinum"					""
@@ -326,80 +326,80 @@
 "PHN"	6869	"Phenoxymethylpenicillin"	"Beta-lactams/penicillins"	"J01CE02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"fepe,peni v,penicillin v,pnv,pv"	"acipen v,apocillin,apopen,beromycin,calcipen,compocillin v,crystapen v,distaquaine v,eskacillian v,eskacillin v,fenacilin,fenospen,meropenin,oracillin,oratren,pc pen vk,penicillin v,penicillinv,phenocillin,phenomycilline,phenopenicillin,robicillin,rocilin,stabicillin,vebecillin,veetids,vegacillin"	2	"g"			""
 "PMR"	5284447	"Pimaricin"	"Antifungals/antimycotics"	"NA"			"natamycin"	"delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricin,pimaricine,pimarizin,synogil,tennecetin"					""
 "PPA"	4831	"Pipemidic acid"	"Quinolones"	"J01MB04"	"Quinolone antibacterials"	"Other quinolones"	"pipz,pizu"	"acide pipemidique,acido pipemidico,acidum pipemidicum,deblaston,dolcol,filtrax,pipedac,pipemid,pipemidate,pipemidic,pipemidic acid,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval"	0.8	"g"			""
-"PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pp"	"isipen,pentcillin,peperacillin,peracin,piperacilina,piperacillin,piperacillin hydrate,piperacillin na,piperacillin sodium,piperacillina,piperacilline,piperacillinum,pipercillin,pipracil,pipril,tazocin"			14	"g"	"25268-4,3972-7"
-"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					""
-"TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"tazocel,tazocillin,tazocin,zosyn"			14	"g"	""
+"PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pp"	"isipen,pentcillin,peperacillin,peracin,piperacilina,piperacillin,piperacillin hydrate,piperacillin na,piperacillin sodium,piperacillina,piperacilline,piperacillinum,pipercillin,pipracil,pipril,tazocin"			14	"g"	"101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1"
+"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			""	""					"54197-9,54198-7,54199-5,55704-1"
+"TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"tazocel,tazocillin,tazocin,zosyn"			14	"g"	"101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
 "PRC"	71978	"Piridicillin"	"Beta-lactams/penicillins"	"NA"			""	"piridicillin"					""
-"PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"	"NA"			""	"pirlimycin,pirlimycina,pirlimycine,pirlimycinum,pirsue"					""
+"PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"	"QJ51FF90"			""	"pirlimycin,pirlimycina,pirlimycine,pirlimycinum,pirsue"					"35829-1,35830-9,35831-7"
 "PIR"	4855	"Piromidic acid"	"Quinolones"	"J01MB03"	"Quinolone antibacterials"	"Other quinolones"	""	"acide piromidique,acido piromidico,acidum piromidicum,actrun c,bactramyl,enterol,gastrurol,panacid,pirodal,piromidate,piromidic acid,piromidicacid,pyrido,reelon,septural,urisept,uropir,zaomeal"	2	"g"			""
-"PVM"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"J01CA02"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"berocillin,pivaloylampicillin,pivampicilina,pivampicillin,pivampicilline,pivampicillinum,pondocillin"	1.05	"g"			""
+"PVM"	33478	"Pivampicillin"	"Beta-lactams/penicillins"	"J01CA02"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"berocillin,pivaloylampicillin,pivampicilina,pivampicillin,pivampicilline,pivampicillinum,pondocillin"	1.05	"g"			"18971-2,415-0,416-8,417-6,418-4"
 "PME"	115163	"Pivmecillinam"	"Beta-lactams/penicillins"	"J01CA08"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"amdinocillin pivoxil,coactabs,hydroxymethyl,pivmecilinamo,pivmecillinam,pivmecillinam hcl,pivmecillinamum"	0.6	"g"			""
-"PLZ"	42613186	"Plazomicin"	"Aminoglycosides"	"J01GB14"			""	"plazomicin,zemdri"					"92024-9"
-"PLB"	49800004	"Polymyxin B"	"Polymyxins"	"A07AA05,J01XB02,S01AA18,S02AA11,S03AA03"	"Other antibacterials"	"Polymyxins"	"pb,pol,polb,poly,poly b,polymixin,polymixin b"	"polimixina b,polumyxin b,polymixin b,polymyxine b"	3	"MU"	0.15	"g"	"17473-0,25269-2"
+"PLZ"	42613186	"Plazomicin"	"Aminoglycosides"	"J01GB14"			""	"plazomicin,zemdri"					"73592-8,73614-0,73637-1,92024-9,94719-2"
+"PLB"	49800004	"Polymyxin B"	"Polymyxins"	"A07AA05,J01XB02,S01AA18,S02AA11,S03AA03"	"Other antibacterials"	"Polymyxins"	"pb,pol,polb,poly,poly b,polymixin,polymixin b"	"polimixina b,polumyxin b,polymixin b,polymyxine b"	3	"MU"	0.15	"g"	"17473-0,18972-0,25269-2,35832-5,419-2,420-0,421-8,422-6"
 "POP"		"Polymyxin B/polysorbate 80"	"Polymyxins"	"NA"			""	""					""
-"POS"	468595	"Posaconazole"	"Antifungals/antimycotics"	"J02AC04"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa"	"noxafil,posaconazole,posaconazole sp,posconazole"	0.3	"g"	0.3	"g"	"53731-6,80545-7"
-"PRA"	9802884	"Pradofloxacin"	"Quinolones"	"NA"			""	"pradofloxacin,pudofloxacin,veraflox"					""
-"PRX"	71455	"Premafloxacin"	"Quinolones"	"NA"			""	"premafloxacin,remafloxacin"					""
-"PMD"	456199	"Pretomanid"	"Antimycobacterials"	"J04AK08"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"oxazine,pretomanid"					""
+"POS"	468595	"Posaconazole"	"Antifungals/antimycotics"	"J02AC04"	"Antimycotics for systemic use"	"Triazole derivatives"	"posa"	"noxafil,posaconazole,posaconazole sp,posconazole"	0.3	"g"	0.3	"g"	"53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
+"PRA"	9802884	"Pradofloxacin"	"Quinolones"	"QJ01MA97"			""	"pradofloxacin,pudofloxacin,veraflox"					"76148-6,87800-9"
+"PRX"	71455	"Premafloxacin"	"Quinolones"	"NA"			""	"premafloxacin,remafloxacin"					"73591-0,73613-2,73636-3"
+"PMD"	456199	"Pretomanid"	"Antimycobacterials"	"J04AK08"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"oxazine,pretomanid"	0.2	"g"			"93850-6"
 "PRM"	6446787	"Primycin"	"Macrolides/lincosamides"	"NA"			""	"primycin"					""
-"PRI"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"J01FG01"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"pris"	"eskalin v,mikamycin,mikamycine,mikamycinum,ostreogrycinum,pristinamycine,pristinamycinum,stafac,stafytracine,staphylomycin,starfac,streptogramin,vernamycin,virgimycin,virgimycine,virginiamycin,virginiamycina,virginiamycine,virginiamycinum"	2	"g"			""
+"PRI"	11979535	"Pristinamycin"	"Macrolides/lincosamides"	"J01FG01"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"pris"	"eskalin v,mikamycin,mikamycine,mikamycinum,ostreogrycinum,pristinamycine,pristinamycinum,stafac,stafytracine,staphylomycin,starfac,streptogramin,vernamycin,virgimycin,virgimycine,virginiamycin,virginiamycina,virginiamycine,virginiamycinum"	2	"g"			"32383-2,35833-3,35834-1,55709-0"
 "PRB"	5903	"Procaine benzylpenicillin"	"Beta-lactams/penicillins"	"J01CE09"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"depocillin,duphapen,hostacillin,hydracillin,jenacillin o,nopcaine,penicillin procaine,retardillin,vetspen,vitablend"			0.6	"g"	""
 "PRP"	92879	"Propicillin"	"Beta-lactams/penicillins"	"J01CE03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"propicilina,propicillin,propicilline,propicillinum"	0.9	"g"			""
 "PKA"	9872451	"Propikacin"	"Aminoglycosides"	"NA"			""	"propikacin,propikacina,propikacine,propikacinum"					""
 "PTH"	666418	"Protionamide"	"Antimycobacterials"	"J04AD01"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"prot"	"ektebin,peteha,prothionamide,prothionamidum,protion,protionamid,protionamida,protionamide,protionamidum,protionizina,tebeform,trevintix,tuberex"	0.75	"g"			""
-"PRU"	65947	"Prulifloxacin"	"Quinolones"	"J01MA17"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"prulifloxacin,pruvel,pufloxacin dioxolil,quisnon"	0.6	"g"			""
-"PZA"	1046	"Pyrazinamide"	"Antimycobacterials"	"J04AK01"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"aldinamid,aldinamide,braccopiral,corsazinmid,dipimide,eprazin,farmizina,isopas,lynamide,novamid,p ezetamid,pezetamid,pharozinamide,piraldina,pirazimida,pirazinamid,pirazinamida,pirazinamide,prazina,pyrafat,pyramide,pyrazide,pyrazinamdie,pyrazinamid,pyrazinamide,pyrazinamidum,pyrazine carboxamide,pyrazineamide,pyrizinamide,rifafour,rozide,tebrazid,tebrazio,tisamid,unipyranamide,zinamide,zinastat"	1.5	"g"			"11001-5,25270-0"
-"QDA"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"J01FG02"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"q/d,qda,qida,quda,rp,syn"	""			1.5	"g"	""
+"PRU"	65947	"Prulifloxacin"	"Quinolones"	"J01MA17"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"prulifloxacin,pruvel,pufloxacin dioxolil,quisnon"	0.6	"g"			"100058-7,76145-2"
+"PZA"	1046	"Pyrazinamide"	"Antimycobacterials"	"J04AK01"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"pyra"	"aldinamid,aldinamide,braccopiral,corsazinmid,dipimide,eprazin,farmizina,isopas,lynamide,novamid,p ezetamid,pezetamid,pharozinamide,piraldina,pirazimida,pirazinamid,pirazinamida,pirazinamide,prazina,pyrafat,pyramide,pyrazide,pyrazinamdie,pyrazinamid,pyrazinamide,pyrazinamidum,pyrazine carboxamide,pyrazineamide,pyrizinamide,rifafour,rozide,tebrazid,tebrazio,tisamid,unipyranamide,zinamide,zinastat"	1.5	"g"			"11001-5,18973-8,20461-0,23632-3,25186-8,25229-6,25270-0,423-4,424-2,425-9,426-7,42935-7,55710-8,55711-6,56026-8,92242-7"
+"QDA"	11979418	"Quinupristin/dalfopristin"	"Macrolides/lincosamides"	"QJ01FG02"	"Macrolides, lincosamides and streptogramins"	"Streptogramins"	"q/d,qda,qida,quda,rp,syn"	""					"23640-6,23641-4,33334-4,35835-8,58712-1"
 "RAC"	56052	"Ractopamine"	"Other antibacterials"	"NA"			""	"optaflexx,paylean,ractopamina,ractopamine,ractopaminum"					""
-"RAM"	16132338	"Ramoplanin"	"Glycopeptides"	"NA"			""	"ramoplanin"					""
-"RZM"	10993211	"Razupenem"	"Carbapenems"	"NA"			""	"razupenem"					""
+"RAM"	16132338	"Ramoplanin"	"Glycopeptides"	"NA"			""	"ramoplanin"					"41710-5,41711-3,41712-1,41737-8"
+"RZM"	10993211	"Razupenem"	"Carbapenems"	"NA"			""	"razupenem"					"73590-2,73612-4,73635-5"
 "RTP"	6918462	"Retapamulin"	"Other antibacterials"	"D06AX13"	"Antibiotics for topical use"	"Other antibiotics for topical use"	"ret"	"altabax,altargo,retapamulin"					""
 "RZF"		"Rezafungin"	"Antifungals"	"NA"			""	"biafungin,rezafungin cation,rezafungin ion"					""
-"RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali,ribociclib"	0.45				""
+"RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali,ribociclib"	0.45	"g"			""
 "RST"	33042	"Ribostamycin"	"Aminoglycosides"	"J01GB10"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	""	"dekamycin iv,hetangmycin,ribastamin,ribostamicina,ribostamycin,ribostamycine,ribostamycinum,vistamycin,xylostatin"			1	"g"	""
 "RID1"	16659285	"Ridinilazole"	"Other antibacterials"	"NA"			""	"ridinilazole"					""
-"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifb"	"alfacid,ansamicin,ansamycin,ansatipin,ansatipine,assatipin,mycobutin,rifabutin,rifabutina,rifabutine,rifabutinum"	0.15	"g"			"24032-5"
+"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifb"	"alfacid,ansamicin,ansamycin,ansatipin,ansatipine,assatipin,mycobutin,rifabutin,rifabutina,rifabutine,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
 "RIF"	135398735	"Rifampicin"	"Antimycobacterials"	"J04AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa"	"abrifam,archidyn,arficin,arzide,azt + rifampin,benemicin,benemycin,dipicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadin i.v,rifadin i.v.,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifamate,rifamicin amp,rifamor,rifampicin,rifampicin sv,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifamycin amp,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,rimycin,sinerdol,tubocin"	0.6	"g"	0.6	"g"	""
 "REI"	135483893	"Rifampicin/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM07"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
 "RFI"		"Rifampicin/isoniazid"	"Antimycobacterials"	"J04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	"rifinah,rimactazid"					""
 "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"	"A07AA13,D06AX15,J04AB03,S01AA16,S02AA12"	"Drugs for treatment of tuberculosis"	"Antibiotics"	""	"aemcolo,rifacin,rifamicina,rifamicine sv,rifamycin,rifamycine,rifamycinum,rifocin,rifocyn,rifomycin,rifomycin sv,tuborin"			0.6	"g"	""
-"RFP"	135403821	"Rifapentine"	"Antimycobacterials"	"J04AB05"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp,rpt"	"cyclopentyl rifampin,prifitin,priftin,rifapentin,rifapentina,rifapentine,rifapentinum"	0.11	"g"			""
-"RFX"	6436173	"Rifaximin"	"Other antibacterials"	"A07AA11,D06AX11"	"Intestinal antiinfectives"	"Antibiotics"	""	"fatroximin,flonorm,lormyx,lumenax,normix,redactiv,rifacol,rifamixin,rifaxidin,rifaximin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan"	0.6	"g"			""
+"RFM"	6324616	"Rifamycin"	"Antimycobacterials"	"A07AA13,D06AX15,J04AB03,S01AA16,S02AA12"	"Drugs for treatment of tuberculosis"	"Antibiotics"	""	"aemcolo,rifacin,rifamicina,rifamicine sv,rifamycin,rifamycine,rifamycinum,rifocin,rifocyn,rifomycin,rifomycin sv,tuborin"	0.8	"g"	0.6	"g"	""
+"RFP"	135403821	"Rifapentine"	"Antimycobacterials"	"J04AB05"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifp,rpt"	"cyclopentyl rifampin,prifitin,priftin,rifapentin,rifapentina,rifapentine,rifapentinum"	0.11	"g"			"100059-5,76627-9"
+"RFX"	6436173	"Rifaximin"	"Other antibacterials"	"A07AA11,D06AX11"	"Intestinal antiinfectives"	"Antibiotics"	""	"fatroximin,flonorm,lormyx,lumenax,normix,redactiv,rifacol,rifamixin,rifaxidin,rifaximin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan"	0.6	"g"			"73589-4,73611-6,73634-8"
 "RIT"	65633	"Ritipenem"	"Carbapenems"	"NA"			""	"ritipenem"					""
 "RIA"	163692	"Ritipenem acoxil"	"Carbapenems"	"NA"			""	"ritipenem acoxil"					""
 "ROK"	5282211	"Rokitamycin"	"Macrolides/lincosamides"	"J01FA12"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"propionylleucomycin,ricamycin,rokicid,rokital,rokitamicina,rokitamycin,rokitamycine,rokitamycinum"	0.8	"g"			""
-"RLT"	54682938	"Rolitetracycline"	"Tetracyclines"	"J01AA09"	"Tetracyclines"	"Tetracyclines"	""	"bristacin,kinteto,reverin,rolitetraciclina,rolitetracycline,rolitetracyclinum,solvocillin,superciclin,synotodecin,synterin,syntetrex,syntetrin,transcycline,velacicline,velacycline"			0.35	"g"	""
-"ROS"	287180	"Rosoxacin"	"Quinolones"	"J01MB01"	"Quinolone antibacterials"	"Other quinolones"	""	"acrosoxacin,eracine,eradacil,eradacin,eradicin,rosoxacin,rosoxacine,rosoxacino,rosoxacinum,roxadyl,winoxacin,winuron"	0.3	"g"			""
-"RXT"		"Roxithromycin"	"Macrolides/lincosamides"	"J01FA06"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi"	"roxithromycin,roxithromycine,roxithromycinum,roxitromicina,rulide"	0.3	"g"			""
+"RLT"	54682938	"Rolitetracycline"	"Tetracyclines"	"J01AA09"	"Tetracyclines"	"Tetracyclines"	""	"bristacin,kinteto,reverin,rolitetraciclina,rolitetracycline,rolitetracyclinum,solvocillin,superciclin,synotodecin,synterin,syntetrex,syntetrin,transcycline,velacicline,velacycline"			0.35	"g"	"18976-1,435-8,436-6,437-4,438-2"
+"ROS"	287180	"Rosoxacin"	"Quinolones"	"J01MB01"	"Quinolone antibacterials"	"Other quinolones"	""	"acrosoxacin,eracine,eradacil,eradacin,eradicin,rosoxacin,rosoxacine,rosoxacino,rosoxacinum,roxadyl,winoxacin,winuron"	0.3	"g"			"18977-9,439-0,440-8,441-6,442-4,55713-2"
+"RXT"		"Roxithromycin"	"Macrolides/lincosamides"	"J01FA06"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"roxi"	"roxithromycin,roxithromycine,roxithromycinum,roxitromicina,rulide"	0.3	"g"			"18978-7,443-2,444-0,445-7,446-5,7046-6"
 "RFL"	58258	"Rufloxacin"	"Quinolones"	"J01MA10"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"rufloxacin,rufloxacin hcl,rufloxacine,rufloxacino,rufloxacinum"	0.2	"g"			""
-"SAL"	3085092	"Salinomycin"	"Other antibacterials"	"NA"			""	"coxistac,procoxacin,salinomicina,salinomycin,salinomycine,salinomycinum"					"87593-0"
-"SAR"	56208	"Sarafloxacin"	"Quinolones"	"NA"			""	"difloxacine,difloxacino,difloxacinum,quinolone der.,saraflox,sarafloxacin,sarafloxacine,sarafloxacino,sarafloxacinum"					""
+"SAL"	3085092	"Salinomycin"	"Other antibacterials"	"QP51BB01"			""	"coxistac,procoxacin,salinomicina,salinomycin,salinomycine,salinomycinum"					"35836-6,35837-4,35838-2,87593-0"
+"SAR"	56208	"Sarafloxacin"	"Quinolones"	"QJ01MA98"			""	"difloxacine,difloxacino,difloxacinum,quinolone der.,saraflox,sarafloxacin,sarafloxacine,sarafloxacino,sarafloxacinum"					"73588-6,73610-8,73633-0"
 "SRC"	54681908	"Sarecycline"	"Tetracyclines"	"J01AA14"	"Tetracyclines"	"Tetracyclines"	""	"sarecycline,seysara"	0.1	"g"			""
 "SRX"	9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"	"NA"			""	"sarmoxicillin"					""
 "SEC"	71815	"Secnidazole"	"Other antibacterials"	"P01AB07"			""	"flagentyl,secnidal,secnidazol,secnidazole,secnidazolum,secnil,sindose,solosec"	2	"g"			""
 "SMF"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"C10BA04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	""					""
-"SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso"	"rickamicin,salvamina,siseptin sulfate,sisomicin,sisomicin sulfate,sisomicina,sisomicine,sisomicinum,sisomin,sisomycin,sissomicin,sizomycin"			0.24	"g"	""
+"SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso"	"rickamicin,salvamina,siseptin sulfate,sisomicin,sisomicin sulfate,sisomicina,sisomicine,sisomicinum,sisomin,sisomycin,sissomicin,sizomycin"			0.24	"g"	"18979-5,447-3,448-1,449-9,450-7,55714-0"
 "SIT"	461399	"Sitafloxacin"	"Quinolones"	"J01MA21"			""	"gracevit,sitafloxacin,sitafloxacinisomer"	0.1	"g"			""
 "SDA"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"J04AA02"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	""	"bactylan,decapasil,lepasen,monopas,nippas,p.a.s. sodium,pamisyl sodium,parasal sodium,pas sodium,pasade,pasnal,passodico,salvis,sanipirol,sodiopas,sodium p.a.s,sodium pas,teebacin,tubersan"	14	"g"	14	"g"	""
-"SOL"	25242512	"Solithromycin"	"Macrolides/lincosamides"	"J01FA16"			""	"solithera,solithromycin"					""
-"SPX"	60464	"Sparfloxacin"	"Quinolones"	"J01MA09"	"Quinolone antibacterials"	"Fluoroquinolones"	"spa,spar"	"esparfloxacino,sparfloxacin,sparfloxacine,sparfloxacinum"	0.2	"g"			""
-"SPT"	15541	"Spectinomycin"	"Other antibacterials"	"J01XX04"	"Other antibacterials"	"Other antibacterials"	"sc,spe,spec,spt"	"actinospectacina,adspec,espectinomicina,prospec,specitinomycin,spectam,spectinomicina,spectinomycin,spectinomycin di hcl,spectinomycine,spectinomycinum,stanilo,togamycin,trobicin"			3	"g"	""
-"SPI"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"J01FA02"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"spir"	"espiramicin,provamycin,rovamycin,rovamycine,sequamycin,spiramycine,spiramycinum"	3	"g"			""
+"SOL"	25242512	"Solithromycin"	"Macrolides/lincosamides"	"J01FA16"			""	"solithera,solithromycin"					"73587-8,73609-0,73632-2"
+"SPX"	60464	"Sparfloxacin"	"Quinolones"	"J01MA09"	"Quinolone antibacterials"	"Fluoroquinolones"	"spa,spar"	"esparfloxacino,sparfloxacin,sparfloxacine,sparfloxacinum"	0.2	"g"			"20397-6,23610-9,23628-1,35839-0,7047-4"
+"SPT"	15541	"Spectinomycin"	"Other antibacterials"	"J01XX04"	"Other antibacterials"	"Other antibacterials"	"sc,spe,spec,spt"	"actinospectacina,adspec,espectinomicina,prospec,specitinomycin,spectam,spectinomicina,spectinomycin,spectinomycin di hcl,spectinomycine,spectinomycinum,stanilo,togamycin,trobicin"			3	"g"	"18980-3,35840-8,451-5,452-3,453-1,454-9"
+"SPI"	6419898	"Spiramycin"	"Macrolides/lincosamides"	"J01FA02"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"spir"	"espiramicin,provamycin,rovamycin,rovamycine,sequamycin,spiramycine,spiramycinum"	3	"g"			"18981-1,455-6,456-4,457-2,458-0,55715-7"
 "SPM"		"Spiramycin/metronidazole"	"Other antibacterials"	"J01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "STR"		"Streptoduocin"	"Aminoglycosides"	"J01GA02"	"Aminoglycoside antibacterials"	"Streptomycins"	""	"ambistrin"			1	"g"	""
-"STR1"	19649	"Streptomycin"	"Aminoglycosides"	"A07AA04,J01GA01"	"Aminoglycoside antibacterials"	"Streptomycins"	"s,stm,str,stre"	"agrept,agrimycin,chemform,estreptomicina,neodiestreptopab,strepcen,streptomicina,streptomycin,streptomycin a,streptomycin spx,streptomycin sulfate,streptomycine,streptomycinum,streptomyzin,vetstrep"			1	"g"	"4039-4"
-"STH"		"Streptomycin-high"	"Aminoglycosides"	"NA"			"sthi,sthl,strepto high,streptomycin high"	""					""
+"STR1"	19649	"Streptomycin"	"Aminoglycosides"	"A07AA04,J01GA01"	"Aminoglycoside antibacterials"	"Streptomycins"	"s,stm,str,stre"	"agrept,agrimycin,chemform,estreptomicina,neodiestreptopab,strepcen,streptomicina,streptomycin,streptomycin a,streptomycin spx,streptomycin sulfate,streptomycine,streptomycinum,streptomyzin,vetstrep"			1	"g"	"18982-9,18983-7,20462-8,23626-5,25185-0,25205-6,25206-4,35841-6,4039-4,42658-5,42659-3,459-8,460-6,461-4,462-2,46719-1,48177-0,6933-6,7048-2,7049-0,96114-4"
+"STH"		"Streptomycin-high"	"Aminoglycosides"	"NA"			"sthi,sthl,strepto high,streptomycin high"	""					"18983-7,35841-6,6933-6,7049-0"
 "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"	""	"betamaze,sulbactam,sulbactam acid,sulbactam free acid,sulbactamum"			1	"g"	""
+"SUL"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"J01CG01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	""	"betamaze,sulbactam,sulbactam acid,sulbactam free acid,sulbactamum"			1	"g"	"41716-2,41717-0,41718-8,41739-4"
 "SBC"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"J01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"kedacillina,sulbenicilina,sulbenicillin,sulbenicilline,sulbenicillinum"			15	"g"	""
 "SUC"	5318	"Sulconazole"	"Antifungals/antimycotics"	"D01AC09"			""	"sulconazol,sulconazole,sulconazolum"					""
-"SUP"	6634	"Sulfachlorpyridazine"	"Other antibacterials"	"NA"			""	"cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone vet,prinzone vet.,solfaclorpiridazina,sonilyn,sulfachlorpyridazine,sulfacloropiridazina,vetisulid"					""
-"SDI"	5215	"Sulfadiazine"	"Trimethoprims"	"J01EC02"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"adiazin,adiazine,cocodiazine,codiazine,cremodiazine,cremotres,debenal,deltazina,diazin,diazolone,diazovit,diazyl,eskadiazine,honey diazine,liquadiazine,microsulfon,neazine,neotrizine,nsulfanilamide,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,sildaflo,silvadene,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazine,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonamides duplex,sulfonsol,sulfose,sulphadiazine,sulphadiazine e,terfonyl,theradiazine,thermazene,trifonamide,triple sulfa,triple sulfas,trisem,truozine,zinc sulfadiazine"	0.6	"g"			"27216-1,59742-7,6907-0"
+"SUP"	6634	"Sulfachlorpyridazine"	"Other antibacterials"	"QJ01EQ12"			""	"cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone vet,prinzone vet.,solfaclorpiridazina,sonilyn,sulfachlorpyridazine,sulfacloropiridazina,vetisulid"					""
+"SDI"	5215	"Sulfadiazine"	"Trimethoprims"	"J01EC02"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	""	"adiazin,adiazine,cocodiazine,codiazine,cremodiazine,cremotres,debenal,deltazina,diazin,diazolone,diazovit,diazyl,eskadiazine,honey diazine,liquadiazine,microsulfon,neazine,neotrizine,nsulfanilamide,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,sildaflo,silvadene,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazine,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonamides duplex,sulfonsol,sulfose,sulphadiazine,sulphadiazine e,terfonyl,theradiazine,thermazene,trifonamide,triple sulfa,triple sulfas,trisem,truozine,zinc sulfadiazine"	0.6	"g"			"18984-5,27216-1,463-0,464-8,465-5,466-3,59742-7,6907-0,7050-8"
 "SLT"	122284	"Sulfadiazine/tetroxoprim"	"Trimethoprims"	"J01EE06"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	"cotetroxazine"					""
 "SLT1"	64932	"Sulfadiazine/trimethoprim"	"Trimethoprims"	"J01EE02"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	"antastmon,cotrimazine,diaziprim forte,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim"					""
-"SUD"	5323	"Sulfadimethoxine"	"Trimethoprims"	"J01ED01"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"agribon,arnosulfan,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamide,omnibon,persulfen,primor,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxine,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfdimethoxine,sulfoplan,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon"	0.5	"g"			""
+"SUD"	5323	"Sulfadimethoxine"	"Trimethoprims"	"J01ED01"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"agribon,arnosulfan,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamide,omnibon,persulfen,primor,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxine,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfdimethoxine,sulfoplan,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon"	0.5	"g"			"87799-3,87803-3"
 "SDM"	5327	"Sulfadimidine"	"Trimethoprims"	"J01EB03"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"azolmetazin,benzene sulfonamide,calfspan,calfspan tablets,cremomethazine,diazil,diazilsulfadine,dimezathine,intradine,kelametazine,mermeth,metazin,neasina,neazina,nsulfanilamide,panazin,pirmazin,primazin,sa iii,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidine,sulfadimidinum,sulfadine,sulfametazina,sulfametazyny,sulfamethazine,sulfamethiazine,sulfamezathine,sulfamidine,sulfasure sr bolus,sulfodimesin,sulfodimezine,sulka k boluses,sulka s boluses,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan"	4	"g"			""
 "SLT2"		"Sulfadimidine/trimethoprim"	"Trimethoprims"	"J01EE05"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
 "SLF"	5344	"Sulfafurazole"	"Trimethoprims"	"J01EB05,S01AB02"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfsz"	"accuzole,alphazole,amidoxal,astrazolo,azo gantrisin,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,dorsulfan warthausen,entusil,entusul,eryzole,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazoi,neoxazol,novazolo,novosaxazole,nsulfanilamide,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxosul tablets,roxoxol,saxosozine,sodizole,solfafurazolo,soxamide,soxazole,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafuraz ole,sulfafurazol,sulfafurazole,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazole,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan,vagilia"	4	"g"	4	"g"	""
@@ -410,7 +410,7 @@
 "SLT3"		"Sulfamerazine/trimethoprim"	"Trimethoprims"	"J01EE07"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	""	""					""
 "SUM"	5327	"Sulfamethazine"	"Other antibacterials"	"NA"			""	"azolmetazin,benzene sulfonamide,calfspan,calfspan tablets,cremomethazine,diazil,diazilsulfadine,dimezathine,intradine,kelametazine,mermeth,metazin,neasina,neazina,nsulfanilamide,panazin,pirmazin,primazin,sa iii,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidine,sulfadimidinum,sulfadine,sulfametazina,sulfametazyny,sulfamethazine,sulfamethiazine,sulfamezathine,sulfamidine,sulfasure sr bolus,sulfodimesin,sulfodimezine,sulka k boluses,sulka s boluses,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan"					"87592-2"
 "SLF4"	5328	"Sulfamethizole"	"Trimethoprims"	"B05CA04,D06BA04,J01EB02,S01AB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfmz"	"ayerlucil,lucosil,methazol,microsul,nsulfanilamide,proklar,renasul,salimol,solfametizolo,sulamethizole,sulfa gram,sulfamethizol,sulfamethizole,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphamethizole,tetracid,thidicur,thiosulfil,thiosulfil forte,ultrasul,urocydal,urodiaton,urolucosil,urosulfin"	4	"g"			"60175-7,60176-5,60177-3"
-"SMX"	5329	"Sulfamethoxazole"	"Trimethoprims"	"J01EC01"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sfmx,sulf"	"azo gantanol,gamazole,gantanol,gantanol ds,metoxal,nsulfanilamide,nsulphanilamide,radonil,septran,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazol,sulfamethoxazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfisomezole,sulmeprim,sulphamethalazole,sulphamethoxazol,sulphamethoxazole,sulphisomezole,urobak"	2	"g"			"10342-4,25271-8,39772-9,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
+"SMX"	5329	"Sulfamethoxazole"	"Trimethoprims"	"J01EC01"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sfmx,sulf"	"azo gantanol,gamazole,gantanol,gantanol ds,metoxal,nsulfanilamide,nsulphanilamide,radonil,septran,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazol,sulfamethoxazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfisomezole,sulmeprim,sulphamethalazole,sulphamethoxazol,sulphamethoxazole,sulphisomezole,urobak"	2	"g"			"10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
 "SLF5"	5330	"Sulfamethoxypyridazine"	"Trimethoprims"	"J01ED05"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"altezol,davosin,depovernil,kineks,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,nsulfanilamide,opinsul,paramid,paramid supra,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,sulfalex,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces"	0.5	"g"			""
 "SLF6"	19596	"Sulfametomidine"	"Trimethoprims"	"J01ED03"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"duroprocin,methofadin,methofazine,nsulfanilamide,solfametomidina,sulfamethomidine,sulfametomidin,sulfametomidina,sulfametomidine,sulfametomidinum"					""
 "SLF7"	5326	"Sulfametoxydiazine"	"Trimethoprims"	"J01ED04"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,longasulf,methoxypyrimal,nsulfanilamide,solfametossidiazina,sulfameter,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorin,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazine,sulfametoxydiazinum,sulphameter,sulphamethoxydiazine,supramid,ultrax"	0.5	"g"			""
@@ -422,63 +422,63 @@
 "SLF11"	5335	"Sulfaphenazole"	"Trimethoprims"	"J01ED08"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	""	"depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,isarol v,merian,microtan pirazolo,nsulfanilamide,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazole,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole"	1	"g"			""
 "SLF12"	5336	"Sulfapyridine"	"Trimethoprims"	"J01EB04"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,septipulmon,solfapiridina,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridine,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon"	1	"g"			"14075-6,55580-5"
 "SNA"	60582	"Sulfasuccinamide"	"Other antibacterials"	"NA"			""	"ambesid,derganil,sulfasuccinamid,sulfasuccinamida,sulfasuccinamide,sulfasuccinamidum"					""
-"SUT"	5340	"Sulfathiazole"	"Trimethoprims"	"D06BA02,J01EB07"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,nsulfanilamide,planomide,poliseptil,sanotiazol,septozol,sodium sulfathiazole,solfatiazolo,streptosilthiazole,sulfamul,sulfathiazol,sulfathiazole,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,triple sulfa,wintrazole"					"87591-4"
+"SUT"	5340	"Sulfathiazole"	"Trimethoprims"	"D06BA02,J01EB07"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,nsulfanilamide,planomide,poliseptil,sanotiazol,septozol,sodium sulfathiazole,solfatiazolo,streptosilthiazole,sulfamul,sulfathiazol,sulfathiazole,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,triple sulfa,wintrazole"					"87591-4,87796-9,87797-7"
 "SLF13"	3000579	"Sulfathiourea"	"Trimethoprims"	"J01EB08"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	""	"badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathiourea,sulfathiouree,sulfatiourea,sulphathiourea"	6	"g"			""
-"SOX"	5344	"Sulfisoxazole"	"Other antibacterials"	"NA"			""	"accuzole,alphazole,amidoxal,astrazolo,azo gantrisin,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,dorsulfan warthausen,entusil,entusul,eryzole,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazoi,neoxazol,novazolo,novosaxazole,nsulfanilamide,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxosul tablets,roxoxol,saxosozine,sodizole,solfafurazolo,soxamide,soxazole,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafuraz ole,sulfafurazol,sulfafurazole,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazole,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan,vagilia"					"9701-4"
-"SSS"	86225	"Sulfonamide"	"Other antibacterials"	"NA"			"sfna"	"anhydron,aquirel,ciclotiazida,ciclotiazide,cyclothiazide,cyclothiazidum,doburil,fluidil,renazide,valmiran"					""
-"SLP"	9950244	"Sulopenem"	"Other antibacterials"	"NA"			""	"sulopenem"					""
+"SOX"	5344	"Sulfisoxazole"	"Other antibacterials"	"NA"			""	"accuzole,alphazole,amidoxal,astrazolo,azo gantrisin,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,dorsulfan warthausen,entusil,entusul,eryzole,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazoi,neoxazol,novazolo,novosaxazole,nsulfanilamide,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxosul tablets,roxoxol,saxosozine,sodizole,solfafurazolo,soxamide,soxazole,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafuraz ole,sulfafurazol,sulfafurazole,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazole,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan,vagilia"					"11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
+"SSS"	86225	"Sulfonamide"	"Other antibacterials"	"NA"			"sfna"	"anhydron,aquirel,ciclotiazida,ciclotiazide,cyclothiazide,cyclothiazidum,doburil,fluidil,renazide,valmiran"					"17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
+"SLP"	9950244	"Sulopenem"	"Other antibacterials"	"NA"			""	"sulopenem"					"55289-3,55290-1,55291-9"
 "SLT6"	444022	"Sultamicillin"	"Beta-lactams/penicillins"	"J01CR04"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	""	"sultamicilina,sultamicillin,sultamicillinum"	1.5	"g"			""
 "SUR"	46700778	"Surotomycin"	"Other antibacterials"	"NA"			""	"surotomycin"					""
-"TAL"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"J01CA15"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"talampicilina,talampicillin,talampicilline,talampicillinum"	2	"g"			""
+"TAL"	71447	"Talampicillin"	"Beta-lactams/penicillins"	"J01CA15"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"talampicilina,talampicillin,talampicilline,talampicillinum"	2	"g"			"18988-6,479-6,480-4,481-2,482-0"
 "TLP"	163307	"Talmetoprim"	"Other antibacterials"	"NA"			""	"talmetoprim"					""
-"TAZ"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"J01CG02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo"	"tazobactam,tazobactam acid,tazobactamum,tazobactum"					""
-"TBP"	9800194	"Tebipenem"	"Carbapenems"	"NA,J01DH06"			""	"tebipenem pivoxil"					""
-"TZD"	11234049	"Tedizolid"	"Oxazolidinones"	"J01XX11"	"Other antibacterials"	"Other antibacterials"	"tedi"	"sivextro,tedizolid,torezolid"	0.2	"g"	0.2	"g"	""
-"TEC"	16131923	"Teicoplanin"	"Glycopeptides"	"J01XA02"	"Other antibacterials"	"Glycopeptide antibacterials"	"tec,tei,teic,tp,tpl,tpn"	"targocid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanin,teicoplanina,teicoplanine,teicoplaninum"			0.4	"g"	"25534-9,25535-6,34378-0,34379-8,4043-6,80968-1"
+"TAZ"	123630	"Tazobactam"	"Beta-lactams/penicillins"	"J01CG02"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	"tazo"	"tazobactam,tazobactam acid,tazobactamum,tazobactum"					"41719-6,41720-4,41721-2,41740-2"
+"TBP"	9800194	"Tebipenem"	"Carbapenems"	"NA,J01DH06"			""	"tebipenem pivoxil"	0.56	"g"			""
+"TZD"	11234049	"Tedizolid"	"Oxazolidinones"	"J01XX11"	"Other antibacterials"	"Other antibacterials"	"tedi"	"sivextro,tedizolid,torezolid"	0.2	"g"	0.2	"g"	"73586-0,73608-2,73631-4"
+"TEC"	16131923	"Teicoplanin"	"Glycopeptides"	"J01XA02"	"Other antibacterials"	"Glycopeptide antibacterials"	"tec,tei,teic,tp,tpl,tpn"	"targocid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanin,teicoplanina,teicoplanine,teicoplaninum"			0.4	"g"	"18989-4,25534-9,25535-6,34378-0,34379-8,4043-6,483-8,484-6,485-3,486-1,7051-6,80968-1"
 "TCM"		"Teicoplanin-macromethod"	"Glycopeptides"	"NA"			""	""					""
-"TLV"	3081362	"Telavancin"	"Glycopeptides"	"J01XA03"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela"	"telavancin,televancin,vibativ"					""
-"TLT"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"J01FA15"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"teli"	"levviax,telithromycin"	0.8	"g"			""
-"TMX"	60021	"Temafloxacin"	"Quinolones"	"J01MA05"	"Quinolone antibacterials"	"Fluoroquinolones"	"tema"	"omniflox,temafloxacin,temafloxacina,temafloxacine,temafloxacinum"	0.8	"g"			""
-"TEM"	171758	"Temocillin"	"Beta-lactams/penicillins"	"J01CA17"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"temo"	"negaban,temocilina,temocillin,temocillina,temocilline,temocillinum"			4	"g"	""
-"TRB"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"D01AE15,D01BA02"	"Antifungals for systemic use"	"Antifungals for systemic use"	"terb"	"corbinal,lamasil,lamisil,lamisil at,lamisil tablet,terbinafina,terbinafine,terbinafinum,terbinex"	0.25	"g"			""
-"TRC"	441383	"Terconazole"	"Antifungals/antimycotics"	"G01AG02"			""	"fungistat,panlomyc,terazol,terconazol,terconazole,terconazolum,tercospor,triaconazole,zazole"					""
+"TLV"	3081362	"Telavancin"	"Glycopeptides"	"J01XA03"	"Other antibacterials"	"Glycopeptide antibacterials"	"tela"	"telavancin,televancin,vibativ"					"72894-9,73630-6,85051-1,88886-7"
+"TLT"	3002190	"Telithromycin"	"Macrolides/lincosamides"	"J01FA15"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"teli"	"levviax,telithromycin"	0.8	"g"			"35843-2,35844-0,35845-7,41722-0"
+"TMX"	60021	"Temafloxacin"	"Quinolones"	"J01MA05"	"Quinolone antibacterials"	"Fluoroquinolones"	"tema"	"omniflox,temafloxacin,temafloxacina,temafloxacine,temafloxacinum"	0.8	"g"			"18990-2,487-9,488-7,489-5,490-3"
+"TEM"	171758	"Temocillin"	"Beta-lactams/penicillins"	"J01CA17"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"temo"	"negaban,temocilina,temocillin,temocillina,temocilline,temocillinum"			4	"g"	"18991-0,491-1,492-9,493-7,494-5,54190-4"
+"TRB"	1549008	"Terbinafine"	"Antifungals/antimycotics"	"D01AE15,D01BA02"	"Antifungals for systemic use"	"Antifungals for systemic use"	"terb"	"corbinal,lamasil,lamisil,lamisil at,lamisil tablet,terbinafina,terbinafine,terbinafinum,terbinex"	0.25	"g"			"10720-1,10721-9,18992-8"
+"TRC"	441383	"Terconazole"	"Antifungals/antimycotics"	"G01AG02"			""	"fungistat,panlomyc,terazol,terconazol,terconazole,terconazolum,tercospor,triaconazole,zazole"					"55196-0"
 "TRZ"	65720	"Terizidone"	"Antimycobacterials"	"J04AK03"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"terivalidin,terizidon,terizidona,terizidone,terizidonum"					""
-"TCY"	54675776	"Tetracycline"	"Tetracyclines"	"A01AB13,D06AA04,J01AA07,S01AA09,S02AA08,S03AA02"	"Tetracyclines"	"Tetracyclines"	"tc,te,tet,tetr"	"abramycin,abricycline,achromycin,achromycin v,actisite,agromicina,ambramicina,ambramycin,amycin,biocycline,bristaciclin,bristaciclina,bristacycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,cyclomycin,cyclopar,cytome,democracin,deschlorobiomycin,dumocyclin,economycin,enterocycline,hostacyclin,lexacycline,limecycline,liquamycin,medocycline,mericycline,micycline,neocycline,oletetrin,omegamycin,orlycycline,panmycin,piracaps,polycycline,polyotic,purocyclina,resteclin,robitet,roviciclina,sigmamycin,solvocin,sumycin,sumycin syrup,supramycin,sustamycin,tetrabid organon,tetrabon,tetrachel,tetraciclina,tetracycl,tetracyclin,tetracycline,tetracycline base,tetracycline i,tetracycline ii,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetramed,tetrasure,tetraverine,tetrazyklin,tetrex,topicycline,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum,vetquamycin"	1	"g"	1	"g"	"25272-6,4045-1,87590-6"
+"TCY"	54675776	"Tetracycline"	"Tetracyclines"	"A01AB13,D06AA04,J01AA07,S01AA09,S02AA08,S03AA02"	"Tetracyclines"	"Tetracyclines"	"tc,te,tet,tetr"	"abramycin,abricycline,achromycin,achromycin v,actisite,agromicina,ambramicina,ambramycin,amycin,biocycline,bristaciclin,bristaciclina,bristacycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,cyclomycin,cyclopar,cytome,democracin,deschlorobiomycin,dumocyclin,economycin,enterocycline,hostacyclin,lexacycline,limecycline,liquamycin,medocycline,mericycline,micycline,neocycline,oletetrin,omegamycin,orlycycline,panmycin,piracaps,polycycline,polyotic,purocyclina,resteclin,robitet,roviciclina,sigmamycin,solvocin,sumycin,sumycin syrup,supramycin,sustamycin,tetrabid organon,tetrabon,tetrachel,tetraciclina,tetracycl,tetracyclin,tetracycline,tetracycline base,tetracycline i,tetracycline ii,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetramed,tetrasure,tetraverine,tetrazyklin,tetrex,topicycline,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum,vetquamycin"	1	"g"	1	"g"	"101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6"
 "TOL"	54691494	"Tetracycline/oleandomycin"	"Other antibacterials"	"J01RA08"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "TET"	65450	"Tetroxoprim"	"Other antibacterials"	"NA"			""	"tetroxoprim,tetroxoprima,tetroxoprime,tetroxoprimum"					""
-"THA"	9568512	"Thiacetazone"	"Oxazolidinones"	"NA"			""	"aktivan,ambathizon,amithiozone,amithizone,amitiozon,benthiozone,benzothiozane,benzothiozon,berculon a,berkazon,citazone,conteben,diasan,diazan,domakol,ilbion,livazone,mirizone neustab,mivizon,myvizone,neotibil,neustab,novakol,nuclon argentinian,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebesone i,tebethion,tebethione,tebezon,thiacetazone,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazone,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal"					""
-"THI"	27200	"Thiamphenicol"	"Amphenicols"	"J01BA02"	"Amphenicols"	"Amphenicols"	""	"descocin,dexawin,dextrosulfenidol,dextrosulphenidol,efnicol,hyrazin,igralin,macphenicol,masatirin,neomyson,racefenicol,racefenicolo,racefenicolum,raceophenidol,racephenicol,rincrol,thiamcol,thiamphenicol,thiamphenicolum,thiocymetin,thiomycetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamicina,urfamycine,vicemycetin"	1.5	"g"	1.5	"g"	""
+"THA"	9568512	"Thiacetazone"	"Oxazolidinones"	"NA"			""	"aktivan,ambathizon,amithiozone,amithizone,amitiozon,benthiozone,benzothiozane,benzothiozon,berculon a,berkazon,citazone,conteben,diasan,diazan,domakol,ilbion,livazone,mirizone neustab,mivizon,myvizone,neotibil,neustab,novakol,nuclon argentinian,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebesone i,tebethion,tebethione,tebezon,thiacetazone,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazone,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal"					"32384-0,54184-7,54204-3"
+"THI"	27200	"Thiamphenicol"	"Amphenicols"	"J01BA02"	"Amphenicols"	"Amphenicols"	""	"descocin,dexawin,dextrosulfenidol,dextrosulphenidol,efnicol,hyrazin,igralin,macphenicol,masatirin,neomyson,racefenicol,racefenicolo,racefenicolum,raceophenidol,racephenicol,rincrol,thiamcol,thiamphenicol,thiamphenicolum,thiocymetin,thiomycetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamicina,urfamycine,vicemycetin"	1.5	"g"	1.5	"g"	"41723-8,41724-6,41725-3,54169-8"
 "TAT"	9568512	"Thioacetazone"	"Antimycobacterials"	"J04AK07"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	""	"aktivan,ambathizon,amithiozone,amitiozon,benthiozone,benzothiozane,benzothiozon,berculon a,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mirizone neustab,mivizon,myvizone,neotibil,neustab,novakol,nuclon argentinian,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebesone i,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazone,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal"					""
 "THI1"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"J04AM04"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
-"TIA"	656958	"Tiamulin"	"Other antibacterials"	"NA"			""	"denagard,thiamutilin,tiamulin,tiamulin pamoate,tiamulina,tiamuline,tiamulinum,tiavet p"					"87589-8"
-"TIC"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"J01CA13"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"tc,ti,tic,tica"	"ticarcilina,ticarcillin,ticarcilline,ticarcillinum,ticillin,timentin"			15	"g"	"25254-4,4054-3,4055-0"
+"TIA"	656958	"Tiamulin"	"Other antibacterials"	"QJ01XQ01"			""	"denagard,thiamutilin,tiamulin,tiamulin pamoate,tiamulina,tiamuline,tiamulinum,tiavet p"					"35846-5,35847-3,35848-1,87589-8"
+"TIC"	36921	"Ticarcillin"	"Beta-lactams/penicillins"	"J01CA13"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"tc,ti,tic,tica"	"ticarcilina,ticarcillin,ticarcilline,ticarcillinum,ticillin,timentin"			15	"g"	"18994-4,18995-1,25254-4,4054-3,4055-0,499-4,500-9,501-7,502-5,503-3,504-1,505-8,506-6,55716-5,55717-3,55718-1,55719-9,7053-2,7054-0"
 "TCC"	6437075	"Ticarcillin/clavulanic acid"	"Beta-lactams/penicillins"	"J01CR03"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"t/c,tcc,ticl,tim,tlc"	"timentin"			15	"g"	""
-"TGC"	54686904	"Tigecycline"	"Tetracyclines"	"J01AA12"	"Tetracyclines"	"Tetracyclines"	"tgc,tig,tige"	"haizheng li xing,tigeciclina,tigecyclin,tigecycline,tigecycline hydrate,tigecyclinum,tigilcycline,tygacil"			0.1	"g"	""
+"TGC"	54686904	"Tigecycline"	"Tetracyclines"	"J01AA12"	"Tetracyclines"	"Tetracyclines"	"tgc,tig,tige"	"haizheng li xing,tigeciclina,tigecyclin,tigecycline,tigecycline hydrate,tigecyclinum,tigilcycline,tygacil"			0.1	"g"	"101499-2,42354-1,42355-8,42356-6,42357-4,55158-0"
 "TBQ"	65592	"Tilbroquinol"	"Quinolones"	"P01AA05"			""	"tilbroquinol,tilbroquinolum"					""
-"TIP"	24860548	"Tildipirosin"	"Macrolides/lincosamides"	"NA"			""	"tildipirosin,zuprevo"					""
-"TIL"	5282521	"Tilmicosin"	"Macrolides/lincosamides"	"NA"			""	"micotil,pulmotil,tilmicosin,tilmicosina,tilmicosine,tilmicosinum"					"87588-0"
-"TIN"	5479	"Tinidazole"	"Other antibacterials"	"J01XD02,P01AB02"	"Other antibacterials"	"Imidazole derivatives"	"tini"	"amtiba,bioshik,ethyl sulfone,fasigin,fasigyn,fasigyntrade mark,fasygin,glongyn,haisigyn,pletil,simplotan,simplotantrade mark,sorquetan,symplotan,tindamax,tindamaxtrade mark,tinidazol,tinidazole,tinidazolum,tricolam,trimonase"	2	"g"	1.5	"g"	""
+"TIP"	24860548	"Tildipirosin"	"Macrolides/lincosamides"	"QJ01FA96"			""	"tildipirosin,zuprevo"					"100060-3,88375-1,88377-7"
+"TIL"	5282521	"Tilmicosin"	"Macrolides/lincosamides"	"QJ01FA91"			""	"micotil,pulmotil,tilmicosin,tilmicosina,tilmicosine,tilmicosinum"					"35849-9,35850-7,35851-5,87588-0"
+"TIN"	5479	"Tinidazole"	"Other antibacterials"	"G01AF21,J01XD02,P01AB02"	"Other antibacterials"	"Imidazole derivatives"	"tini"	"amtiba,bioshik,ethyl sulfone,fasigin,fasigyn,fasigyntrade mark,fasygin,glongyn,haisigyn,pletil,simplotan,simplotantrade mark,sorquetan,symplotan,tindamax,tindamaxtrade mark,tinidazol,tinidazole,tinidazolum,tricolam,trimonase"	2	"g"	1.5	"g"	"54928-7,55720-7,55721-5,55722-3"
 "TCR"	3001386	"Tiocarlide"	"Antimycobacterials"	"J04AD02"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	""	"amixyl,datanil,disocarban,disoxyl,isoxyl,thiocarlide,tiocarlid,tiocarlida,tiocarlide,tiocarlidum"	7	"g"			""
 "TDC"	10247721	"Tiodonium chloride"	"Other antibacterials"	"NA"			""	"cloruro de tiodonio,tiodonii chloridum,tiodonium chloride"					""
 "TXC"	65788	"Tioxacin"	"Quinolones"	"NA"			""	"tioxacin,tioxacine,tioxacino,tioxacinum,tioxic acid"					""
-"TIZ"	394397	"Tizoxanide"	"Other antibacterials"	"NA"			""	"ntzdes"					""
-"TOB"	36294	"Tobramycin"	"Aminoglycosides"	"J01GB01,S01AA12"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"nn,tm,to,tob,tobr"	"bethkis,brulamycin,deoxykanamycin b,distobram,gernebcin,gotabiotic,kitabis,kitabis pak,nebcin,nebicin,nebramycin,nebramycin vi,obramycin,sybryx,tenebrimycin,tenemycin,tobacin,tobi podhaler,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycin,tobramycin base,tobramycin sulfate,tobramycine,tobramycinum,tobrased,tobrasone,tobrex"			0.24	"g"	"13584-8,17808-7,22750-4,22751-2,22752-0,31094-6,31095-3,31096-1,35239-3,35670-9,4057-6,4058-4,4059-2,50927-3,52962-8,59380-6,80966-5"
+"TIZ"	394397	"Tizoxanide"	"Other antibacterials"	"NA"			""	"ntzdes"					"73585-2,73607-4,73629-8"
+"TOB"	36294	"Tobramycin"	"Aminoglycosides"	"J01GB01,S01AA12"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"nn,tm,to,tob,tobr"	"bethkis,brulamycin,deoxykanamycin b,distobram,gernebcin,gotabiotic,kitabis,kitabis pak,nebcin,nebicin,nebramycin,nebramycin vi,obramycin,sybryx,tenebrimycin,tenemycin,tobacin,tobi podhaler,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycin,tobramycin base,tobramycin sulfate,tobramycine,tobramycinum,tobrased,tobrasone,tobrex"			0.24	"g"	"101496-8,13584-8,17808-7,18996-9,22750-4,22751-2,22752-0,25227-0,25800-4,31094-6,31095-3,31096-1,35239-3,35670-9,4057-6,4058-4,4059-2,507-4,508-2,509-0,50927-3,510-8,52962-8,59380-6,7055-7,80966-5"
 "TOH"		"Tobramycin-high"	"Aminoglycosides"	"NA"			"tobra high,tobramycin high,tohl"	""					""
-"TFX"	5517	"Tosufloxacin"	"Quinolones"	"J01MA22"			""	"tosufloxacin"	0.45	"g"			""
-"TMP"	5578	"Trimethoprim"	"Trimethoprims"	"J01EA01"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"t,tmp,tr,tri,trim,w"	"abaprim,alprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacterial,bacticel,bactifor,bactin,bactoprim,bactramin,bactrim,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,colizole ds,conprim,cotrimel,cotrimoxizole,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,idotrim,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lagatrim forte,lastrim,lescot,methoprim,metoprim,monoprim,monotrim,monotrimin,novotrimel,omstat,oraprim,pancidim,polytrim,priloprim,primosept,primsol,proloprim,protrin,purbal,resprim,resprim forte,roubac,roubal,salvatrim,septrin ds,septrin forte,septrin s,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfamethoprim,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,tmp smx,toprim,trimanyl,trimethioprim,trimethopim,trimethoprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexazole,trimexol,trimezol,trimogal,trimono,trimopan,trimpex,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim"	0.4	"g"	0.4	"g"	"11005-6,17747-7,25273-4,32342-8,4079-0,4080-8,4081-6,55584-7,80552-3,80973-1"
-"SXT"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"J01EE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"cot,cotrim,sxt,t/s,trsu,trsx,ts"	"abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bacterial forte,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrim ds,bactrim forte,bactrim pediatric,bactrimel,bactrizol,bactromin,bactropin,baktar,belcomycine,berlocid,bibacrim,biseptol,chemitrim,chemotrim,ciplin,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colomycin,coly-mycin,cotribene,cotrim d.s.,cotrim eu rho,cotrim holsen,cotrim.l.u.t.,cotrimaxazol,cotrimazole,cotrimhexal,cotrimoxazol,cotrimoxazol al,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,esteprim,eusaprim,fectrim,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,jenamoxazol,kemoprim,kepinol,kepinol forte,laratrim,linaris,maxtrim,microtrim,microtrim forte,mikrosid,momentol,oecotrim,oriprim,oxaprim,pantoprim,polymyxin e,polymyxin e. sulfate,primazole,promixin,septra,septra ds,septra grape,septrim,septrin,servitrim,sigaprim,sigaprin,sulfatrim pediatric,sulfotrim,sulfotrimin,sulmeprim pediatric,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,totazina,tribakin,trifen,trigonyl,trimesulf,trimetho comp,trimethoprimsulfa,trimetoger,trimexazol,trimforte,trimosulfa,uroplus,uroplus ds,uroplus ss"					""
-"TRL"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"J01FA08"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"acetyloleandomycin,aovine,cyclamycin,evramicina,matromicina,matromycin t,micotil,oleandocetine,oleandomycin,t.a.o.,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycin,troleandomycine,troleandomycinum,viamicina,wytrion"	1	"g"			""
+"TFX"	5517	"Tosufloxacin"	"Quinolones"	"J01MA22,S01AE09"			""	"tosufloxacin"	0.45	"g"			"100061-1,76146-0"
+"TMP"	5578	"Trimethoprim"	"Trimethoprims"	"J01EA01"	"Sulfonamides and trimethoprim"	"Trimethoprim and derivatives"	"t,tmp,tr,tri,trim,w"	"abaprim,alprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacterial,bacticel,bactifor,bactin,bactoprim,bactramin,bactrim,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,colizole ds,conprim,cotrimel,cotrimoxizole,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,idotrim,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lagatrim forte,lastrim,lescot,methoprim,metoprim,monoprim,monotrim,monotrimin,novotrimel,omstat,oraprim,pancidim,polytrim,priloprim,primosept,primsol,proloprim,protrin,purbal,resprim,resprim forte,roubac,roubal,salvatrim,septrin ds,septrin forte,septrin s,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfamethoprim,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,tmp smx,toprim,trimanyl,trimethioprim,trimethopim,trimethoprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexazole,trimexol,trimezol,trimogal,trimono,trimopan,trimpex,triprim,trisul,trisulcom,trisulfam,trisural,uretrim,urobactrim,utetrin,velaten,wellcoprim,wellcoprin,xeroprim,zamboprim"	0.4	"g"	0.4	"g"	"101495-0,11005-6,17747-7,18997-7,18998-5,20387-7,23614-1,23631-5,25273-4,32342-8,4079-0,4080-8,4081-6,511-6,512-4,513-2,514-0,515-7,516-5,517-3,518-1,55584-7,7056-5,7057-3,80552-3,80973-1"
+"SXT"	358641	"Trimethoprim/sulfamethoxazole"	"Trimethoprims"	"J01EE01"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"cot,cotrim,sxt,t/s,trsu,trsx,ts"	"abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bacterial forte,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrim ds,bactrim forte,bactrim pediatric,bactrimel,bactrizol,bactromin,bactropin,baktar,belcomycine,berlocid,bibacrim,biseptol,chemitrim,chemotrim,ciplin,colimycin,colimycin sulphate,colisticin,colistimethate,colistimethate sodium,colistin sulfate,colistin sulphate,colomycin,coly-mycin,cotribene,cotrim d.s.,cotrim eu rho,cotrim holsen,cotrim.l.u.t.,cotrimaxazol,cotrimazole,cotrimhexal,cotrimoxazol,cotrimoxazol al,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,esteprim,eusaprim,fectrim,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,jenamoxazol,kemoprim,kepinol,kepinol forte,laratrim,linaris,maxtrim,microtrim,microtrim forte,mikrosid,momentol,oecotrim,oriprim,oxaprim,pantoprim,polymyxin e,polymyxin e. sulfate,primazole,promixin,septra,septra ds,septra grape,septrim,septrin,servitrim,sigaprim,sigaprin,sulfatrim pediatric,sulfotrim,sulfotrimin,sulmeprim pediatric,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,totazina,tribakin,trifen,trigonyl,trimesulf,trimetho comp,trimethoprimsulfa,trimetoger,trimexazol,trimforte,trimosulfa,uroplus,uroplus ds,uroplus ss"					"101495-0,18998-5,20387-7,23631-5,25273-4,32342-8,4081-6,515-7,516-5,517-3,518-1,7057-3"
+"TRL"	202225	"Troleandomycin"	"Macrolides/lincosamides"	"J01FA08"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	""	"acetyloleandomycin,aovine,cyclamycin,evramicina,matromicina,matromycin t,micotil,oleandocetine,oleandomycin,t.a.o.,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycin,troleandomycine,troleandomycinum,viamicina,wytrion"	1	"g"			"18999-3,519-9,520-7,521-5,522-3"
 "TRO"	55886	"Trospectomycin"	"Other antibacterials"	"NA"			""	"rubidiumnitrate,trospectinomycin,trospectomicina,trospectomycin,trospectomycine,trospectomycinum"					""
-"TVA"	62959	"Trovafloxacin"	"Quinolones"	"J01MA13"	"Quinolone antibacterials"	"Fluoroquinolones"	"trov"	"trovafloxacin,trovan"	0.2	"g"	0.2	"g"	""
-"TUL"	9832301	"Tulathromycin"	"Macrolides/lincosamides"	"NA"			""	"draxxin,tulathrmycin a,tulathromycin,tulathromycin a"					""
-"TYL"	5280440	"Tylosin"	"Macrolides/lincosamides"	"NA"			""	"fradizine,tilosina,tylocine,tylosin,tylosin a,tylosine,tylosinum"					"87587-2"
-"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"	"NA"			"tvn"	"tylvalosin"					""
+"TVA"	62959	"Trovafloxacin"	"Quinolones"	"J01MA13"	"Quinolone antibacterials"	"Fluoroquinolones"	"trov"	"trovafloxacin,trovan"	0.2	"g"	0.2	"g"	"23642-2,23643-0,35855-6,7058-1"
+"TUL"	9832301	"Tulathromycin"	"Macrolides/lincosamides"	"QJ01FA94"			""	"draxxin,tulathrmycin a,tulathromycin,tulathromycin a"					"76149-4,87798-5"
+"TYL"	5280440	"Tylosin"	"Macrolides/lincosamides"	"QJ01FA90,QJ51FA90"			""	"fradizine,tilosina,tylocine,tylosin,tylosin a,tylosine,tylosinum"					"35856-4,35857-2,35858-0,87587-2"
+"TYL1"	6441094	"Tylvalosin"	"Macrolides/lincosamides"	"QJ01FA92"			"tvn"	"tylvalosin"					"101526-2,87586-4"
 "PRU1"	124225	"Ulifloxacin (Prulifloxacin)"	"Other antibacterials"	"NA"			""	"ulifloxacin"					""
-"VAN"	14969	"Vancomycin"	"Glycopeptides"	"A07AA09,J01XA01,S01AA28"	"Other antibacterials"	"Glycopeptide antibacterials"	"va,van,vanc"	"vancocin,vancocin hcl,vancoled,vancomicina,vancomycin,vancomycin hcl,vancomycine,vancomycinum,vancor,viomycin derivative"	2	"g"	2	"g"	"13586-3,13587-1,20578-1,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,59381-4,97657-1"
+"VAN"	14969	"Vancomycin"	"Glycopeptides"	"A07AA09,J01XA01,S01AA28"	"Other antibacterials"	"Glycopeptide antibacterials"	"va,van,vanc"	"vancocin,vancocin hcl,vancoled,vancomicina,vancomycin,vancomycin hcl,vancomycine,vancomycinum,vancor,viomycin derivative"	2	"g"	2	"g"	"13586-3,13587-1,19000-9,20578-1,23615-8,25228-8,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,523-1,524-9,525-6,526-4,59381-4,7059-9,92241-9,97657-1"
 "VAM"		"Vancomycin-macromethod"	"Glycopeptides"	"NA"			""	""					""
-"VIO"	135398671	"Viomycin"	"Antimycobacterials"	"NA"			""	"celiomycin,florimycin,floromycin,tuberactinomycin b,vinacetin a,vioactane,viomicina,viomycin,viomycine,viomycinum"					""
+"VIO"	135398671	"Viomycin"	"Antimycobacterials"	"NA"			""	"celiomycin,florimycin,floromycin,tuberactinomycin b,vinacetin a,vioactane,viomicina,viomycin,viomycine,viomycinum"					"19001-7,23616-6,527-2,528-0,529-8,530-6"
 "VIR"	11979535	"Virginiamycine"	"Other antibacterials"	"NA"			""	"eskalin,eskalin v,micamicina,mikamycin,mikamycine,mikamycinum,ostreogricina,ostreogrycin,ostreogrycine,ostreogrycinum,pristinamicina,pristinamycin,pristinamycine,pristinamycinum,pyostacine,stafac,stafytracine,staphylomycin,stapyocine,starfac,streptogramin,vernamycin,virgimycin,virgimycine,virginiamicina,virginiamycin,virginiamycina,virginiamycine,virginiamycinum"					""
-"VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vrc"	"pfizer,vfend i.v.,voriconazol,voriconazole,voriconazole vfend,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"38370-3,53902-3,73676-9,80553-1,80651-3"
+"VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vrc"	"pfizer,vfend i.v.,voriconazol,voriconazole,voriconazole vfend,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
 "XBR"	72144	"Xibornol"	"Other antibacterials"	"J01XX02"	"Other antibacterials"	"Other antibacterials"	""	"bactacine,bracen,nanbacine,xibornol,xibornolo,xibornolum"					""
 "ZID"	77846445	"Zidebactam"	"Other antibacterials"	"NA"			""	"zidebactam"					""
 "ZFD"		"Zoliflodacin"		"NA"			""	"zoliflodacin"					""

data-raw/antivirals.txt

@@ -1,121 +1,121 @@
 "av"	"name"	"atc"	"cid"	"atc_group"	"synonyms"	"oral_ddd"	"oral_units"	"iv_ddd"	"iv_units"	"loinc"
-"ABA"	"Abacavir"	"J05AF06"	441300	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"abacavir sulfate,avacavir,ziagen"	0.6	"g"			"29113-8,78772-1,78773-9,79134-3,80118-3"
+"ABA"	"Abacavir"	"J05AF06"	441300	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"abacavir sulfate,avacavir,ziagen"	0.6	"g"			"29113-8,30273-7,30287-7,30303-2,78772-1,78773-9,79134-3,80118-3"
 "ACI"	"Aciclovir"	"J05AB01"	135398513	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"acicloftal,aciclovier,aciclovirum,activir,acyclofoam,acycloguanosine,acyclovir,acyclovir lauriad,avaclyr,cargosil,cyclovir,genvir,gerpevir,hascovir,maynar,novirus,poviral,sitavig,sitavir,vipral,viropump,virorax,zovirax,zyclir"	4	"g"	4	"g"	""
 "ADD"	"Adefovir dipivoxil"	"J05AF08"	60871	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"adefovir di,adefovir di ester,adefovir dipivoxyl,adefovir pivoxil,adefovirdipivoxl,bisadenine,bispmea,hepsera,preveon,youheding"	10	"mg"			""
 "AME"	"Amenamevir"	"J05AX26"	11397521	"Other antivirals"	"amenalief"	0.4	"g"			""
-"AMP"	"Amprenavir"	"J05AE05"	65016	"Protease inhibitors"	"agenerase,carbamate,prozei"	1.2	"g"			"29114-6,31028-4,78791-1"
+"AMP"	"Amprenavir"	"J05AE05"	65016	"Protease inhibitors"	"agenerase,carbamate,prozei"	1.2	"g"			"29114-6,30296-8,30297-6,30299-2,31028-4,49623-2,78791-1"
 "ASU"	"Asunaprevir"	"J05AP06"	16076883	"Antivirals for treatment of HCV infections"	"sunvepra,sunvepratrade"	0.2	"g"			""
-"ATA"	"Atazanavir"	"J05AE08"	148192	"Protease inhibitors"	"atazanavir base,latazanavir,reyataz,zrivada"	0.3	"g"			"41470-6,78796-0,78797-8,80142-3,80143-1"
+"ATA"	"Atazanavir"	"J05AE08"	148192	"Protease inhibitors"	"atazanavir base,latazanavir,reyataz,zrivada"	0.3	"g"			"41403-7,41470-6,41993-7,49618-2,49668-7,57907-8,78796-0,78797-8,80142-3,80143-1"
 "ATA+COBI"	"Atazanavir/cobicistat"	"J05AR15"	86583336	"Antivirals for treatment of HIV infections, combinations"	""					""
-"ATA+RIT"	"Atazanavir/ritonavir"	"J05AR23"	25134325	"Antivirals for treatment of HIV infections, combinations"	""	0.3	"g"			""
+"ATA+RIT"	"Atazanavir/ritonavir"	"J05AR23"	25134325	"Antivirals for treatment of HIV infections, combinations"	""	0.3	"g"			"49618-2,57907-8"
 "BAM"	"Baloxavir marboxil"	"J05AX25"	124081896	"Other antivirals"	"xofluza"	40	"mg"			""
-"BOC"	"Boceprevir"	"J05AP03"	10324367	"Antivirals for treatment of HCV infections"	"victrelis"	2.4	"g"			""
+"BOC"	"Boceprevir"	"J05AP03"	10324367	"Antivirals for treatment of HCV infections"	"victrelis"	2.4	"g"			"72859-2"
 "BRIN"	"Brincidofovir"	"J05AB17"	483477	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"cidofovir prodrug,tembexa"					""
 "BRIV"	"Brivudine"	"J05AB15"	446727	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"bridic,brivox,brivudin,brivudina,brivudinum,brvdurd,helpin,zerpex,zostex"	0.125	"g"			""
 "BUL"	"Bulevirtide"	"J05AX28"		"Other antivirals"	""					""
-"CAB"	"Cabotegravir"	"J05AJ04"	54713659	"Integrase inhibitors"	"cabenuva"	30	"mg"	10	"mg"	""
-"CID"	"Cidofovir"	"J05AB12"	60613	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"cidofovir anhydrous,cidofovir gel,cidofovir hydrate,cidofovirum,forvade,hpmpc dihydrate,phosphonic acid,vistide"			25	"mg"	""
+"CAB"	"Cabotegravir"	"J05AJ04"	54713659	"Integrase inhibitors"	"cabenuva"	30	"mg"	10	"mg"	"96566-5"
+"CID"	"Cidofovir"	"J05AB12"	60613	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"cidofovir anhydrous,cidofovir gel,cidofovir hydrate,cidofovirum,forvade,hpmpc dihydrate,phosphonic acid,vistide"			25	"mg"	"33628-9,72855-0,72856-8"
 "CLE"	"Clevudine"	"J05AF12"	73115	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"levovir,revovir"	30	"mg"			""
 "COBL"	"Coblopasvir"	"J05AP12"	58316387	"Antivirals for treatment of HCV infections"	""					""
-"DAC"	"Daclatasvir"	"J05AP07"	25154714	"Antivirals for treatment of HCV infections"	"daklinza"	60	"mg"			""
+"DAC"	"Daclatasvir"	"J05AP07"	25154714	"Antivirals for treatment of HCV infections"	"daklinza"	60	"mg"			"82379-9"
 "DAC+ASU+BEC"	"Daclatasvir/asunaprevir/beclabuvir"	"J05AP58"		"Antivirals for treatment of HCV infections"	""					""
-"DAR"	"Darunavir"	"J05AE10"	213039	"Protease inhibitors"	"carbamate,darunavirum,derunavir,prezista,prezista naive"	1.2	"g"			"57954-0"
+"DAR"	"Darunavir"	"J05AE10"	213039	"Protease inhibitors"	"carbamate,darunavirum,derunavir,prezista,prezista naive"	1.2	"g"			"49630-7,49666-1,55091-3,57954-0,57955-7"
 "DAR+COBI"	"Darunavir/cobicistat"	"J05AR14"	57327017	"Antivirals for treatment of HIV infections, combinations"	""					""
-"DAR+RIT"	"Darunavir/ritonavir"	"J05AR26"		"Antivirals for treatment of HIV infections, combinations"	""					""
+"DAR+RIT"	"Darunavir/ritonavir"	"J05AR26"		"Antivirals for treatment of HIV infections, combinations"	""					"49630-7,57955-7"
 "DAS"	"Dasabuvir"	"J05AP09"	56640146	"Antivirals for treatment of HCV infections"	""	0.5	"g"			""
 "DAS+OMB+PAR+RIT"	"Dasabuvir/ombitasvir/paritaprevir/ritonavir"	"J05AP52"		"Antivirals for treatment of HCV infections"	""					""
-"DEL"	"Delavirdine"	"J05AG02"	5625	"Non-nucleoside reverse transcriptase inhibitors"	"piperazine,rescriptor"	1.2	"g"			"27082-7,29115-3"
-"DID"	"Didanosine"	"J05AF02"	135398739	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"didanosina,didanosinum,dideoxyinosine,hypoxanthine ddn,videx ec"	0.4	"g"			"29116-1,48307-3"
-"DOL"	"Dolutegravir"	"J05AJ03"	54726191	"Integrase inhibitors"	"dolutegravir  dtg,soltegravir,tivicay"	50	"mg"			""
+"DEL"	"Delavirdine"	"J05AG02"	5625	"Non-nucleoside reverse transcriptase inhibitors"	"piperazine,rescriptor"	1.2	"g"			"27082-7,29115-3,30276-0,30290-1,30305-7"
+"DID"	"Didanosine"	"J05AF02"	135398739	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"didanosina,didanosinum,dideoxyinosine,hypoxanthine ddn,videx ec"	0.4	"g"			"29116-1,30270-3,30284-4,30300-8,48307-3"
+"DOL"	"Dolutegravir"	"J05AJ03"	54726191	"Integrase inhibitors"	"dolutegravir  dtg,soltegravir,tivicay"	50	"mg"			"101412-5,72857-6"
 "DOL+RIL"	"Dolutegravir/rilpivirine"	"J05AR21"	131801472	"Antivirals for treatment of HIV infections, combinations"	""					""
-"DOR"	"Doravirine"	"J05AG06"	58460047	"Non-nucleoside reverse transcriptase inhibitors"	"pifeltro"	0.1	"g"			""
-"EFA"	"Efavirenz"	"J05AG03"	64139	"Non-nucleoside reverse transcriptase inhibitors"	"efavirenz teva,efavirenzum,eravirenz,stocrin,strocin,sustiva,viraday"	0.6	"g"			"29117-9,33928-3,51907-4,51908-2"
-"ELB"	"Elbasvir"	"J05AP10"	71661251	"Antivirals for treatment of HCV infections"	"methyl carbamate"	50	"mg"			""
+"DOR"	"Doravirine"	"J05AG06"	58460047	"Non-nucleoside reverse transcriptase inhibitors"	"pifeltro"	0.1	"g"			"91897-9"
+"EFA"	"Efavirenz"	"J05AG03"	64139	"Non-nucleoside reverse transcriptase inhibitors"	"efavirenz teva,efavirenzum,eravirenz,stocrin,strocin,sustiva,viraday"	0.6	"g"			"29117-9,30277-8,30291-9,30306-5,33928-3,51907-4,51908-2"
+"ELB"	"Elbasvir"	"J05AP10"	71661251	"Antivirals for treatment of HCV infections"	"methyl carbamate"	50	"mg"			"82376-5"
 "ELB+GRA"	"Elbasvir/grazoprevir"	"J05AP54"	91669168	"Antivirals for treatment of HCV infections"	"zepatier"					""
-"ELV"	"Elvitegravir"	"J05AJ02"	5277135	"Integrase inhibitors"	"vitekta"					"88986-5"
-"EMT"	"Emtricitabine"	"J05AF09"	60877	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"coviracil,emtricitabinum,emtritabine,emtriva,racivir"	0.2	"g"			""
+"ELV"	"Elvitegravir"	"J05AJ02"	5277135	"Integrase inhibitors"	"vitekta"					"72526-7,88986-5"
+"EMT"	"Emtricitabine"	"J05AF09"	60877	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"coviracil,emtricitabinum,emtritabine,emtriva,racivir"	0.2	"g"			"41402-9,49669-5"
 "EMT+TEA"	"Emtricitabine/tenofovir alafenamide"	"J05AR17"	90469070	"Antivirals for treatment of HIV infections, combinations"	"descovy"					""
 "EMT+TEA+BIC"	"Emtricitabine/tenofovir alafenamide/bictegravir"	"J05AR20"		"Antivirals for treatment of HIV infections, combinations"	""					""
-"EMT+TEA+RIL"	"Emtricitabine/tenofovir alafenamide/rilpivirine"	"J05AR19"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "EMT+TEA+DAR+COBI"	"Emtricitabine/tenofovir alafenamide/darunavir/cobicistat"	"J05AR22"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "EMT+TEA+ELV+COBI"	"Emtricitabine/tenofovir alafenamide/elvitegravir/cobicistat"	"J05AR18"		"Antivirals for treatment of HIV infections, combinations"	""					""
+"EMT+TEA+RIL"	"Emtricitabine/tenofovir alafenamide/rilpivirine"	"J05AR19"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "EMT+TED+EFA"	"Emtricitabine/tenofovir disoproxil/efavirenz"	"J05AR06"		"Antivirals for treatment of HIV infections, combinations"	""					""
-"EMT+TED+RIL"	"Emtricitabine/tenofovir disoproxil/rilpivirine"	"J05AR08"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "EMT+TED+ELV+COBI"	"Emtricitabine/tenofovir disoproxil/elvitegravir/cobicistat"	"J05AR09"		"Antivirals for treatment of HIV infections, combinations"	""					""
-"ENF"	"Enfuvirtide"	"J05AX07"	16130199	"Other antivirals"	"enfurvitide,fuzeon,pentafuside"			0.18	"g"	""
+"EMT+TED+RIL"	"Emtricitabine/tenofovir disoproxil/rilpivirine"	"J05AR08"		"Antivirals for treatment of HIV infections, combinations"	""					""
+"ENF"	"Enfuvirtide"	"J05AX07"	16130199	"Other antivirals"	"enfurvitide,fuzeon,pentafuside"			0.18	"g"	"72858-4,82719-6"
 "ENI"	"Enisamium iodide"	"J05AX17"	10089466	"Other antivirals"	"amizon"	1.5	"g"			""
-"ENT"	"Entecavir"	"J05AF10"	135398508	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"baraclude,entecavir anhydrous"	0.5	"mg"			""
-"ETR"	"Etravirine"	"J05AG04"	193962	"Non-nucleoside reverse transcriptase inhibitors"	"dapy deriv,etravine,intelence"	0.4	"g"			"57961-5"
+"ENT"	"Entecavir"	"J05AF10"	135398508	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"baraclude,entecavir anhydrous"	0.5	"mg"			"56791-7"
+"ETR"	"Etravirine"	"J05AG04"	193962	"Non-nucleoside reverse transcriptase inhibitors"	"dapy deriv,etravine,intelence"	0.4	"g"			"52749-9,57961-5,72558-0"
 "FAL"	"Faldaprevir"	"J05AP04"	42601552	"Antivirals for treatment of HCV infections"	""					""
-"FAM"	"Famciclovir"	"J05AB09"	3324	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"famciclovirum,famvir,oravir"	0.75	"g"			""
+"FAM"	"Famciclovir"	"J05AB09"	3324	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"famciclovirum,famvir,oravir"	0.75	"g"			"72839-4"
 "FAV"	"Favipiravir"	"J05AX27"	492405	"Other antivirals"	"avigan,fapilavir,favilavir"	1.6	"g"			""
-"FOSA"	"Fosamprenavir"	"J05AE07"	131536	"Protease inhibitors"	"amprenavir phosphate,carbamate,lexiva,telzir"	1.4	"g"			""
-"FOSC"	"Foscarnet"	"J05AD01"	3415	"Phosphonic acid derivatives"	"forscarnet,foscarmet,foscavir,phosphonoformate,phosphonoformic acid"			6.5	"g"	""
+"FOSA"	"Fosamprenavir"	"J05AE07"	131536	"Protease inhibitors"	"amprenavir phosphate,carbamate,lexiva,telzir"	1.4	"g"			"42500-9,43736-8,51409-1,57965-6"
+"FOSC"	"Foscarnet"	"J05AD01"	3415	"Phosphonic acid derivatives"	"forscarnet,foscarmet,foscavir,phosphonoformate,phosphonoformic acid"			6.5	"g"	"256-8,42317-8,72834-5"
 "FOSF"	"Fosfonet"	"J05AD02"	546	"Phosphonic acid derivatives"	"fosfonet sodium,fosfonoacetate,fosfonoacetic acid,phosphonacetate,phosphonacetic acid,phosphonoaceticacid"					""
 "FOST"	"Fostemsavir"	"J05AX29"	11319217	"Other antivirals"	"rukobia"	1.2	"g"			""
-"GAN"	"Ganciclovir"	"J05AB06"	135398740	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"citovirax,cymevan,cymeven,cymevene,cytovene,ganciclovirum,gancyclovir,hydroxyacyclovir,virgan,vitrasert,zirgan"	3	"g"	0.5	"g"	"15367-6,25256-9,59798-9,59799-7,60077-5,60078-3"
+"GAN"	"Ganciclovir"	"J05AB06"	135398740	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"citovirax,cymevan,cymeven,cymevene,cytovene,ganciclovirum,gancyclovir,hydroxyacyclovir,virgan,vitrasert,zirgan"	3	"g"	0.5	"g"	"15367-6,25256-9,265-9,59798-9,59799-7,60077-5,60078-3,72854-3,72861-8"
 "GLE+PIB"	"Glecaprevir/pibrentasvir"	"J05AP57"	85471918	"Antivirals for treatment of HCV infections"	""					""
-"GRA"	"Grazoprevir"	"J05AP11"	44603531	"Antivirals for treatment of HCV infections"	""	0.1	"g"			""
+"GRA"	"Grazoprevir"	"J05AP11"	44603531	"Antivirals for treatment of HCV infections"	""	0.1	"g"			"82523-2"
 "IBA"	"Ibalizumab"	"J05AX23"		"Other antivirals"	""					""
 "IDO"	"Idoxuridine"	"J05AB02"	5905	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"antizona,dendrid,heratil,herplex,idossuridina,idoxene,idoxuridin,idoxuridina,idoxuridinum,iduoculos,iduridin,iododeoxyridine,iododeoxyuridine,iodoxuridine,joddeoxiuridin,kerecid,stoxil,virudox"					""
-"IND"	"Indinavir"	"J05AE02"	5362440	"Protease inhibitors"	"compound j,crixivan,indinavir anhydrous,propolis+indinavir"	2.4	"g"			"29118-7,31033-4,51918-1"
+"IND"	"Indinavir"	"J05AE02"	5362440	"Protease inhibitors"	"compound j,crixivan,indinavir anhydrous,propolis+indinavir"	2.4	"g"			"29118-7,30278-6,30292-7,30307-3,31033-4,49619-0,51918-1,57984-7"
 "INP"	"Inosine pranobex"	"J05AX05"	135449284	"Other antivirals"	"aviral,delimmun,groprinosin,immunovir,imunovir,imunoviral,inosiplex,isoprinosin,isoprinosina,isoprinosine,isoviral,methisoprinol,modimmunal,pranosina,pranosine,viruxan"	3	"g"			""
-"LAM"	"Lamivudine"	"J05AF05"	60825	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"epivir,hepitec,heptivir,heptodin,heptovir,lamivir,lamivudeine,lamivudine teva,lamivudinum,virolam,zeffix"	0.3	"g"			"29119-5,49226-4"
+"LAM"	"Lamivudine"	"J05AF05"	60825	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"epivir,hepitec,heptivir,heptodin,heptovir,lamivir,lamivudeine,lamivudine teva,lamivudinum,virolam,zeffix"	0.3	"g"			"29119-5,30269-5,30283-6,30298-4,49226-4,49620-8"
 "LAM+ABA"	"Lamivudine/abacavir"	"J05AR02"		"Antivirals for treatment of HIV infections, combinations"	""					""
+"LAM+ABA+DOL"	"Lamivudine/abacavir/dolutegravir"	"J05AR13"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+DOL"	"Lamivudine/dolutegravir"	"J05AR25"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+RAL"	"Lamivudine/raltegravir"	"J05AR16"	73386700	"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+TED"	"Lamivudine/tenofovir disoproxil"	"J05AR12"		"Antivirals for treatment of HIV infections, combinations"	""					""
-"LAM+ABA+DOL"	"Lamivudine/abacavir/dolutegravir"	"J05AR13"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+TED+DOL"	"Lamivudine/tenofovir disoproxil/dolutegravir"	"J05AR27"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+TED+DOR"	"Lamivudine/tenofovir disoproxil/doravirine"	"J05AR24"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAM+TED+EFA"	"Lamivudine/tenofovir disoproxil/efavirenz"	"J05AR11"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "LAN"	"Laninamivir"	"J05AH04"	502272	"Neuraminidase inhibitors"	""					""
 "LEN"	"Lenacapavir"	"J05AX31"	133082658	"Other antivirals"	""					""
 "LET"	"Letermovir"	"J05AX18"	45138674	"Other antivirals"	"acetic acid,prevymis"	0.48	"g"	0.48	"g"	""
-"LOP+RIT"	"Lopinavir/ritonavir"	"J05AR10"	11979606	"Antivirals for treatment of HIV infections, combinations"	"aluvia,kaletra,lopimune"	0.8	"g"			""
+"LOP+RIT"	"Lopinavir/ritonavir"	"J05AR10"	11979606	"Antivirals for treatment of HIV infections, combinations"	"aluvia,kaletra,lopimune"	0.8	"g"			"42000-0,57997-9"
 "LYS"	"Lysozyme"	"J05AX02"	16130991	"Other antivirals"	""					""
 "MARA"	"Maraviroc"	"J05AX09"	3002977	"Other antivirals"	"celsentri,selzentry"	0.6	"g"			"88987-3"
-"MARI"	"Maribavir"	"J05AX10"	471161	"Other antivirals"	"benzimidavir,camvia"					""
+"MARI"	"Maribavir"	"J05AX10"	471161	"Other antivirals"	"benzimidavir,camvia"					"72853-5"
 "MET"	"Metisazone"	"J05AA01"	667492	"Thiosemicarbazones"	"kemoviran,marboran,marborane,methisazon,methisazone,methsazone,metisazon,metisazona,metisazonum,viruzona"					""
 "MOR"	"Moroxydine"	"J05AX01"	71655	"Other antivirals"	"bimolin,moroxidina,moroxydinum,virugon,virumin,wirumin"	0.3	"g"			""
-"NEL"	"Nelfinavir"	"J05AE04"	64143	"Protease inhibitors"	"viracept"	2.25	"g"			"29120-3,32647-0,35113-0,51923-1"
-"NEV"	"Nevirapine"	"J05AG01"	4463	"Non-nucleoside reverse transcriptase inhibitors"	"nevirapine anhydrous,nevirapine teva,nevirapine),viramune,viramune ir,viramune xr"	0.4	"g"			"29121-1,32646-2,51925-6"
+"NEL"	"Nelfinavir"	"J05AE04"	64143	"Protease inhibitors"	"viracept"	2.25	"g"			"29120-3,30280-2,30294-3,30309-9,32647-0,35113-0,51923-1"
+"NEV"	"Nevirapine"	"J05AG01"	4463	"Non-nucleoside reverse transcriptase inhibitors"	"nevirapine anhydrous,nevirapine teva,nevirapine),viramune,viramune ir,viramune xr"	0.4	"g"			"29121-1,30275-2,30289-3,30311-5,32646-2,51925-6"
 "OMB+PAR+RIT"	"Ombitasvir/paritaprevir/ritonavir"	"J05AP53"		"Antivirals for treatment of HCV infections"	""					""
-"OSE"	"Oseltamivir"	"J05AH02"	65028	"Neuraminidase inhibitors"	"agucort,tamiflu,tamvir"	0.15	"g"			""
+"OSE"	"Oseltamivir"	"J05AH02"	65028	"Neuraminidase inhibitors"	"agucort,tamiflu,tamvir"	0.15	"g"			"60440-5,60441-3"
 "PEN"	"Penciclovir"	"J05AB13"	135398748	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"adenovir,denavir,penciceovir,penciclovirum,pencyclovir,vectavir"					"60140-1,60141-9"
 "PAIE"	"Pentanedioic acid imidazolyl ethanamide"	"J05AX21"	9942657	"Other antivirals"	"ingamine"	90	"mg"			""
 "PER"	"Peramivir"	"J05AH03"	154234	"Neuraminidase inhibitors"	"peramiflu,peramivir anhydrous,rapiacta,rapivab"			0.6	"g"	""
 "PLE"	"Pleconaril"	"J05AX06"	1684	"Other antivirals"	"picovir,pleconarilis"					""
-"RAL"	"Raltegravir"	"J05AJ01"	54671008	"Integrase inhibitors"	"isentress"	0.8	"g"			"72835-2"
+"RAL"	"Raltegravir"	"J05AJ01"	54671008	"Integrase inhibitors"	"isentress"	0.8	"g"			"61198-8,72525-9,72835-2"
 "REM"	"Remdesivir"	"J05AB16"	121304016	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"veklury"			0.1	"g"	""
 "RIB"	"Ribavirin"	"J05AP01"	37542	"Antivirals for treatment of HCV infections"	"copegus,cotronak,ravanex,rebetol,rebetron,rebretron,ribacine,ribamide,ribamidil,ribamidyl,ribasphere,ribavirin capsules,ribavirin mylan,ribavirin teva,ribavirina,ribavirine,ribavirinum,tribavirin,varazid,vilona,viramid,virazid,virazide,virazole"	1	"g"			"41469-8"
-"RIL"	"Rilpivirine"	"J05AG05"	6451164	"Non-nucleoside reverse transcriptase inhibitors"	"edurant,rilpivirina"	25	"mg"	15	"mg"	"80547-3"
+"RIL"	"Rilpivirine"	"J05AG05"	6451164	"Non-nucleoside reverse transcriptase inhibitors"	"edurant,rilpivirina"	25	"mg"	15	"mg"	"68463-9,72557-2,80547-3"
 "RIM"	"Rimantadine"	"J05AC02"	5071	"Cyclic amines"	"ethanamine,rimant,rimantadin,rimantadin a,rimantadina,rimantadinum"	0.2	"g"			""
-"RIT"	"Ritonavir"	"J05AE03"	392622	"Protease inhibitors"	"empetus,norvir,norvir softgel,ritomune,ritonavirum,ritovir,viekirax,viriton"	1.2	"g"			"29122-9,31027-6,51929-8,51930-6"
-"SAQ"	"Saquinavir"	"J05AE01"	441243	"Protease inhibitors"	"fortovase,invirase,saquinavirum"	1.8	"g"			"19051-2,29123-7,51932-2"
-"SIM"	"Simeprevir"	"J05AP05"	24873435	"Antivirals for treatment of HCV infections"	"olysio,simeprevir sodium"	0.15	"g"			""
-"SOF"	"Sofosbuvir"	"J05AP08"	45375808	"Antivirals for treatment of HCV infections"	"hepcinat,hepcvir,sovaldi,sovihep"	0.4	"g"			""
+"RIT"	"Ritonavir"	"J05AE03"	392622	"Protease inhibitors"	"empetus,norvir,norvir softgel,ritomune,ritonavirum,ritovir,viekirax,viriton"	1.2	"g"			"29122-9,30279-4,30293-5,30308-1,31027-6,51929-8,51930-6"
+"SAQ"	"Saquinavir"	"J05AE01"	441243	"Protease inhibitors"	"fortovase,invirase,saquinavirum"	1.8	"g"			"19051-2,29123-7,30281-0,30295-0,30310-7,49621-6,51932-2,58024-1"
+"SIM"	"Simeprevir"	"J05AP05"	24873435	"Antivirals for treatment of HCV infections"	"olysio,simeprevir sodium"	0.15	"g"			"82522-4"
+"SOF"	"Sofosbuvir"	"J05AP08"	45375808	"Antivirals for treatment of HCV infections"	"hepcinat,hepcvir,sovaldi,sovihep"	0.4	"g"			"82382-3"
 "SOF+LED"	"Sofosbuvir/ledipasvir"	"J05AP51"	72734365	"Antivirals for treatment of HCV infections"	"harvoni"					""
 "SOF+VEL"	"Sofosbuvir/velpatasvir"	"J05AP55"	91885554	"Antivirals for treatment of HCV infections"	"epclusa,epclusa tablet"					""
 "SOF+VEL+VOX"	"Sofosbuvir/velpatasvir/voxilaprevir"	"J05AP56"		"Antivirals for treatment of HCV infections"	""					""
-"STA"	"Stavudine"	"J05AF04"	18283	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"estavudina,sanilvudine,stavudinum,zerit xr,zerut xr"	80	"mg"			"29124-5,49227-2"
+"STA"	"Stavudine"	"J05AF04"	18283	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"estavudina,sanilvudine,stavudinum,zerit xr,zerut xr"	80	"mg"			"29124-5,30272-9,30286-9,30302-4,49227-2"
 "STA+LAM+NEV"	"Stavudine/lamivudine/nevirapine"	"J05AR07"	15979285	"Antivirals for treatment of HIV infections, combinations"	""					""
 "TEC"	"Tecovirimat"	"J05AX24"	16124688	"Other antivirals"	""					""
-"TELA"	"Telaprevir"	"J05AP02"	3010818	"Antivirals for treatment of HCV infections"	"incivek,incivo,telavic"	2.25	"g"			""
-"TELB"	"Telbivudine"	"J05AF11"	159269	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"epavudine,sebivo,telbivudin,tyzeka"	0.6	"g"			""
+"TELA"	"Telaprevir"	"J05AP02"	3010818	"Antivirals for treatment of HCV infections"	"incivek,incivo,telavic"	2.25	"g"			"72860-0"
+"TELB"	"Telbivudine"	"J05AF11"	159269	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"epavudine,sebivo,telbivudin,tyzeka"	0.6	"g"			"56792-5"
 "TEA"	"Tenofovir alafenamide"	"J05AF13"	9574768	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"vemlidy"	25	"mg"			""
 "TED"	"Tenofovir disoproxil"	"J05AF07"	5481350	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"bispmpa,pmpa prodrug,tenofovir,tenofovir bis,tenofovirdisoproxil,viread"	0.245	"g"			""
 "TED+EMT"	"Tenofovir disoproxil/emtricitabine"	"J05AR03"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "TIL"	"Tilorone"	"J05AX19"	5475	"Other antivirals"	"amixin ic,tiloron,tilorona,tiloronum"	0.125	"g"			""
-"TIP"	"Tipranavir"	"J05AE09"	54682461	"Protease inhibitors"	"aptivus"	1	"g"			"57383-2"
+"TIP"	"Tipranavir"	"J05AE09"	54682461	"Protease inhibitors"	"aptivus"	1	"g"			"42535-5,43737-6,49622-4,49667-9,57383-2,58029-0"
 "TRO"	"Tromantadine"	"J05AC03"	64377	"Cyclic amines"	"tromantadina,tromantadinum"					""
 "UMI"	"Umifenovir"	"J05AX13"	131411	"Other antivirals"	"arbidol,arbidol base"	0.8	"g"			""
 "VALA"	"Valaciclovir"	"J05AB11"	135398742	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"talavir,valacv,valacyclovir,valcivir,valcyclovir,valtrex,virval,zelitrex"	3	"g"			""
 "VALG"	"Valganciclovir"	"J05AB14"	135413535	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"cymeval"	0.9	"g"			"74960-6"
 "VID"	"Vidarabine"	"J05AB03"	21704	"Nucleosides and nucleotides excl. reverse transcriptase inhibitors"	"adenine arabinoside,araadenosine,arabinoside adenine,arabinosyl adenine,arabinosyladenine,spongoadenosine,vidarabin,vidarabina,vidarabine anhydrous,vidarabinum,vira a,vira atm"			0.7	"g"	""
-"ZAL"	"Zalcitabine"	"J05AF03"	24066	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"dideoxycytidine,interferon ad + ddc,zalcitibine"	2.25	"mg"			"29125-2"
-"ZAN"	"Zanamivir"	"J05AH01"	60855	"Neuraminidase inhibitors"	"modified sialic acid,relenza,zanamavir,zanamivi,zanamivirhydrate"			1.2	"g"	""
-"ZID"	"Zidovudine"	"J05AF01"	35370	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"azidothymidine,beta interferon,compound s,propolis+azt,retrovir,trizivir,zidovudina,zidovudinum"	0.6	"g"	0.6	"g"	"29126-0,6894-0"
+"ZAL"	"Zalcitabine"	"J05AF03"	24066	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"dideoxycytidine,interferon ad + ddc,zalcitibine"	2.25	"mg"			"29125-2,30271-1,30285-1,30301-6"
+"ZAN"	"Zanamivir"	"J05AH01"	60855	"Neuraminidase inhibitors"	"modified sialic acid,relenza,zanamavir,zanamivi,zanamivirhydrate"			1.2	"g"	"75029-9"
+"ZID"	"Zidovudine"	"J05AF01"	35370	"Nucleoside and nucleotide reverse transcriptase inhibitors"	"azidothymidine,beta interferon,compound s,propolis+azt,retrovir,trizivir,zidovudina,zidovudinum"	0.6	"g"	0.6	"g"	"29126-0,30268-7,30282-8,531-4,6894-0"
 "ZID+LAM"	"Zidovudine/lamivudine"	"J05AR01"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "ZID+LAM+ABA"	"Zidovudine/lamivudine/abacavir"	"J05AR04"		"Antivirals for treatment of HIV infections, combinations"	""					""
 "ZID+LAM+NEV"	"Zidovudine/lamivudine/nevirapine"	"J05AR05"		"Antivirals for treatment of HIV infections, combinations"	""					""

data-raw/av.md5

@@ -1 +1 @@
-009fea3738cdb6390dccd470cb27f015
+1bb751091ed77d3d8c8c0ccad3583483

data-raw/clin_break.md5

@@ -1 +1 @@
-b0c1c3ddb9f8a23aedff6208e9f8d32a
+25f9e2b995124710eb121cc4e62eba16

data-raw/eucast_rules.tsv

@@ -2,7 +2,7 @@
 # For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
 # aminoglycosides, aminopenicillins, antifungals, antimycobacterials, betalactams, carbapenems, cephalosporins, cephalosporins_1st, cephalosporins_2nd, cephalosporins_3rd, cephalosporins_4th, cephalosporins_5th, cephalosporins_except_CAZ, fluoroquinolones, glycopeptides, glycopeptides_except_lipo, lincosamides, lipoglycopeptides, macrolides, oxazolidinones, penicillins, polymyxins, quinolones, streptogramins, tetracyclines, tetracyclines_except_TGC, trimethoprims, ureidopenicillins
 # and all separate EARS-Net letter codes such as AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
-# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
+# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or 'genus_species' or 'gramstain'.
 # 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 and later
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 9 LINES SKIPPED <<<<<

data-raw/extractATCs.R

@@ -4,7 +4,7 @@ library(tidyr)
 library(AMR)
 # we need J01, J02 and J04 (J03 does not exist)
 
-url <- "https://www.whocc.no/atc_ddd_index/?code={code}&showdescription=no"
+url <- "https://atcddd.fhi.no/atc_ddd_index/?code={code}&showdescription=no"
 complete_vector <- character(0)
 for (Jxx in c("J01", "J02", "J04")) {
   site <- gsub("{code}", Jxx, url, fixed = TRUE)

data-raw/loinc.R

@@ -31,8 +31,8 @@
 
 # Steps to reproduce:
 # 1. Create a fake account at https://loinc.org (sad you have to create one...)
-# 2. Download the CSV from https://loinc.org/download/loinc-complete/ (Loinc_2.67_Text_2.67.zip)
-# 3. Read Loinc.csv that's in zip folder LoincTable
+# 2. Download the CSV from https://loinc.org/download/loinc-complete/ 
+# 3. Read file LoincTable/Loinc.csv
 loinc_df <- read.csv("data-raw/Loinc.csv",
   row.names = NULL,
   stringsAsFactors = FALSE
@@ -42,31 +42,62 @@ loinc_df <- read.csv("data-raw/Loinc.csv",
 library(dplyr)
 library(cleaner)
 library(AMR)
-loinc_df %>% freq(CLASS) # to find the drugs
-loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
-ab_names <- antibiotics %>%
-  pull(name) %>%
-  paste0(collapse = "|") %>%
-  paste0("(", ., ")")
+# to find the drugs:
+loinc_df %>%
+  filter(COMPONENT %like% "ampicillin|fluconazol|meropenem") %>%
+  count(CLASS, sort = TRUE)
+loinc_df <- loinc_df %>%
+  filter(CLASS %in% c("DRUG/TOX", "ABXBACT")) %>% 
+  mutate(name = generalise_antibiotic_name(COMPONENT), .before = 1)
 
+# antibiotics
 antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
 for (i in seq_len(nrow(antibiotics))) {
   message(i)
   loinc_ab <- loinc_df %>%
-    filter(COMPONENT %like% paste0("^", antibiotics$name[i])) %>%
+    filter(name %like% paste0("^", generalise_antibiotic_name(antibiotics$name[i]))) %>%
     pull(LOINC_NUM)
   if (length(loinc_ab) > 0) {
     antibiotics$loinc[i] <- list(loinc_ab)
   }
 }
+
+# antivirals
+antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
+for (i in seq_len(nrow(antivirals))) {
+  message(i)
+  loinc_ab <- loinc_df %>%
+    filter(name %like% paste0("^", generalise_antibiotic_name(antivirals$name[i]))) %>%
+    pull(LOINC_NUM)
+  if (length(loinc_ab) > 0) {
+    antivirals$loinc[i] <- list(loinc_ab)
+  }
+}
+
 # sort and fix for empty values
 for (i in 1:nrow(antibiotics)) {
-  loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
-  antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
+  loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc", drop = TRUE][[1]]))))
+  loinc <- loinc[loinc != ""]
+  antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
 }
+for (i in 1:nrow(antivirals)) {
+  loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
+  loinc <- loinc[loinc != ""]
+  antivirals[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
+}
+
+antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE))
+antibiotics <- dplyr::arrange(antibiotics, name)
+
+antivirals <- dataset_UTF8_to_ASCII(as.data.frame(antivirals, stringsAsFactors = FALSE))
+antivirals <- dplyr::arrange(antivirals, name)
 
 # remember to update R/aa_globals.R for the documentation
 
 dim(antibiotics) # for R/data.R
-usethis::use_data(antibiotics, overwrite = TRUE)
+usethis::use_data(antibiotics, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
 rm(antibiotics)
+
+dim(antivirals) # for R/data.R
+usethis::use_data(antivirals, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
+rm(antivirals)

data-raw/reproduction_of_antibiotics.R

@@ -754,12 +754,20 @@ antibiotics <- antibiotics %>%
 
 # update ATC codes from WHOCC website -------------------------------------
 
-# last time checked: 2022-10-29
+# last time checked: 2024-02-22
 
 library(rvest)
 updated_atc <- as.list(antibiotics$atc)
 
-get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
+get_atcs <- function(ab_name, type = "human") {
+  if (type == "human") {
+    url <- "https://atcddd.fhi.no/atc_ddd_index/"
+  } else if (type == "veterinary") {
+    url <- "https://atcddd.fhi.no/atcvet/atcvet_index/"  
+  } else {
+    stop("invalid type")
+  }
+  
   ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
 
   # we will do a search on their website, which means:
@@ -780,6 +788,7 @@ get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
     html_node("table") %>%
     # transform it to an R data set
     html_table(header = FALSE)
+  
   # and get the ATCs (first column) of only exact hits
   unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE]))
 }
@@ -790,7 +799,10 @@ for (i in seq_len(nrow(antibiotics))) {
     " - Downloading ", antibiotics$name[i],
     appendLF = FALSE
   )
-  atcs <- get_atcs(antibiotics$name[i])
+  atcs <- get_atcs(antibiotics$name[i], type = "human")
+  if (all(is.na(atcs))) {
+    atcs <- get_atcs(antibiotics$name[i], type = "veterinary")
+  }
   if (length(atcs) > 0) {
     updated_atc[[i]] <- atcs
     message(" (", length(atcs), " results)")
@@ -805,7 +817,7 @@ antibiotics$atc <- updated_atc
 
 # update DDDs from WHOCC website ------------------------------------------
 
-# last time checked: 2022-10-29
+# last time checked: 2024-02-22
 ddd_oral <- rep(NA_real_, nrow(antibiotics))
 ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
 ddd_iv <- rep(NA_real_, nrow(antibiotics))
@@ -851,6 +863,8 @@ antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors
 class(antibiotics$ab) <- c("ab", "character")
 antibiotics <- dplyr::arrange(antibiotics, name)
 
+# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
+
 # make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
 for (i in 1:nrow(antibiotics)) {
   abb <- as.character(sort(unique(tolower(antibiotics[i, "abbreviations", drop = TRUE][[1]]))))
@@ -866,7 +880,6 @@ for (i in 1:nrow(antibiotics)) {
   }
 }
 
-# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
 
 usethis::use_data(antibiotics, overwrite = TRUE, version = 2, compress = "xz")
 rm(antibiotics)

data-raw/reproduction_of_antivirals.R

@@ -34,7 +34,7 @@ library(rvest)
 # get all data from the WHOCC website
 get_atc_table <- function(atc_group) {
   # give as input J0XXX, like atc_group = "J05AB"
-  downloaded <- read_html(paste0("https://www.whocc.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
+  downloaded <- read_html(paste0("https://atcddd.fhi.no/atc_ddd_index/?code=", atc_group, "&showdescription=no"))
   table_title <- downloaded %>%
     html_nodes(paste0('a[href^="./?code=', atc_group, '&"]')) %>%
     html_text()
@@ -62,7 +62,7 @@ get_atc_table <- function(atc_group) {
   )
 }
 
-# these are the relevant groups for input: https://www.whocc.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
+# these are the relevant groups for input: https://atcddd.fhi.no/atc_ddd_index/?code=J05A (J05 only contains J05A)
 atc_groups <- c("J05AA", "J05AB", "J05AC", "J05AD", "J05AE", "J05AF", "J05AG", "J05AH", "J05AJ", "J05AP", "J05AR", "J05AX")
 
 # get the first
@@ -142,33 +142,7 @@ antivirals <- bind_cols(
 class(antivirals$av) <- c("av", "character")
 antivirals <- antivirals %>% AMR:::dataset_UTF8_to_ASCII()
 
-# add loinc, see 'data-raw/loinc.R'
-loinc_df <- read.csv("data-raw/Loinc.csv",
-  row.names = NULL,
-  stringsAsFactors = FALSE
-)
-
-loinc_df <- loinc_df %>% filter(CLASS == "DRUG/TOX")
-av_names <- antivirals %>%
-  pull(name) %>%
-  paste0(collapse = "|") %>%
-  paste0("(", ., ")")
-
-antivirals$loinc <- as.list(rep(NA_character_, nrow(antivirals)))
-for (i in seq_len(nrow(antivirals))) {
-  message(i)
-  loinc_ab <- loinc_df %>%
-    filter(COMPONENT %like% paste0("^", antivirals$name[i])) %>%
-    pull(LOINC_NUM)
-  if (length(loinc_ab) > 0) {
-    antivirals$loinc[i] <- list(loinc_ab)
-  }
-}
-# sort and fix for empty values
-for (i in 1:nrow(antivirals)) {
-  loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
-  antivirals[i, "loinc"][[1]] <- ifelse(length(loinc[!loinc == ""]) == 0, list(""), list(loinc))
-}
+# ! add loinc, run 'data-raw/loinc.R' !
 
 # de-duplicate synonyms
 for (i in 1:nrow(antivirals)) {

data-raw/reproduction_of_clinical_breakpoints.R

@@ -192,7 +192,7 @@ devtools::load_all()
 
 # BREAKPOINTS ----
 
-# now that we have the right MO codes, get the breakpoints and convert them
+# now that we have the correct MO codes, get the breakpoints and convert them
 
 whonet_breakpoints %>% 
   count(GUIDELINES, BREAKPOINT_TYPE) %>% 
@@ -213,7 +213,10 @@ unknown <- breakpoints %>%
 breakpoints %>% 
   filter(code %in% unknown) %>% 
   count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
-# these codes are currently (2023-07-08): clu, kma. No clue, so remove them:
+# 2024-02-22: clu and kma are know (see below), fix the PBI one
+breakpoints$mo[breakpoints$ORGANISM_CODE == "PBI"] <- as.mo("Parabacteroides")
+breakpoints$ORGANISM_CODE[breakpoints$ORGANISM_CODE == "PBI"] <- "Parabacteroides"
+# 2023-07-08: these codes are currently: clu, kma. No clue (are not in MO list of WHONET), so remove them:
 breakpoints <- breakpoints %>% 
   filter(!is.na(mo))
 
@@ -236,6 +239,7 @@ breakpoints_new <- breakpoints %>%
   transmute(
     guideline = paste(GUIDELINES, YEAR),
     type = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(BREAKPOINT_TYPE)),
+    host = ifelse(BREAKPOINT_TYPE == "ECOFF", "ECOFF", tolower(HOST)),
     method = TEST_METHOD,
     site = SITE_OF_INFECTION,
     mo,
@@ -263,15 +267,15 @@ breakpoints_new <- breakpoints %>%
     gsub("–", "-", ., fixed = TRUE)) %>%
   arrange(desc(guideline), mo, ab, type, method) %>%
   filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
-  distinct(guideline, type, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
+  distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
 
 # check the strange duplicates
 breakpoints_new %>% 
-  mutate(id = paste(guideline, type, ab, mo, method, site)) %>% 
+  mutate(id = paste(guideline, type, host, ab, mo, method, site)) %>% 
   filter(id %in% .$id[which(duplicated(id))])
 # remove duplicates
 breakpoints_new <- breakpoints_new %>% 
-  distinct(guideline, type, ab, mo, method, site, .keep_all = TRUE)
+  distinct(guideline, type, host, ab, mo, method, site, .keep_all = TRUE)
 
 # fix reference table names
 breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
@@ -284,6 +288,13 @@ breakpoints_new <- breakpoints_new %>%
 breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_S", drop = TRUE]))
 breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.double(as.disk(breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R", drop = TRUE]))
 
+# regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - remove them
+breakpoints_new <- breakpoints_new |> 
+  filter(host %unlike% "foal") |> 
+  mutate(host = ifelse(host %like% "horse", "horse", host))
+
+# FIXES FOR WHONET ERRORS ----
+
 # WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
 # instead, clean based on MIC factor levels
 m <- unique(as.double(as.mic(levels(as.mic(1)))))
@@ -298,25 +309,29 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 5
 breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
 
 # fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
-clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
+breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
 # Haemophilus same error (must only be H. influenzae)
-clinical_breakpoints$mo[clinical_breakpoints$mo == "B_HMPHL" & clinical_breakpoints$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
+breakpoints_new$mo[breakpoints_new$mo == "B_HMPHL" & breakpoints_new$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
 # EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
-clinical_breakpoints <- clinical_breakpoints %>% 
+breakpoints_new <- breakpoints_new %>% 
   bind_rows(
-    clinical_breakpoints %>%
+    breakpoints_new %>%
       filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>% 
       mutate(mo = as.mo("B_HMPHL_PRNF"))
   ) %>% 
-  arrange(desc(guideline), mo, ab, type, method)
+  arrange(desc(guideline), mo, ab, type, host, method)
 # Achromobacter denitrificans is in WHONET included in their A. xylosoxidans table, must be removed
-clinical_breakpoints <- clinical_breakpoints %>% filter(mo != as.mo("Achromobacter denitrificans"))
+breakpoints_new <- breakpoints_new %>% filter(mo != as.mo("Achromobacter denitrificans"))
 # WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
-clinical_breakpoints <- clinical_breakpoints %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
+breakpoints_new <- breakpoints_new %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
 # Nitrofurantoin in Staph (EUCAST) only applies to S. saprophyticus, while WHONET has the DISK correct but the MIC on genus level
-clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STPHY" & clinical_breakpoints$ab == "NIT" & clinical_breakpoints$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
-# determine rank again
-clinical_breakpoints <- clinical_breakpoints %>% 
+breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT" & breakpoints_new$guideline %like% "EUCAST"] <- as.mo("B_STPHY_SPRP")
+# WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
+# UPDATE 2024-02-22: fixed now
+# breakpoints_new$breakpoint_S[breakpoints_new$mo == "B_[ORD]_ENTRBCTR" & breakpoints_new$ab == "SAM" & breakpoints_new$guideline %like% "CLSI 2023" & breakpoints_new$method == "MIC"] <- 8
+
+# determine rank again now that some changes were made on taxonomic level (genus -> species)
+breakpoints_new <- breakpoints_new %>% 
   mutate(rank_index = case_when(
     is.na(mo_rank(mo, keep_synonyms = TRUE)) ~ 6, # for UNKNOWN, B_GRAMN, B_ANAER, B_ANAER-NEG, etc.
     mo_rank(mo, keep_synonyms = TRUE) %like% "(infra|sub)" ~ 1,
@@ -328,12 +343,11 @@ clinical_breakpoints <- clinical_breakpoints %>%
     TRUE ~ 6
   ))
 
-
 # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
 # EUCAST 2022 guideline: S <= 8 and R > 8
 #           WHONET file: S <= 8 and R >= 16
 breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
-# this will make an MIC of 12 I, which should be R, so:
+# this will make an MIC of 12 I, which should be R according to EUCAST, so:
 breakpoints_new <- breakpoints_new %>%
   mutate(breakpoint_R = ifelse(guideline %like% "EUCAST" & method == "MIC" & log2(breakpoint_R) - log2(breakpoint_S) != 0,
     pmax(breakpoint_S, breakpoint_R / 2),
@@ -346,9 +360,12 @@ breakpoints_new <- breakpoints_new %>%
     breakpoint_R + 1,
     breakpoint_R
   ))
-# fix missing R breakpoint where there is an S breakpoint
+# fill missing R breakpoint where there is an S breakpoint
 breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
 
+
+# CHECKS AND SAVE TO PACKAGE ----
+
 # check again
 breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 # compare with current version
@@ -361,8 +378,6 @@ breakpoints_new %>% filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCA
 dim(breakpoints_new)
 dim(clinical_breakpoints)
 
-# SAVE TO PACKAGE ----
-
 clinical_breakpoints <- breakpoints_new
 clinical_breakpoints <- clinical_breakpoints %>% dataset_UTF8_to_ASCII()
 usethis::use_data(clinical_breakpoints, overwrite = TRUE, compress = "xz", version = 2)

data-raw/reproduction_of_microorganisms.R

@@ -150,12 +150,14 @@ df_remove_nonASCII <- function(df) {
 
 # to retrieve LPSN and authors from LPSN website
 get_lpsn_and_author <- function(rank, name) {
+  name <- gsub("^Candidatus ", "", name)
   url <- paste0("https://lpsn.dsmz.de/", tolower(rank), "/", tolower(name))
   page_txt <- tryCatch(read_html(url), error = function(e) NULL)
   if (is.null(page_txt)) {
     warning("No LPSN found for ", tolower(rank), " '", name, "'")
     lpsn <- NA_character_
     ref <- NA_character_
+    status <- "unknown"
   } else {
     page_txt <- page_txt %>%
       html_element("#detail-page") %>%
@@ -164,9 +166,33 @@ get_lpsn_and_author <- function(rank, name) {
     ref <- page_txt %>%
       gsub(".*?Name: (.*[0-9]{4}?).*", "\\1", ., perl = FALSE) %>%
       gsub(name, "", ., fixed = TRUE) %>%
+      gsub("^\"?Candidatus ?\"?", "", .) %>%
       trimws()
+    status <- trimws(gsub(".*Nomenclatural status:[\r\n\t ]*([a-zA-Z, ]+)[\r\n\t].*", "\\1", page_txt, perl = FALSE))
+    if ((status %like% "validly published" & status %unlike% "not valid") | status %like% "[\r\n\t]") {
+      # we used to take "accepted" for every LPSN record, also candidates. Now only for missing values and explicit accepted ones.
+      status <- "accepted"
+    } else {
+      status <- "not validly published"
+    }
+  }
+  c("lpsn" = lpsn, "ref" = ref, "status" = status)
+}
+
+# this will e.g. take the family from the root genus record, and gives all species that family
+get_top_lvl <- function(current, rank, rank_target) {
+  if (!rank_target %in% rank) {
+    current[1]
+  } else {
+    out <- current[rank == rank_target][1]
+    if (out %in% c("", NA)) {
+      out <- names(sort(table(current[which(!current %in% c("", NA))]), decreasing = TRUE)[1])
+      if (is.null(out)) {
+        out <- ""
+      }
+    }
+    out
   }
-  c("lpsn" = lpsn, "ref" = ref)
 }
 
 # MB/ August 2022: useless, does not contain full taxonomy, e.g. LPSN::request(cred, category = "family") is empty.
@@ -208,11 +234,12 @@ include_fungal_orders_ids <- taxonomy_gbif.bak %>%
 include_fungal_orders <- taxonomy_gbif.bak %>%
   filter(taxonID %in% c(include_fungal_orders_ids$taxonID, include_fungal_orders_ids$acceptedNameUsageID)) %>%
   distinct(order) %>%
-  pull(order)
+  pull(order) |> 
+  sort()
 
 # check some columns to validate below filters
-sort(table(taxonomy_gbif.bak$taxonomicStatus))
-sort(table(taxonomy_gbif.bak$taxonRank))
+taxonomy_gbif.bak$taxonomicStatus |> table() |> sort() |> as.data.frame()
+taxonomy_gbif.bak$taxonRank |> table() |> sort() |> as.data.frame()
 
 taxonomy_gbif <- taxonomy_gbif.bak %>%
   # immediately filter rows we really never want
@@ -223,10 +250,7 @@ taxonomy_gbif <- taxonomy_gbif.bak %>%
     #  include these kingdoms (no Chromista)
     kingdom %in% c("Archaea", "Bacteria", "Protozoa") |
       # include all of these fungal orders
-      order %in% c(
-        "Eurotiales", "Microascales", "Mucorales", "Saccharomycetales",
-        "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"
-      ) |
+      order %in% include_fungal_orders |
       # and all of these important genera (see "data-raw/_pre_commit_hook.R")
       # (they also contain bacteria and protozoa, but these will get prevalence = 2 later on)
       genus %in% AMR:::MO_PREVALENT_GENERA
@@ -289,9 +313,6 @@ taxonomy_gbif
 
 taxonomy_lpsn.bak <- vroom(file_lpsn)
 
-# check some columns to validate below filters
-sort(table(is.na(taxonomy_lpsn.bak$record_lnk))) # accepted = TRUE
-
 taxonomy_lpsn <- taxonomy_lpsn.bak %>%
   transmute(
     genus = genus_name,
@@ -309,6 +330,10 @@ taxonomy_lpsn <- taxonomy_lpsn.bak %>%
     lpsn_renamed_to = as.character(record_lnk)
   ) %>%
   mutate(source = "LPSN")
+
+# integrity tests
+sort(table(taxonomy_lpsn$rank))
+sort(table(taxonomy_lpsn$status))
 taxonomy_lpsn
 
 # download additional taxonomy to the domain/kingdom level (their API is not sufficient...)
@@ -322,17 +347,22 @@ taxonomy_lpsn_missing <- tibble(
 )
 for (page in LETTERS) {
   # this will not alter `taxonomy_lpsn` yet
-  message("Downloading page ", page, "...", appendLF = FALSE)
+  message("Downloading page ", page, "...", appendLF = TRUE)
   url <- paste0("https://lpsn.dsmz.de/genus?page=", page)
-  x <- read_html(url) %>%
+  x <- tryCatch(read_html(url),
+                error = function(e) {
+                  message("Waiting 10 seconds because of error: ", e$message)
+                  Sys.sleep(10)
+                  read_html(url)
+                })
+  x <- x %>%
     # class "main-list" is the main table
     html_element(".main-list") %>%
     # get every list element with a set <id> attribute
     html_elements("li[id]")
+  pb <- progress_bar$new(total = length(x), format = "[:bar] :current/:total :eta")
   for (i in seq_len(length(x))) {
-    if (i %% 25 == 0) {
-      message(".", appendLF = FALSE)
-    }
+    pb$tick()
     elements <- x[[i]] %>% html_elements("a")
     hrefs <- elements %>% html_attr("href")
     ranks <- hrefs %>% gsub(".*/(.*?)/.*", "\\1", .)
@@ -344,21 +374,26 @@ for (page in LETTERS) {
     names <- names[ranks != "species"]
     ranks <- ranks[ranks != "species"]
     ranks[ranks == "domain"] <- "kingdom"
-
-    df <- names %>%
-      tibble() %>%
-      t() %>%
-      as_tibble(.name_repair = "unique") %>%
-      setNames(ranks) %>%
-      # no candidates please
-      filter(genus %unlike% "^(Candidatus|\\[)")
+    
+    suppressMessages(
+      df <- names %>%
+        tibble() %>%
+        t() %>%
+        as_tibble(.name_repair = "unique") %>%
+        setNames(ranks) %>%
+        # no candidates please
+        filter(genus %unlike% "^(Candidatus|\\[)")
+    )
 
     taxonomy_lpsn_missing <- taxonomy_lpsn_missing %>%
       bind_rows(df)
   }
-  message(length(x), " entries incl. candidates (cleaned total: ", nrow(taxonomy_lpsn_missing), ")")
+  message("  => ", length(x), " entries incl. candidates (cleaned total: ", nrow(taxonomy_lpsn_missing), ")")
 }
-taxonomy_lpsn_missing
+taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> distinct()
+# had to pick the right genus/family combination here:
+taxonomy_lpsn_missing <- taxonomy_lpsn_missing |> filter(!(genus == "Pusillimonas" & family == "Oscillospiraceae"))
+taxonomy_lpsn.bak2 <- taxonomy_lpsn.bak
 
 taxonomy_lpsn <- taxonomy_lpsn %>%
   left_join(taxonomy_lpsn_missing, by = "genus") %>%
@@ -367,8 +402,10 @@ taxonomy_lpsn <- taxonomy_lpsn %>%
   mutate_all(function(x) ifelse(x %like_case% " no ", NA_character_, x))
 
 taxonomy_lpsn.bak2 <- taxonomy_lpsn
-# download family directly from LPSN website using scraping
-pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$family)))
+# download family directly from LPSN website using scraping, by using get_lpsn_and_author()
+# try it first:
+# get_lpsn_and_author("genus", "Escherichia")
+pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$family)), format = "[:bar] :current/:total :eta")
 for (f in unique(taxonomy_lpsn$family)) {
   pb$tick()
   if (is.na(f)) next
@@ -381,14 +418,14 @@ for (f in unique(taxonomy_lpsn$family)) {
       order = taxonomy_lpsn$order[which(taxonomy_lpsn$family == f)[1]],
       family = f,
       rank = "family",
-      status = "accepted",
+      status = unname(tax_info["status"]),
       source = "LPSN",
       lpsn = unname(tax_info["lpsn"]),
       ref = unname(tax_info["ref"])
     ))
 }
 # download order directly from LPSN website using scraping
-pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$order)))
+pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$order)), format = "[:bar] :current/:total :eta")
 for (o in unique(taxonomy_lpsn$order)) {
   pb$tick()
   if (is.na(o)) next
@@ -400,14 +437,14 @@ for (o in unique(taxonomy_lpsn$order)) {
       class = taxonomy_lpsn$class[which(taxonomy_lpsn$order == o)[1]],
       order = o,
       rank = "order",
-      status = "accepted",
+      status = unname(tax_info["status"]),
       source = "LPSN",
       lpsn = unname(tax_info["lpsn"]),
       ref = unname(tax_info["ref"])
     ))
 }
 # download class directly from LPSN website using scraping
-pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$class)))
+pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$class)), format = "[:bar] :current/:total :eta")
 for (cc in unique(taxonomy_lpsn$class)) {
   pb$tick()
   if (is.na(cc)) next
@@ -418,14 +455,14 @@ for (cc in unique(taxonomy_lpsn$class)) {
       phylum = taxonomy_lpsn$phylum[which(taxonomy_lpsn$class == cc)[1]],
       class = cc,
       rank = "class",
-      status = "accepted",
+      status = unname(tax_info["status"]),
       source = "LPSN",
       lpsn = unname(tax_info["lpsn"]),
       ref = unname(tax_info["ref"])
     ))
 }
 # download phylum directly from LPSN website using scraping
-pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$phylum)))
+pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$phylum)), format = "[:bar] :current/:total :eta")
 for (p in unique(taxonomy_lpsn$phylum)) {
   pb$tick()
   if (is.na(p)) next
@@ -435,14 +472,14 @@ for (p in unique(taxonomy_lpsn$phylum)) {
       kingdom = taxonomy_lpsn$kingdom[which(taxonomy_lpsn$phylum == p)[1]],
       phylum = p,
       rank = "phylum",
-      status = "accepted",
+      status = unname(tax_info["status"]),
       source = "LPSN",
       lpsn = unname(tax_info["lpsn"]),
       ref = unname(tax_info["ref"])
     ))
 }
 # download kingdom directly from LPSN website using scraping
-pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$kingdom)))
+pb <- progress_bar$new(total = length(unique(taxonomy_lpsn$kingdom)), format = "[:bar] :current/:total :eta")
 for (k in unique(taxonomy_lpsn$kingdom)) {
   pb$tick()
   if (is.na(k)) next
@@ -451,7 +488,7 @@ for (k in unique(taxonomy_lpsn$kingdom)) {
     bind_rows(tibble(
       kingdom = k,
       rank = "kingdom",
-      status = "accepted",
+      status = unname(tax_info["status"]),
       source = "LPSN",
       lpsn = unname(tax_info["lpsn"]),
       ref = unname(tax_info["ref"])
@@ -469,6 +506,7 @@ saveRDS(taxonomy_gbif, "data-raw/taxonomy_gbif.rds", version = 2)
 saveRDS(taxonomy_lpsn, "data-raw/taxonomy_lpsn.rds", version = 2)
 # this allows to always get back to this point by simply loading the files from data-raw/.
 
+
 # Add full names ----------------------------------------------------------
 
 taxonomy_gbif <- taxonomy_gbif %>%
@@ -515,29 +553,28 @@ taxonomy_lpsn$lpsn_parent[taxonomy_lpsn$rank == "subspecies"] <- taxonomy_lpsn$l
 
 # Combine the datasets ----------------------------------------------------
 
-# basis must be LPSN as it's most recent
-taxonomy <- taxonomy_lpsn %>%
-  # join GBIF identifiers to them
-  left_join(taxonomy_gbif %>% select(kingdom, fullname, starts_with("gbif")),
-    by = c("kingdom", "fullname")
-  )
-
-# for everything else, add the GBIF data
-taxonomy <- taxonomy %>%
-  bind_rows(taxonomy_gbif %>%
-    filter(!paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname))) %>%
-  arrange(fullname) %>%
-  filter(fullname != "")
+taxonomy <- taxonomy_lpsn |>
+  # start by adding GBIF to the bottom
+  bind_rows(taxonomy_gbif) |> 
+  # group on unique species
+  group_by(kingdom, fullname) |>
+  # fill the NAs in LPSN/GBIF fields and ref with the other source (so LPSN: 123 and GBIF: NA will become LPSN: 123 and GBIF: 123)
+  mutate(across(matches("^(lpsn|gbif|ref)"), function(x) rep(x[!is.na(x)][1], length(x)))) |>
+  # ungroup again
+  ungroup() |> 
+  # only keep unique species per kingdom
+  distinct(kingdom, fullname, .keep_all = TRUE) |> 
+  arrange(fullname)
 
 # get missing entries from existing microorganisms data set
-taxonomy <- taxonomy %>%
-  bind_rows(AMR::microorganisms %>%
+taxonomy.old <- AMR::microorganisms %>%
     select(all_of(colnames(taxonomy))) %>%
     filter(
       !paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
       # these will be added later:
-      source != "manually added"
-    )) %>%
+      source != "manually added")
+taxonomy <- taxonomy %>%
+  bind_rows(taxonomy.old) %>%
   arrange(fullname) %>%
   filter(fullname != "")
 
@@ -557,6 +594,29 @@ taxonomy <- taxonomy %>%
   ))
 table(taxonomy$rank, useNA = "always")
 
+# at this point, it happens that some genera within kingdoms have multiple families / orders, etc., see here:
+taxonomy |> filter(genus != "") |> group_by(kingdom, genus) |> filter(n_distinct(family) > 1) |> View()
+# so make this universal
+taxonomy <- taxonomy |> 
+  group_by(kingdom, genus) |> 
+  mutate(family = get_top_lvl(family, rank, "genus")) |> 
+  group_by(kingdom, family) |>
+  mutate(order = get_top_lvl(order, rank, "family")) |> 
+  group_by(kingdom, order) |>
+  mutate(class = get_top_lvl(class, rank, "order")) |> 
+  group_by(kingdom, class) |>
+  mutate(phylum = get_top_lvl(phylum, rank, "class")) |> 
+  ungroup()
+# and remove the taxonomy where it must remain empty
+taxonomy <- taxonomy |> 
+  mutate(phylum = ifelse(rank %in% c("kingdom"), "", phylum),
+         class = ifelse(rank %in% c("kingdom", "phylum"), "", class),
+         order = ifelse(rank %in% c("kingdom", "phylum", "class"), "", order),
+         family = ifelse(rank %in% c("kingdom", "phylum", "class", "order"), "", family),
+         genus = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family"), "", genus),
+         species = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus"), "", species),
+         subspecies = ifelse(rank %in% c("kingdom", "phylum", "class", "order", "family", "genus", "species"), "", subspecies))
+
 
 # Save intermediate results (0) -------------------------------------------
 
@@ -575,28 +635,23 @@ current_gbif <- taxonomy_gbif.bak %>%
   )
 
 # add missing kingdoms
-taxonomy <- taxonomy %>%
-  bind_rows(
-    taxonomy %>%
-      filter(kingdom != "") %>%
-      distinct(kingdom) %>%
-      mutate(
-        fullname = kingdom,
-        rank = "kingdom",
-        status = "accepted",
-        source = "manually added"
-      ) %>%
-      filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
-      left_join(
-        current_gbif %>%
-          select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
-        by = c("kingdom", "rank")
-      ) %>%
-      mutate(source = ifelse(!is.na(gbif), "GBIF", source))
-  )
+taxonomy_all_missing <- taxonomy %>%
+  filter(kingdom != "") %>%
+  distinct(kingdom) %>%
+  mutate(
+    fullname = kingdom,
+    rank = "kingdom"
+  ) %>%
+  filter(!paste(kingdom, rank) %in% paste(taxonomy$kingdom, taxonomy$rank)) %>%
+  left_join(
+    current_gbif %>%
+      select(kingdom, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
+    by = c("kingdom", "rank")
+  ) %>%
+  mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
+         status = ifelse(!is.na(gbif), "accepted", "unknown"))
 
 # 2 = phylum ... 6 = genus
-taxonomy_all_missing <- NULL
 for (i in 2:6) {
   i_name <- colnames(taxonomy)[i + 1]
   message("Adding missing: ", i_name, "... ", appendLF = FALSE)
@@ -606,25 +661,20 @@ for (i in 2:6) {
     select(kingdom:(i + 1)) %>%
     mutate(
       fullname = .[[ncol(.)]],
-      rank = i_name,
-      status = "accepted",
-      source = "manually added"
+      rank = i_name
     ) %>%
-    filter(!paste(kingdom, .[[ncol(.) - 4]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
+    filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
     # get GBIF identifier where available
     left_join(
       current_gbif %>%
         select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
       by = c("kingdom", "rank", i_name)
     ) %>%
-    mutate(source = ifelse(!is.na(gbif), "GBIF", source))
+    mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
+           status = ifelse(!is.na(gbif), "accepted", "unknown"))
   message("n = ", nrow(to_add))
-  if (is.null(taxonomy_all_missing)) {
-    taxonomy_all_missing <- to_add
-  } else {
-    taxonomy_all_missing <- taxonomy_all_missing %>%
-      bind_rows(to_add)
-  }
+  taxonomy_all_missing <- taxonomy_all_missing %>%
+    bind_rows(to_add)
 }
 taxonomy_all_missing %>% View()
 
@@ -652,7 +702,7 @@ taxonomy <- taxonomy %>%
   select(-fullname_rank, -rank_index) %>%
   arrange(fullname)
 
-# now also add missing species (requires combination with genus)
+# now also add missing species that have subspecies (requires combination with genus)
 taxonomy <- taxonomy %>%
   bind_rows(
     taxonomy %>%
@@ -661,9 +711,7 @@ taxonomy <- taxonomy %>%
       select(kingdom:species) %>%
       mutate(
         fullname = paste(genus, species),
-        rank = "species",
-        status = "accepted",
-        source = "manually added"
+        rank = "species"
       ) %>%
       filter(!paste(kingdom, genus, species, rank) %in% paste(taxonomy$kingdom, taxonomy$genus, taxonomy$species, taxonomy$rank)) %>%
       # get GBIF identifier where available
@@ -672,13 +720,15 @@ taxonomy <- taxonomy %>%
           select(kingdom, genus, species = specificEpithet, rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
         by = c("kingdom", "rank", "genus", "species")
       ) %>%
-      mutate(source = ifelse(!is.na(gbif), "GBIF", source))
+      mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
+             status = ifelse(!is.na(gbif), "accepted", "unknown"))
   )
 
 
 # remove NAs from taxonomy again, and keep unique full names
 taxonomy <- taxonomy %>%
   mutate(across(kingdom:subspecies, function(x) ifelse(is.na(x), "", x))) %>%
+  arrange(kingdom, fullname, ref) |>
   distinct(kingdom, fullname, .keep_all = TRUE) %>%
   filter(kingdom != "")
 
@@ -691,12 +741,11 @@ saveRDS(taxonomy, "data-raw/taxonomy1.rds")
 # Get previously manually added entries -----------------------------------
 
 manually_added <- AMR::microorganisms %>%
-  filter(source == "manually added", !paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname)) %>%
+  filter(source == "manually added",
+         !paste(kingdom, fullname) %in% paste(taxonomy$kingdom, taxonomy$fullname),
+         !rank %in% c("kingdom", "phylum", "class", "order", "family")) %>%
   select(fullname:subspecies, ref, source, rank)
 
-manually_added <- manually_added %>%
-  bind_rows(salmonellae)
-
 # get latest taxonomy for those entries
 for (g in unique(manually_added$genus[manually_added$genus != "" & manually_added$genus %in% taxonomy$genus])) {
   manually_added$family[which(manually_added$genus == g)] <- taxonomy$family[which(taxonomy$genus == g & is.na(taxonomy$lpsn))][1]
@@ -716,11 +765,14 @@ for (p in unique(manually_added$phylum[manually_added$phylum != "" & manually_ad
 
 manually_added <- manually_added %>%
   mutate(
-    status = "accepted",
+    status = "unknown",
     rank = ifelse(fullname %like% "unknown", "(unknown rank)", rank)
   )
 manually_added
 
+# these are now included in the new taxonomy, check them
+manually_added |> filter(fullname %in% taxonomy$fullname)
+
 taxonomy <- taxonomy %>%
   # here also the 'unknowns' are added, such as "(unknown fungus)"
   bind_rows(manually_added) %>%
@@ -728,6 +780,31 @@ taxonomy <- taxonomy %>%
 
 table(taxonomy$rank, useNA = "always")
 
+# Get LPSN data for records missing from `taxonomy_lpsn` ------------------
+
+# Weirdly enough, some LPSN records were lacking from `taxonomy_lpsn`, 
+# such as family Thiotrichaceae and its order Thiotrichales. When running
+# get_lpsn_and_author("family", "Thiotrichaceae") you do get a result.
+# So check every non-LPSN records from the kingdom of Bacteria and add it
+gbif_bacteria <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
+added <- 0
+pb <- progress_bar$new(total = length(gbif_bacteria), format = "[:bar] :current/:total :eta")
+for (record in gbif_bacteria) {
+  pb$tick()
+  lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
+                              name = taxonomy$fullname[record])
+  if (is.na(lpsn["lpsn"])) {
+    next
+  } else {
+    added <- added + 1
+    taxonomy$source[record] <- "LPSN"
+    taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
+    taxonomy$ref[record] <- unname(lpsn["ref"])
+    taxonomy$status[record] <- unname(lpsn["status"])
+  }
+}
+message(added, " GBIF records altered to latest LPSN")
+taxbak <- taxonomy
 
 # Clean scientific reference ----------------------------------------------
 
@@ -737,7 +814,7 @@ taxonomy <- taxonomy %>%
 
 # Get the latest upper taxonomy from LPSN for non-LPSN data ---------------
 
-# (e.g., phylum above class "Bacilli" was still "Firmicutes", should be "Bacillota" in 2022)
+# (e.g., phylum above class "Bacilli" was still "Firmicutes" in 2023, should be "Bacillota")
 for (k in unique(taxonomy$kingdom[taxonomy$kingdom != ""])) {
   message("Fixing GBIF taxonomy for kingdom ", k, ".", appendLF = FALSE)
   i <- 0
@@ -765,17 +842,25 @@ for (k in unique(taxonomy$kingdom[taxonomy$kingdom != ""])) {
 }
 
 # we need to fix parent GBIF identifiers
-taxonomy$gbif_parent[taxonomy$rank == "phylum" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "class" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "order" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "family" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "genus" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "species" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species" & !is.na(taxonomy$gbif)], taxonomy$fullname)]
-taxonomy$gbif_parent[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)], taxonomy$species[taxonomy$rank == "subspecies" & !is.na(taxonomy$gbif)]), taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
+# and LPSN parents
+taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
 
 # these still have no record in our data set:
-all(taxonomy$lpsn_parent %in% taxonomy$lpsn)
-all(taxonomy$gbif_parent %in% taxonomy$gbif)
+which(!taxonomy$lpsn_parent %in% taxonomy$lpsn)
+which(!taxonomy$gbif_parent %in% taxonomy$gbif)
 
 # fix rank
 taxonomy <- taxonomy %>%
@@ -794,6 +879,7 @@ taxonomy <- taxonomy %>%
 
 # Add prevalence ----------------------------------------------------------
 
+taxonomy_lpsn.bak3 <- taxonomy
 pathogens <- read_excel(file_bartlett, sheet = "Tab 6 Full List")
 
 # get all established, both old and current taxonomic names
@@ -902,6 +988,7 @@ mo_kingdom <- taxonomy %>%
     kingdom == "Protozoa" ~ "P",
     TRUE ~ ""
   ))
+
 # phylum until family are abbreviated with 8 characters and prefixed with their rank
 
 # Phylum - keep old and fill up for new ones
@@ -1196,58 +1283,120 @@ taxonomy <- taxonomy %>%
 taxonomy %>%
   filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE]) %>%
   View()
+
+# fullnames must be unique, we'll keep the most relevant ones only
 taxonomy <- taxonomy %>%
   mutate(rank_index = case_when(
     kingdom == "Bacteria" ~ 1,
     kingdom == "Fungi" ~ 2,
     kingdom == "Protozoa" ~ 3,
     kingdom == "Archaea" ~ 4,
-    TRUE ~ 5
+    kingdom == "Animalia" ~ 5,
+    TRUE ~ 6
   )) %>%
   arrange(fullname, rank_index) %>%
   distinct(fullname, .keep_all = TRUE) %>%
   select(-rank_index) %>%
   filter(mo != "")
 
+# keep the codes from manually added ones
+manual_mos <- as.character(AMR::microorganisms$mo)[match(taxonomy$fullname[taxonomy$source == "manually added"], AMR::microorganisms$fullname)]
+taxonomy$mo[taxonomy$source == "manually added"][!is.na(manual_mos)] <- manual_mos[!is.na(manual_mos)]
+
 # this must not exist:
 taxonomy %>%
   filter(mo %like% "__") %>%
   View()
 taxonomy <- taxonomy %>% filter(mo %unlike% "__")
+taxonomy_lpsn.bak4 <- taxonomy
 
 
 # Some integrity checks ---------------------------------------------------
 
 # are mo codes unique?
-taxonomy %>% filter(mo %in% .[duplicated(mo), "mo", drop = TRUE])
-taxonomy <- taxonomy %>% distinct(mo, .keep_all = TRUE)
+taxonomy %>% filter(mo %in% .[duplicated(mo), "mo", drop = TRUE]) |> arrange(mo) |> View()
+# no, there are not, so sort on MO and keep the first
+taxonomy <- taxonomy %>% arrange(mo) |> distinct(mo, .keep_all = TRUE)
 
+taxonomy <- taxonomy |> 
+  mutate(fullname = case_match(rank,
+                               "phylum" ~ phylum,
+                               "class" ~ class,
+                               "order" ~ order,
+                               "family" ~ family,
+                               .default = fullname))
 # are fullnames unique?
 taxonomy %>% filter(fullname %in% .[duplicated(fullname), "fullname", drop = TRUE])
 
 # are all GBIFs available?
 taxonomy %>%
-  filter(!gbif_parent %in% gbif) %>%
-  count(rank)
-# try to find the right gbif IDs
-taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")] <- taxonomy$gbif[match(taxonomy$genus[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "species")], taxonomy$genus)]
-taxonomy$gbif_parent[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")] <- taxonomy$gbif[match(taxonomy$phylum[which(!taxonomy$gbif_parent %in% taxonomy$gbif & taxonomy$rank == "class")], taxonomy$phylum)]
-taxonomy %>%
-  filter(!gbif_parent %in% gbif) %>%
-  count(rank)
+  filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
+  count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
+        rank)
 
-# are all LPSNs available?
+# so fix again all parent GBIF identifiers
+taxonomy$gbif_parent[taxonomy$rank == "phylum"] <- taxonomy$gbif[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "class"] <- taxonomy$gbif[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "order"] <- taxonomy$gbif[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "family"] <- taxonomy$gbif[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "genus"] <- taxonomy$gbif[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "species"] <- taxonomy$gbif[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
+taxonomy$gbif_parent[taxonomy$rank == "subspecies"] <- taxonomy$gbif[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
+# and LPSN identifiers
+taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
+
+# check again
 taxonomy %>%
-  filter(!lpsn_parent %in% lpsn) %>%
-  count(rank)
-# make GBIF refer to newest renaming according to LPSN
-taxonomy$gbif_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))] <- taxonomy$gbif[match(taxonomy$lpsn_renamed_to[which(!is.na(taxonomy$gbif_renamed_to) & !is.na(taxonomy$lpsn_renamed_to))], taxonomy$lpsn)]
+  filter((!gbif_parent %in% gbif) | (!lpsn_parent %in% lpsn)) %>%
+  count(source = ifelse(!gbif_parent %in% gbif, "GBIF", "LPSN"),
+        rank)
+
+
 
 # Save intermediate results (3) -------------------------------------------
 
 saveRDS(taxonomy, "data-raw/taxonomy3.rds")
 
 
+# Redo LPSN missings and parents ------------------------------------------
+
+gbif_bacteria_second_run <- which(taxonomy$kingdom == "Bacteria" & taxonomy$source == "GBIF" & taxonomy$rank %in% c("phylum", "class", "order", "family"))
+gbif_bacteria_second_run <- gbif_bacteria_second_run[!gbif_bacteria_second_run %in% gbif_bacteria]
+added <- 0
+pb <- progress_bar$new(total = length(gbif_bacteria_second_run), format = "[:bar] :current/:total :eta")
+for (record in gbif_bacteria_second_run) {
+  pb$tick()
+  lpsn <- get_lpsn_and_author(rank = taxonomy$rank[record],
+                              name = taxonomy$fullname[record])
+  if (is.na(lpsn["lpsn"])) {
+    next
+  } else {
+    added <- added + 1
+    taxonomy$source[record] <- "LPSN"
+    taxonomy$lpsn[record] <- unname(lpsn["lpsn"])
+    taxonomy$ref[record] <- unname(lpsn["ref"])
+    taxonomy$status[record] <- unname(lpsn["status"])
+  }
+}
+message(added, " GBIF records altered to latest LPSN")
+taxbak <- taxonomy
+taxonomy$lpsn_parent[taxonomy$rank == "phylum"] <- taxonomy$lpsn[match(taxonomy$kingdom[taxonomy$rank == "phylum"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "class"] <- taxonomy$lpsn[match(taxonomy$phylum[taxonomy$rank == "class"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "order"] <- taxonomy$lpsn[match(taxonomy$class[taxonomy$rank == "order"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "family"] <- taxonomy$lpsn[match(taxonomy$order[taxonomy$rank == "family"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "genus"] <- taxonomy$lpsn[match(taxonomy$family[taxonomy$rank == "genus"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "species"] <- taxonomy$lpsn[match(taxonomy$genus[taxonomy$rank == "species"], taxonomy$fullname)]
+taxonomy$lpsn_parent[taxonomy$rank == "subspecies"] <- taxonomy$lpsn[match(paste(taxonomy$genus[taxonomy$rank == "subspecies"], taxonomy$species[taxonomy$rank == "subspecies"]), taxonomy$fullname)]
+
+# TODO: there is no order Eggerthellales anymore
+
+
 # Remove unwanted taxonomic entries from Protoza/Fungi --------------------
 
 # this must be done after the microbial ID generation, since it will otherwise generate a lot of different IDs
@@ -1256,12 +1405,12 @@ taxonomy <- taxonomy %>%
     # Protozoa:
     !(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence == 3),
     # Fungi:
-    !(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3),
+    !(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 3 & rank %in% c("genus", "species", "subspecies")),
     !(genus %in% c("Phoma", "Leptosphaeria", "Physarum") & rank %in% c("species", "subspecies")), # only genus of this rare fungus, with resp. 1300 and 800 species
     # (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
     # Animalia:
     !genus %in% c("Lucilia", "Lumbricus"),
-    !(class == "Insecta" & rank %in% c("species", "subspecies")), # keep only genus of insects
+    !(class == "Insecta" & rank %in% c("species", "subspecies")), # keep only genus of insects, not all of their (sub)species
     !(genus == "Amoeba" & kingdom == "Animalia"),
     !(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")), # only genus of the many hundreds of mosquitoes species
     kingdom != "Plantae"
@@ -1270,7 +1419,8 @@ taxonomy <- taxonomy %>%
 # no ghost families, orders classes, phyla
 taxonomy <- taxonomy %>%
   group_by(kingdom, family) %>%
-  filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
+  # (but keep the ghost families of bacteria)
+  filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom" | kingdom == "Bacteria") %>%
   group_by(kingdom, order) %>%
   filter(n() > 1 | fullname %like% "unknown" | rank == "kingdom") %>%
   group_by(kingdom, class) %>%
@@ -1280,6 +1430,34 @@ taxonomy <- taxonomy %>%
   ungroup()
 
 
+for (i in which(colnames(taxonomy) %in% c("phylum", "class", "order", "family")) - 1) {
+  i_name <- colnames(taxonomy)[i + 1]
+  message("Adding missing: ", i_name, "... ", appendLF = FALSE)
+  to_add <- taxonomy %>%
+    filter(.[[i + 1]] != "") %>%
+    distinct(kingdom, .[[i + 1]], .keep_all = TRUE) %>%
+    select(kingdom:(i + 1)) %>%
+    mutate(
+      fullname = .[[ncol(.)]],
+      rank = i_name
+    ) %>%
+    filter(!paste(kingdom, .[[ncol(.) - 2]], rank) %in% paste(taxonomy$kingdom, taxonomy[[i + 1]], taxonomy$rank)) %>%
+    # get GBIF identifier where available
+    left_join(
+      current_gbif %>%
+        select(kingdom, all_of(i_name), rank = taxonRank, ref = scientificNameAuthorship, gbif = taxonID, gbif_parent = parentNameUsageID),
+      by = c("kingdom", "rank", i_name)
+    ) %>%
+    mutate(source = ifelse(!is.na(gbif), "GBIF", "manually added"),
+           status = ifelse(!is.na(gbif), "accepted", "unknown"))
+  message("n = ", nrow(to_add))
+  # taxonomy_all_missing <- taxonomy_all_missing %>%
+  #   bind_rows(to_add)
+}
+
+
+
+
 message(
   "\nCongratulations! The new taxonomic table will contain ", format(nrow(taxonomy), big.mark = " "), " rows.\n",
   "This was ", format(nrow(AMR::microorganisms), big.mark = " "), " rows.\n"

data-raw/translations.tsv

@@ -278,3 +278,10 @@ Macrolides/lincosamides	FALSE	TRUE	TRUE	FALSE	大环内酯类/林可酰胺类	Ma
 Other antibacterials	FALSE	TRUE	TRUE	FALSE	其他抗菌剂	Ostatní antibakteriální látky	Andre antibakterielle stoffer	Overige antibiotica	Muut antibakteeriset aineet	Autres antibactériens	Andere Antibiotika	Άλλα αντιβακτηριακά	Altri antibatterici	その他の抗菌薬	Andre antibakterielle midler	Inne środki przeciwbakteryjne	Outros antibacterianos	Alte antibacteriene	Другие антибактериальные препараты	Otros antibacterianos	Andra antibakteriella medel	Diğer antibakteriyeller	Інші антибактеріальні засоби
 Polymyxins	FALSE	TRUE	TRUE	FALSE	多粘菌素类	Polymyxiny	Polymyxiner	Polymyxines	Polymysiinit	Polymyxines	Polymyxine	Πολυμυξίνες	Polimixine	ポリミキシン	Polymyxiner	Polimyksyny	Polimixinas	Polimixine	Полимиксины	Polimixinas	Polymyxiner	Polimiksinler	Поліміксини
 Quinolones	FALSE	TRUE	TRUE	FALSE	喹诺酮类	Chinolony	Kinoloner	Quinolonen	Kinolonit	Quinolones	Quinolone	Κινολόνες	Chinoloni	キノロン	Kinoloner	Quinolony	Quinolones	Quinolone	Хинолоны	Quinolonas	Kinoloner	Kinolonlar	Хінолони
+aquatic|fish	FALSE	FALSE	FALSE	FALSE	水生|条鱼|鱼	vodní|ryba|ryby	akvatisk|fisk	aquatisch|vis|vissen	vesieliö|kala|kalaa	aquatique|poisson|poissons	wasser|fisch|fische	υδρόβια|ψάρι|ψάρια	acquatico|pesce|pesci	アクアティック|1匹|魚	akvatisk|fisk	wodny|ryba|ryby	aquático|peixe|peixes	acvatic|pește|pești	водные|рыба|рыбы	acuático|pez|peces	vattenlevande|fisk|fiskar	sucul|balık	водний|риба|рибки
+cattle|bovine	FALSE	FALSE	FALSE	FALSE	牛|牛	skot	kvæg	vee|rund	karja|nauta	bovins|bovin	rinder	βοοειδή	bovini|bovino	牛|ウシ	storfe|storfe	bydło|bydło	bovinos|bovino	bovine|bovine	крупный рогатый скот|крупный рогатый скот	bovino|bovino	nötkreatur|nötkreatur	sığır|büyükbaş hayvan	велика рогата худоба|бичачий
+cat|cats|feline	FALSE	FALSE	FALSE	FALSE	猫|猫|猫科动物	kočka|kočky|kočky	kat|katte|kat	kat|katten|katachtig	kissa|kissat|kissa	chat|chats|félin	katze|katzen	γάτα|γάτες|αιλουροειδή	gatto|gatti|felino	猫|猫|ネコ	katt	kot|koty	gato|gatos|felino	pisică|pisici|felină	кошка|кошки|кошка	gato|gatos|felino	katt|katter|kattdjur	kedi|kediler|kedi	кіт|коти|котячий
+dog|dogs|canine	FALSE	FALSE	FALSE	FALSE	狗|狗|犬类	pes|psi|psí	hund|hunde	hond|honden	koira|koirat|koira	chien|canine	hund|hunde|hund	σκύλος|σκύλοι|σκύλος	cane|cani|canino	犬|犬|イヌ	hund	pies|psy|pies	cão|cães|canino	câine|câini|canin	собака|собаки|собака	perro|perros|canino	hund|hundar	köpek|köpekler	пес|собаки|собачий
+horse|horses|equine	FALSE	FALSE	FALSE	FALSE	马|马|马	kůň|koně|koně	hest|heste	paard|paarden	hevonen|hevoset|hevoset	cheval|chevaux|équine	pferd|pferde	άλογο|άλογα|ιπποειδή	cavallo|cavalli|equino	馬|馬|馬	hest	koń|konie|koń	cavalo|cavalos|equinos	cal|cai|ecvideu	лошадь|лошади|лошадь	caballo|caballos|equino	häst|hästar|häst	at|atlar|atçılık	кінь|коні|конячий
+bird|birds|poultry	FALSE	FALSE	FALSE	FALSE	鸟类|鸟类|家禽	ptáci|ptáci|drůbež	fugl|fugle|fjerkræ	vogel|vogels|pluimvee	lintu|linnut|siipikarja	oiseaux|oiseaux|volaille	vogel|vögel|geflügel	πουλιά|πουλιά|πουλερικά	uccello|uccelli|pollame	鳥|鳥|家禽	fugl|fugler|fjørfe	ptak|ptaki|drób	aves|aves|aves de capoeira	pasăre|păsări|păsări de curte	птица|птицы|домашняя птица	aves|aves|aves de corral	fågel|fåglar|fjäderfä	kuş|kuşlar|kümes hayvanları	птах|птахів|птиця
+swine|swines	FALSE	FALSE	FALSE	FALSE	猪|猪	prasata|prasata	svin	varken|varkens	sika|sikaa	porcine|porcs	schwein|schweine	χοίροι|χοίροι	suino|suini	豚|豚|頭	svin	trzoda chlewna|świnie	suínos	porc|porcine	свинья|свиньи	porcino|porcinos	svin	domuz|domuz	свиня|свині

index.md

@@ -1,8 +1,9 @@
 # The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
 
+* Provides an **all-in-one solution** for AMR data analysis in a One Health approach
 * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
 * Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
-* Applies all recent **CLSI and EUCAST clinical breakpoints** for MICs and disk zones
+* Applies all recent **CLSI and EUCAST clinical and veterinary breakpoints** for  MICs and disk zones
 * Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
 * Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC** and **SNOMED CT**
 * Works on Windows, macOS and Linux with **all versions of R** since R-3.0 and is completely **dependency-free**, highly suitable for places with **limited resources**
@@ -240,7 +241,8 @@ It will be downloaded and installed automatically. For RStudio, click on the men
 
 #### Latest development version
 
-[![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?branch=main)
+[![check-recent](https://github.com/msberends/AMR/workflows/check-old/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?branch=main)
+[![check-recent](https://github.com/msberends/AMR/workflows/check-recent/badge.svg?branch=main)](https://codecov.io/gh/msberends/AMR?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/main/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=main)
 

inst/tinytest/test-_deprecated.R

@@ -27,38 +27,4 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-sir <- random_sir(100)
-rsi <- sir
-class(rsi) <- gsub("sir", "rsi", class(rsi))
-mic <- random_mic(100)
-disk <- random_disk(100)
 
-expect_identical(summary(sir), summary(rsi))
-expect_identical(c(sir), c(rsi))
-
-expect_identical(suppressWarnings(suppressMessages(as.rsi(as.character(rsi)))),
-                 suppressWarnings(suppressMessages(as.sir(as.character(sir)))))
-expect_identical(suppressWarnings(suppressMessages(as.rsi(mic, mo = "Escherichia coli", ab = "CIP"))),
-                 suppressWarnings(suppressMessages(as.sir(mic, mo = "Escherichia coli", ab = "CIP"))))
-expect_identical(suppressWarnings(suppressMessages(as.rsi(disk, mo = "Escherichia coli", ab = "CIP"))),
-                 suppressWarnings(suppressMessages(as.sir(disk, mo = "Escherichia coli", ab = "CIP"))))
-expect_identical(suppressWarnings(suppressMessages(as.rsi(data.frame(CIP = mic, mo = "Escherichia coli")))),
-                 suppressWarnings(suppressMessages(as.sir(data.frame(CIP = mic, mo = "Escherichia coli")))))
-
-expect_identical(suppressWarnings(n_rsi(example_isolates$CIP)),
-                 suppressWarnings(n_sir(example_isolates$CIP)))
-
-expect_identical(suppressWarnings(rsi_df(example_isolates)),
-                 suppressWarnings(sir_df(example_isolates)))
-
-expect_identical(suppressWarnings(is.rsi.eligible(example_isolates)),
-                 suppressWarnings(is_sir_eligible(example_isolates)))
-
-if (AMR:::pkg_is_available("ggplot2")) {
-  expect_equal(suppressWarnings(ggplot_rsi(example_isolates[, c("CIP", "GEN", "TOB")])),
-               suppressWarnings(ggplot_sir(example_isolates[, c("CIP", "GEN", "TOB")])))
-  
-  p <- ggplot2::ggplot(example_isolates[, c("CIP", "GEN", "TOB")])
-  expect_equal(suppressWarnings(p + geom_rsi() + scale_rsi_colours() + labels_rsi_count() + facet_rsi() + theme_rsi()),
-               suppressWarnings(p + geom_sir() + scale_sir_colours() + labels_sir_count() + facet_sir() + theme_sir()))
-}

inst/tinytest/test-ab_property.R

@@ -63,11 +63,10 @@ expect_stdout(print(ab_name("amox", language = NULL)))
 expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
 expect_equal(
   ab_loinc("ampicillin"),
-  c("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5")
+  c("101477-8", "101478-6", "18864-9", "18865-6", "20374-5", "21066-6", "23618-2", "27-3", "28-1", "29-9", "30-7", "31-5", "32-3", "33-1", "3355-5", "33562-0", "33919-2", "34-9", "43883-8", "43884-6", "6979-9", "6980-7", "87604-5")
 )
 
-expect_true(ab_url("AMX") %like% "whocc.no")
-# expect_warning(ab_url("ASP"))
+expect_true(ab_url("AMX") %like% "fhi[.]no")
 
 expect_identical(
   colnames(set_ab_names(example_isolates[, 17:22])),

inst/tinytest/test-antibiogram.R

@@ -78,19 +78,19 @@ ab6 <- antibiogram(example_isolates,
                    syndromic_group = "ward")
 
 # with a custom language, though this will be determined automatically
-# (i.e., this table will be in Spanish on Spanish systems)
+# (i.e., this table will be in Dutch on Dutch systems)
 ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
 ab7 <- antibiogram(ex1,
                    antibiotics = aminoglycosides(),
                    ab_transform = "name",
                    syndromic_group = ifelse(ex1$ward == "ICU",
-                                            "UCI", "No UCI"),
-                   language = "es")
+                                            "IC", "Geen IC"),
+                   language = "nl")
 
 expect_inherits(ab6, "antibiogram")
 expect_inherits(ab7, "antibiogram")
 expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
-expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
+expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikacine", "Gentamicine", "Tobramycine"))
 
 # Weighted-incidence syndromic combination antibiogram (WISCA) ---------
 

inst/tinytest/test-av_property.R

@@ -57,8 +57,7 @@ expect_stdout(print(av_name("acic", language = NULL)))
 expect_equal(av_name("29113-8", language = NULL), "Abacavir")
 expect_equal(
   av_loinc("Abacavir"),
-  c("29113-8", "78772-1", "78773-9", "79134-3", "80118-3")
+  c("29113-8", "30273-7", "30287-7", "30303-2", "78772-1", "78773-9", "79134-3", "80118-3")
 )
 
-expect_true(av_url("ACI") %like% "whocc.no")
-# expect_warning(av_url("ASP"))
+expect_true(av_url("ACI") %like% "fhi[.]no")