(v2.1.1.9050) vctrs fix for sir, small documentation fixes

.github/prehooks/commit-msg

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

.github/prehooks/pre-commit

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 # ==================================================================== #
 # TITLE:                                                               #
@@ -29,12 +29,32 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
-echo "Running pre-commit hook..."
+########################################
+# This script runs before every commit #
+########################################
+
+# try to fetch the commit message from the standard location
+COMMIT_MSG_PATH=".git/COMMIT_EDITMSG"
+if [ -f "$COMMIT_MSG_PATH" ]; then
+  COMMIT_MSG=$(cat "$COMMIT_MSG_PATH")
+else
+  echo "Commit message file not found."
+  exit 1
+fi
+# check the commit message, cancel commit if needed
+if [[ "$COMMIT_MSG" =~ \(no-check\)|\(no-checks\)|\(no-verify\) ]]; then
+  echo "Not running pre-commit checks:"
+  echo "Commit message contains '(no-check)', '(no-checks)', or '(no-verify)."
+  echo ""
+  exit 0
+fi
+
+echo "Running pre-commit checks..."
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 if command -v Rscript > /dev/null; then
   if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
-    Rscript -e "source('data-raw/_pre_commit_hook.R')"
+    Rscript -e "source('data-raw/_pre_commit_checks.R')"
     currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
     echo "- Adding changed files in ./data-raw and ./man to this commit"
     git add data-raw/*
@@ -69,16 +89,10 @@ 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

.github/workflows/check-old.yaml

@@ -49,6 +49,7 @@ jobs:
           # Test all old versions of R >= 3.0, we support them all!
           # For these old versions, dependencies and vignettes will not be checked.
           # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
+          - {os: ubuntu-latest, r: '3.6', allowfail: false}
           # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8
           - {os: ubuntu-latest, r: '3.4', allowfail: false}
           - {os: ubuntu-latest, r: '3.3', allowfail: false}

.github/workflows/check-recent.yaml

@@ -58,15 +58,15 @@ jobs:
           - {os: ubuntu-latest,  r: 'devel', allowfail: false}
 
           # current 'release' version, check all major OSes:
-          - {os: macOS-latest,   r: '4.3', allowfail: false}
-          - {os: windows-latest, r: '4.3', allowfail: false}
-          - {os: ubuntu-latest,  r: '4.3', allowfail: false}
+          - {os: macOS-latest,   r: 'release', allowfail: false}
+          - {os: windows-latest, r: 'release', allowfail: false}
+          - {os: ubuntu-latest,  r: 'release', allowfail: false}
 
           # older versions (see also check-old.yaml for even older versions):
+          - {os: ubuntu-latest, r: '4.3', allowfail: false}
           - {os: ubuntu-latest, r: '4.2', allowfail: false}
           - {os: ubuntu-latest, r: '4.1', allowfail: false}
-          - {os: ubuntu-latest, r: '4.0', allowfail: false}
-          - {os: ubuntu-latest, r: '3.6', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
+          - {os: ubuntu-latest, r: '4.0', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

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: 2.1.1.9050
+Date: 2024-06-15
 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 +24,35 @@ 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.double,sir)
 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 +62,15 @@ 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)
@@ -123,14 +78,13 @@ 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,ab_selector)
 S3method(print,av)
 S3method(print,bug_drug_combinations)
 S3method(print,custom_eucast_rules)
@@ -141,46 +95,27 @@ 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 +123,6 @@ 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 +161,6 @@ 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 +206,17 @@ 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 +227,6 @@ 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)
@@ -307,7 +234,6 @@ 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)
@@ -329,6 +255,7 @@ export(mo_fullname)
 export(mo_gbif)
 export(mo_genus)
 export(mo_gramstain)
+export(mo_group_members)
 export(mo_info)
 export(mo_is_anaerobic)
 export(mo_is_gram_negative)
@@ -360,8 +287,8 @@ export(mo_uncertainties)
 export(mo_url)
 export(mo_year)
 export(mrgn)
-export(n_rsi)
 export(n_sir)
+export(nitrofurans)
 export(not_intrinsic_resistant)
 export(oxazolidinones)
 export(pca)
@@ -376,16 +303,18 @@ export(proportion_df)
 export(quinolones)
 export(random_disk)
 export(random_mic)
-export(random_rsi)
 export(random_sir)
+export(rescale_mic)
 export(reset_AMR_locale)
 export(resistance)
 export(resistance_predict)
+export(rifamycins)
 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 +328,6 @@ export(skewness)
 export(streptogramins)
 export(susceptibility)
 export(tetracyclines)
-export(theme_rsi)
 export(theme_sir)
 export(translate_AMR)
 export(trimethoprims)

NEWS.md

@@ -1,3 +1,66 @@
+# AMR 2.1.1.9050
+
+*(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
+* `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI. Also, to get quantitative values, `as.double()` or a `sir` object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become `NA`). Other functions using `sir` classes (e.g., `summary()`) are updated to reflect the change to contain NI and SDD.
+* 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 `rescale_mic()`, which allows to rescale 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.
+* Function `mo_group_members()` to retrieve the member microorganisms of a microorganism group. For example, `mo_group_members("Strep group C")` returns a vector of all microorganisms that are in that group.
+* Clinical breakpoints and intrinsic resistance of EUCAST 2024 and CLSI 2024 have been added to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 (v14.0) is now the new default guideline for all MIC and disks diffusion interpretations.
+
+## Changed
+* For SIR interpretation, it is now possible to use column names for argument `ab`, `mo`, and `uti`: `as.sir(..., ab = "column1", mo = "column2", uti = "column3")`. This greatly improves the flexibility for users.
+* Extended the antibiotic selectors with `nitrofurans()` and `rifamycins()`
+* `antibiotics` data set:
+  * Added "clindamycin inducible screening" as `CLI1`. Since clindamycin is a lincosamide, the antibiotic selector `lincosamides()` now contains the argument `only_treatable = TRUE` (similar to other antibiotic selectors that contain non-treatable drugs)
+  * Added Amorolfine (`AMO`, D01AE16), which is now also part of the `antifungals()` selector
+* For MICs:
+  * Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
+  * Added new argument `keep_operators` to `as.mic()`. This can be `"all"` (default), `"none"`, or `"edges"`. This argument is also available in the new `rescale_mic()` and `scale_*_mic()` functions.
+  * 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`.
+  * Sorting of MIC values (using `sort()`) was fixed in the same manner; `<0.001` now gets sorted before `0.001`, and `>0.001` gets sorted after `0.001`.
+* Updated `italicise_taxonomy()` to support HTML output
+* `custom_eucast_rules()` now supports multiple antibiotics and antibiotic groups to be affected by a single rule
+* `mo_info()` now contains an extra element `group_members`, with the contents of the new `mo_group_members()` function
+* 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
+* Fix for using a manual value for `mo_transform` in `antibiogram()`
+* Fix for mapping 'high level' antibiotics in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
+* Improved overall algorithm of `as.ab()` for better performance and accuracy
+* Improved overall algorithm of `as.mo()` for better performance and accuracy. Specifically, more weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species.
+* When using antibiotic selectors such as `aminoglycosides()` that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using `only_treatable = FALSE`
+* Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
+
+## 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
@@ -63,7 +126,7 @@ The 'RSI functions' will be removed in a future version, but not before late 202
 
 ### New antibiogram function
 
-With the new `antibiogram()` function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker *et al.* (2021, DOI [10.1177/20499361211011373](https://doi.org/10.1177/20499361211011373)) and Barbieri *et al.* (2021, DOI [10.1186/s13756-021-00939-2](https://doi.org/10.1186/s13756-021-00939-2)).
+With the new `antibiogram()` function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker *et al.* (2021, DOI 10.1177/20499361211011373) and Barbieri *et al.* (2021, DOI 10.1186/s13756-021-00939-2).
 
 The help page for `antibiogram()` extensively elaborates on use cases, and `antibiogram()` also supports printing in R Markdown and Quarto, with support for 20 languages.
 
@@ -120,7 +183,7 @@ 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 +196,7 @@ 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 +254,4 @@ 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

@@ -28,7 +28,7 @@
 # ==================================================================== #
 
 # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
-# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
+# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
 EUCAST_VERSION_BREAKPOINTS <- list(
   # "13.0" = list(
   #   version_txt = "v13.0",
@@ -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",
@@ -158,6 +161,7 @@ globalVariables(c(
   "microorganisms",
   "microorganisms.codes",
   "mo",
+  "n",
   "name",
   "new",
   "numerator",
@@ -183,8 +187,10 @@ globalVariables(c(
   "total",
   "txt",
   "type",
+  "uti_index",
   "value",
   "varname",
+  "x",
   "xvar",
   "y",
   "year",

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,
@@ -515,6 +524,9 @@ word_wrap <- function(...,
     # otherwise, give a 'click to run' popup
     parts[cmds & parts %unlike% "[.]"] <- font_url(url = paste0("ide:run:AMR::", parts[cmds & parts %unlike% "[.]"]),
                                                    txt = parts[cmds & parts %unlike% "[.]"])
+    # text starting with `?` must also lead to the help page
+    parts[parts %like% "^[?]"] <- font_url(url = paste0("ide:help:AMR::", gsub("()", "", gsub("^[?]", "", parts[parts %like% "^[?]"]), fixed = TRUE)),
+                                           txt = parts[parts %like% "^[?]"])
     msg <- paste0(parts, collapse = "`")
   }
   msg <- gsub("`(.+?)`", font_grey_bg("\\1"), msg)
@@ -680,7 +692,7 @@ create_eucast_ab_documentation <- function() {
   ab <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AMR_env$AB_lookup$ab) {
       # separate drugs, such as `AMX`
@@ -734,6 +746,10 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
     # class 'sir' should be sorted like this
     v <- c("S", "I", "R")
   }
+  if (identical(v, c("I", "NI", "R", "S", "SDD"))) {
+    # class 'sir' should be sorted like this
+    v <- c("S", "SDD", "I", "R", "NI")
+  }
   # oxford comma
   if (last_sep %in% c(" or ", " and ") && length(v) > 2) {
     last_sep <- paste0(",", last_sep)
@@ -826,7 +842,7 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
     return(invisible())
   }
 
-  if (!is.null(allow_class)) {
+  if (!is.null(allow_class) && !(suppressWarnings(all(is.na(object))) && allow_NA == TRUE)) {
     stop_ifnot(inherits(object, allow_class), "argument `", obj_name,
       "` must be ", format_class(allow_class, plural = isTRUE(has_length > 1)),
       ", i.e. not be ", format_class(class(object), plural = isTRUE(has_length > 1)),
@@ -862,12 +878,20 @@ 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
     )
@@ -1028,10 +1052,15 @@ get_current_column <- function() {
     if (tryCatch(!is.null(env$i), error = function(e) FALSE)) {
       if (!is.null(env$tibble_vars)) {
         # for mutate_if()
+        # TODO remove later, was part of older dplyr versions (at least not in dplyr 1.1.4)
         env$tibble_vars[env$i]
       } else {
         # for mutate(across())
-        df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
+        if (!is.null(env$data) && is.data.frame(env$data)) {
+          df <- env$data
+        } else {
+          df <- tryCatch(get_current_data(NA, 0), error = function(e) NULL)
+        }
         if (is.data.frame(df)) {
           colnames(df)[env$i]
         } else {
@@ -1316,6 +1345,10 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, clear = TRUE, title
     if (!is.null(progress_bar)) {
       # so we use progress::progress_bar
       # a close()-method was also added, see below for that
+      title <- trimws2(title)
+      if (title != "") {
+        title <- paste0(title, " ")
+      }
       pb <- progress_bar$new(
         format = paste0(title,
                         ifelse(only_bar_percent == TRUE, "[:bar] :percent", "[:bar] :percent (:current/:total,:eta)")),
@@ -1512,14 +1545,14 @@ add_MO_lookup_to_AMR_env <- function() {
     MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 3
 
     # the fullname lowercase, important for the internal algorithms in as.mo()
-    MO_lookup$fullname_lower <- tolower(trimws(paste(
+    MO_lookup$fullname_lower <- tolower(trimws2(paste(
       MO_lookup$genus,
       MO_lookup$species,
       MO_lookup$subspecies
     )))
     ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
     MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
-    MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
+    MO_lookup$fullname_lower <- trimws2(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
     # special for Salmonella - they have cities as subspecies but not the species (enterica) in the fullname:
     MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")] <- gsub(" enterica ", " ", MO_lookup$fullname_lower[which(MO_lookup$subspecies %like_case% "^[A-Z]")], fixed = TRUE)
 
@@ -1551,7 +1584,7 @@ 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$chmatch(x, table, ...), error = function(e) base::match(x, table, ...))
   } else {
     base::match(x, table, ...)
   }
@@ -1559,7 +1592,7 @@ match <- function(x, table, ...) {
 `%in%` <- function(x, table) {
   if (!is.null(AMR_env$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
@@ -107,7 +107,10 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     ))
   }
 
-  initial_search <- is.null(list(...)$initial_search)
+  loop_time <- list(...)$loop_time
+  if (is.null(loop_time)) {
+    loop_time <- 1
+  }
   already_regex <- isTRUE(list(...)$already_regex)
   fast_mode <- isTRUE(list(...)$fast_mode)
 
@@ -117,8 +120,8 @@ 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) {
@@ -131,16 +134,21 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   x_unknown_ATCs <- character(0)
 
   note_if_more_than_one_found <- function(found, index, from_text) {
-    if (isTRUE(initial_search) && isTRUE(length(from_text) > 1)) {
-      abnames <- ab_name(from_text, tolower = TRUE, initial_search = FALSE)
+    if (loop_time == 1 && isTRUE(length(from_text) > 1)) {
+      abnames <- ab_name(from_text, tolower = TRUE, loop_time = loop_time + 1)
       if (ab_name(found[1L], language = NULL) %like% "(clavulanic acid|(avi|tazo|mono|vabor)bactam)") {
         abnames <- abnames[!abnames %in% c("clavulanic acid", "avibactam", "tazobactam", "vaborbactam", "monobactam")]
       }
       if (length(abnames) > 1) {
-        message_(
-          "More than one result was found for item ", index, ": ",
-          vector_and(abnames, quotes = FALSE)
-        )
+        if (toupper(paste(abnames, collapse = " ")) %in% AMR_env$AB_lookup$generalised_name) {
+          # if the found values combined is a valid AB, return that
+          found <- AMR_env$AB_lookup$ab[match(toupper(paste(abnames, collapse = " ")), AMR_env$AB_lookup$generalised_name)][1]
+        } else {
+          message_(
+            "More than one result was found for item ", index, ": ",
+            vector_and(abnames, quotes = FALSE)
+          )
+        }
       }
     }
     found[1L]
@@ -174,13 +182,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   x_new[is.na(x)] <- NA
   already_known[is.na(x)] <- FALSE
 
-  if (isTRUE(initial_search) && sum(already_known) < length(x)) {
+  if (loop_time == 1 && sum(already_known) < length(x)) {
     progress <- progress_ticker(n = sum(!already_known), n_min = 25, print = info) # start if n >= 25
     on.exit(close(progress))
   }
 
   for (i in which(!already_known)) {
-    if (isTRUE(initial_search)) {
+    if (loop_time == 1) {
       progress$tick()
     }
 
@@ -202,7 +210,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     }
 
     if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
-      from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]]),
+      from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 1, translate_ab = FALSE)[[1]]),
         error = function(e) character(0)
       )
     } else {
@@ -314,13 +322,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     }
 
     # INITIAL SEARCH - More uncertain results ----
-
-    if (isTRUE(initial_search) && fast_mode == FALSE) {
-      # only run on first try
+    if (loop_time <= 2 && fast_mode == FALSE) {
+      # only run on first and second try
 
       # try by removing all spaces
       if (x[i] %like% " ") {
-        found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub(" +", "", x[i], perl = TRUE), loop_time = loop_time + 2))
         if (length(found) > 0 && !is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -329,7 +336,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
 
       # try by removing all spaces and numbers
       if (x[i] %like% " " || x[i] %like% "[0-9]") {
-        found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
         if (length(found) > 0 && !is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -355,7 +362,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
         )[[1]],
         collapse = "/"
       )
-      x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
+      x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
       if (!is.na(x_translated_guess)) {
         x_new[i] <- x_translated_guess
         next
@@ -367,7 +374,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
           strsplit(x_translated, "[^A-Z0-9 ]"),
           function(y) {
             for (i in seq_len(length(y))) {
-              y_name <- suppressWarnings(ab_name(y[i], language = NULL, initial_search = FALSE))
+              y_name <- suppressWarnings(ab_name(y[i], language = NULL, loop_time = loop_time + 2))
               y[i] <- ifelse(!is.na(y_name),
                 y_name,
                 y[i]
@@ -378,7 +385,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
         )[[1]],
         collapse = "/"
       )
-      x_translated_guess <- suppressWarnings(as.ab(x_translated, initial_search = FALSE))
+      x_translated_guess <- suppressWarnings(as.ab(x_translated, loop_time = loop_time + 2))
       if (!is.na(x_translated_guess)) {
         x_new[i] <- x_translated_guess
         next
@@ -386,7 +393,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
 
       # try by removing all trailing capitals
       if (x[i] %like_case% "[a-z]+[A-Z]+$") {
-        found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), initial_search = FALSE))
+        found <- suppressWarnings(as.ab(gsub("[A-Z]+$", "", x[i], perl = TRUE), loop_time = loop_time + 2))
         if (!is.na(found)) {
           x_new[i] <- note_if_more_than_one_found(found, i, from_text)
           next
@@ -394,7 +401,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       }
 
       # keep only letters
-      found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), initial_search = FALSE))
+      found <- suppressWarnings(as.ab(gsub("[^A-Z]", "", x[i], perl = TRUE), loop_time = loop_time + 2))
       if (!is.na(found)) {
         x_new[i] <- note_if_more_than_one_found(found, i, from_text)
         next
@@ -405,7 +412,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       if (flag_multiple_results == TRUE) {
         found <- from_text[1L]
       } else {
-        found <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L]),
+        found <- tryCatch(suppressWarnings(ab_from_text(x[i], loop_time = loop_time + 2, translate_ab = FALSE)[[1]][1L]),
           error = function(e) NA_character_
         )
       }
@@ -415,12 +422,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       }
 
       # first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
-      found <- suppressWarnings(as.ab(substr(x[i], 1, 5), initial_search = FALSE))
-      if (!is.na(found) && ab_group(found, initial_search = FALSE) %unlike% "cephalosporins") {
+      found <- suppressWarnings(as.ab(substr(x[i], 1, 5), loop_time = loop_time + 2))
+      if (!is.na(found) && ab_group(found, loop_time = loop_time + 1) %unlike% "cephalosporins") {
         x_new[i] <- note_if_more_than_one_found(found, i, from_text)
         next
       }
-      found <- suppressWarnings(as.ab(substr(x[i], 1, 7), initial_search = FALSE))
+      found <- suppressWarnings(as.ab(substr(x[i], 1, 7), loop_time = loop_time + 2))
       if (!is.na(found)) {
         x_new[i] <- note_if_more_than_one_found(found, i, from_text)
         next
@@ -428,7 +435,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
 
       # make all consonants facultative
       search_str <- gsub("([BCDFGHJKLMNPQRSTVWXZ])", "\\1*", x[i], perl = TRUE)
-      found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
+      found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 2, already_regex = TRUE))
       # keep at least 4 normal characters
       if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 4) {
         found <- NA
@@ -440,7 +447,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
 
       # make all vowels facultative
       search_str <- gsub("([AEIOUY])", "\\1*", x[i], perl = TRUE)
-      found <- suppressWarnings(as.ab(search_str, initial_search = FALSE, already_regex = TRUE))
+      found <- suppressWarnings(as.ab(search_str, loop_time = loop_time + 2, already_regex = TRUE))
       # keep at least 5 normal characters
       if (nchar(gsub(".\\*", "", search_str, perl = TRUE)) < 5) {
         found <- NA
@@ -456,7 +463,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       x_spelling <- gsub("I+", "[AEIOU]+", x_spelling, fixed = TRUE)
       x_spelling <- gsub("O+", "[AEIOU]+", x_spelling, fixed = TRUE)
       x_spelling <- gsub("U+", "[AEIOU]+", x_spelling, fixed = TRUE)
-      found <- suppressWarnings(as.ab(x_spelling, initial_search = FALSE, already_regex = TRUE))
+      found <- suppressWarnings(as.ab(x_spelling, loop_time = loop_time + 2, already_regex = TRUE))
       if (!is.na(found)) {
         x_new[i] <- note_if_more_than_one_found(found, i, from_text)
         next
@@ -473,7 +480,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
           # ending part:
           substr(x[i], j + 2, nchar(x[i]))
         )
-        found <- suppressWarnings(as.ab(x_switched, initial_search = FALSE))
+        found <- suppressWarnings(as.ab(x_switched, loop_time = loop_time + 1))
         if (!is.na(found)) {
           break
         }
@@ -482,18 +489,18 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
         x_new[i] <- found[1L]
         next
       }
-    } # end of initial_search = TRUE
+    } # end of loop_time <= 2
 
     # not found
     x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
   }
 
-  if (isTRUE(initial_search) && sum(already_known) < length(x)) {
+  if (loop_time == 1 && sum(already_known) < length(x)) {
     close(progress)
   }
 
   # save to package env to save time for next time
-  if (isTRUE(initial_search)) {
+  if (loop_time == 1) {
     AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$x %in% x), , drop = FALSE]
     AMR_env$ab_previously_coerced <- unique(rbind_AMR(
       AMR_env$ab_previously_coerced,
@@ -518,6 +525,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
     x_unknown,
     AMR_env$ab_previously_coerced$x_bak[which(AMR_env$ab_previously_coerced$x %in% x & is.na(AMR_env$ab_previously_coerced$ab))]
   )
+  x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
   if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
       "in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
@@ -645,12 +653,14 @@ generalise_antibiotic_name <- function(x) {
   x <- gsub("_(MIC|RSI|SIR|DIS[CK])$", "", x, perl = TRUE)
   # remove disk concentrations, like LVX_NM -> LVX
   x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
-  # remove part between brackets if that's followed by another string
-  x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # keep only max 1 space
   x <- trimws2(gsub(" +", " ", x, perl = TRUE))
   # non-character, space or number should be a slash
-  x <- gsub("[^A-Z0-9 -]", "/", x, perl = TRUE)
+  x <- gsub("[^A-Z0-9 -)(]", "/", x, perl = TRUE)
+  # correct for 'high level' antibiotics
+  x <- gsub("([^A-Z0-9/ -]+)?(HIGH(.?LE?VE?L)?|[^A-Z0-9/]H[^A-Z0-9]?L)([^A-Z0-9 -]+)?", "-HIGH", x, perl = TRUE)
+  # remove part between brackets if that's followed by another string
+  x <- gsub("(.*)+ [(].*[)]", "\\1", x)
   # spaces around non-characters must be removed: amox + clav -> amox/clav
   x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
   x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x, perl = TRUE)

R/ab_from_text.R

@@ -129,6 +129,10 @@ ab_from_text <- function(text,
       text_split_all <- text_split_all[nchar(text_split_all) >= 4 & grepl("[a-z]+", text_split_all)]
       result <- lapply(text_split_all, function(text_split) {
         progress$tick()
+        text_split <- text_split[text_split %like% "[A-Z]" & text_split %unlike% "[0-9]"]
+        if (length(text_split) == 0) {
+          return(as.ab(NA_character_))
+        }
         suppressWarnings(
           as.ab(text_split, ...)
         )

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

@@ -57,59 +57,31 @@
 #' example_isolates
 #'
 #'
-#' # Examples sections below are split into 'base R', 'dplyr', and 'data.table':
-#'
-#'
-#' # base R ------------------------------------------------------------------
-#'
-#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
-#' example_isolates[, carbapenems()]
-#'
-#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
-#' example_isolates[, c("mo", aminoglycosides())]
-#'
-#' # select only antibiotic columns with DDDs for oral treatment
-#' example_isolates[, administrable_per_os()]
-#'
-#' # filter using any() or all()
-#' example_isolates[any(carbapenems() == "R"), ]
-#' subset(example_isolates, any(carbapenems() == "R"))
-#'
-#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
-#' example_isolates[any(carbapenems()), ]
-#' example_isolates[all(carbapenems()), ]
-#'
-#' # filter with multiple antibiotic selectors using c()
-#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
-#'
-#' # filter + select in one go: get penicillins in carbapenem-resistant strains
-#' example_isolates[any(carbapenems() == "R"), penicillins()]
-#'
-#' # You can combine selectors with '&' to be more specific. For example,
-#' # penicillins() would select benzylpenicillin ('peni G') and
-#' # administrable_per_os() would select erythromycin. Yet, when combined these
-#' # drugs are both omitted since benzylpenicillin is not administrable per os
-#' # and erythromycin is not a penicillin:
-#' example_isolates[, penicillins() & administrable_per_os()]
-#'
-#' # ab_selector() applies a filter in the `antibiotics` data set and is thus
-#' # very flexible. For instance, to select antibiotic columns with an oral DDD
-#' # of at least 1 gram:
-#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
-#'
+#' # Examples sections below are split into 'dplyr', 'base R', and 'data.table':
+#' 
 #' \donttest{
 #' # dplyr -------------------------------------------------------------------
+#' 
+#' if (require("dplyr")) {
+#'.  example_isolates %>% select(carbapenems())
+#' }
 #'
 #' if (require("dplyr")) {
-#'   tibble(kefzol = random_sir(5)) %>%
-#'     select(cephalosporins())
+#'   # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
+#'   example_isolates %>% select(mo, aminoglycosides())
+#' }
+#'
+#' if (require("dplyr")) {
+#'   # select only antibiotic columns with DDDs for oral treatment
+#'.  example_isolates %>% select(administrable_per_os())
 #' }
 #'
 #' if (require("dplyr")) {
 #'   # get AMR for all aminoglycosides e.g., per ward:
 #'   example_isolates %>%
 #'     group_by(ward) %>%
-#'     summarise(across(aminoglycosides(), resistance))
+#'     summarise(across(aminoglycosides(),
+#'                      resistance))
 #' }
 #' if (require("dplyr")) {
 #'   # You can combine selectors with '&' to be more specific:
@@ -121,7 +93,8 @@
 #'   example_isolates %>%
 #'     filter(mo_genus() %in% c("Escherichia", "Klebsiella")) %>%
 #'     group_by(ward) %>%
-#'     summarise(across(not_intrinsic_resistant(), resistance))
+#'     summarise_at(not_intrinsic_resistant(),
+#'                  resistance)
 #' }
 #' if (require("dplyr")) {
 #'   # get susceptibility for antibiotics whose name contains "trim":
@@ -187,6 +160,44 @@
 #' }
 #'
 #'
+#' # base R ------------------------------------------------------------------
+#'
+#' # select columns 'IPM' (imipenem) and 'MEM' (meropenem)
+#' example_isolates[, carbapenems()]
+#'
+#' # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
+#' example_isolates[, c("mo", aminoglycosides())]
+#'
+#' # select only antibiotic columns with DDDs for oral treatment
+#' example_isolates[, administrable_per_os()]
+#'
+#' # filter using any() or all()
+#' example_isolates[any(carbapenems() == "R"), ]
+#' subset(example_isolates, any(carbapenems() == "R"))
+#'
+#' # filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
+#' example_isolates[any(carbapenems()), ]
+#' example_isolates[all(carbapenems()), ]
+#'
+#' # filter with multiple antibiotic selectors using c()
+#' example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
+#'
+#' # filter + select in one go: get penicillins in carbapenem-resistant strains
+#' example_isolates[any(carbapenems() == "R"), penicillins()]
+#'
+#' # You can combine selectors with '&' to be more specific. For example,
+#' # penicillins() would select benzylpenicillin ('peni G') and
+#' # administrable_per_os() would select erythromycin. Yet, when combined these
+#' # drugs are both omitted since benzylpenicillin is not administrable per os
+#' # and erythromycin is not a penicillin:
+#' example_isolates[, penicillins() & administrable_per_os()]
+#'
+#' # ab_selector() applies a filter in the `antibiotics` data set and is thus
+#' # very flexible. For instance, to select antibiotic columns with an oral DDD
+#' # of at least 1 gram:
+#' example_isolates[, ab_selector(oral_ddd > 1 & oral_units == "g")]
+#'
+#'
 #' # data.table --------------------------------------------------------------
 #'
 #' # data.table is supported as well, just use it in the same way as with
@@ -226,10 +237,6 @@ 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 +249,6 @@ 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 +280,6 @@ 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 +287,6 @@ 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 +294,6 @@ 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 +301,6 @@ 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 +309,6 @@ 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 +317,6 @@ 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 +324,6 @@ 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 +331,6 @@ 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 +338,6 @@ 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 +345,6 @@ 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 +352,6 @@ 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 +359,6 @@ 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 +366,6 @@ 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)
 }
 
@@ -422,32 +373,21 @@ 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)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @export
-lincosamides <- function(only_sir_columns = FALSE, ...) {
+lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  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)
+  meet_criteria(only_treatable, allow_class = "logical", has_length = 1)
+  ab_select_exec("lincosamides", only_sir_columns = only_sir_columns, only_treatable = only_treatable)
 }
 
 #' @rdname antibiotic_class_selectors
 #' @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)
 }
 
@@ -455,21 +395,20 @@ 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)
 }
 
+#' @rdname antibiotic_class_selectors
+#' @export
+nitrofurans <- function(only_sir_columns = FALSE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("nitrofurans", only_sir_columns = only_sir_columns)
+}
+
 #' @rdname antibiotic_class_selectors
 #' @export
 oxazolidinones <- function(only_sir_columns = FALSE, ...) {
   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 +416,6 @@ 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)
 }
 
@@ -489,43 +424,34 @@ 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)
 }
 
-#' @rdname antibiotic_class_selectors
-#' @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(...)$only_rsi_columns
-  }
-  ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
-}
-
 #' @rdname antibiotic_class_selectors
 #' @export
 quinolones <- function(only_sir_columns = FALSE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-  if ("only_rsi_columns" %in% names(list(...))) {
-    deprecation_warning("only_rsi_columns", "only_sir_columns", is_function = FALSE)
-    only_sir_columns <- list(...)$only_rsi_columns
-  }
   ab_select_exec("quinolones", only_sir_columns = only_sir_columns)
 }
 
+#' @rdname antibiotic_class_selectors
+#' @export
+rifamycins <- function(only_sir_columns = FALSE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("rifamycins", only_sir_columns = only_sir_columns)
+}
+
+#' @rdname antibiotic_class_selectors
+#' @export
+streptogramins <- function(only_sir_columns = FALSE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("streptogramins", only_sir_columns = only_sir_columns)
+}
+
 #' @rdname antibiotic_class_selectors
 #' @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 +459,6 @@ 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 +466,6 @@ 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 +567,10 @@ 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 +581,7 @@ 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))
@@ -687,9 +605,9 @@ ab_select_exec <- function(function_name,
 
   # untreatable drugs
   if (only_treatable == TRUE) {
-    untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
+    untreatable <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$name %like% "-high|EDTA|polysorbate|macromethod|screening|nacubactam"), "ab", drop = TRUE]
     if (any(untreatable %in% names(ab_in_data))) {
-      if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
+      if (message_not_thrown_before(function_name, "ab_class", "untreatable")) {
         warning_(
           "in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
           vector_and(
@@ -699,8 +617,7 @@ ab_select_exec <- function(function_name,
             ),
             quotes = FALSE,
             sort = TRUE
-          ), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
-          "This warning will be shown once per session."
+          ), ". They can be included using `", function_name, "(only_treatable = FALSE)`."
         )
       }
       ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
@@ -719,7 +636,7 @@ ab_select_exec <- function(function_name,
     } else if (isTRUE(function_name == "antimycobacterials")) {
       abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")]
     } else {
-      # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_hook.R
+      # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_checks.R
       # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
       abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))
       # manually added codes from add_custom_antimicrobials() must also be supported
@@ -773,6 +690,16 @@ ab_select_exec <- function(function_name,
   )
 }
 
+#' @method print ab_selector
+#' @export
+#' @noRd
+print.ab_selector <- function(x, ...) {
+  warning_("It should never be needed to print an antibiotic selector class. Are you using data.table? Then add the argument `with = FALSE`, see our examples at `?ab_selector`.",
+           immediate = TRUE)
+  cat("Class 'ab_selector'\n")
+  print(as.character(x), quote = FALSE)
+}
+
 #' @method c ab_selector
 #' @export
 #' @noRd
@@ -784,10 +711,10 @@ c.ab_selector <- function(...) {
 
 all_any_ab_selector <- function(type, ..., na.rm = TRUE) {
   cols_ab <- c(...)
-  result <- cols_ab[toupper(cols_ab) %in% c("S", "I", "R")]
+  result <- cols_ab[toupper(cols_ab) %in% c("S", "SDD", "I", "R", "NI")]
   if (length(result) == 0) {
     message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
-    result <- c("S", "I", "R")
+    result <- c("S", "SDD", "I", "R", "NI")
   }
   cols_ab <- cols_ab[!cols_ab %in% result]
   df <- get_current_data(arg_name = NA, call = -3)
@@ -896,7 +823,7 @@ any.ab_selector_any_all <- function(..., na.rm = FALSE) {
     }
   }
   # this is `!=`, so turn around the values
-  sir <- c("S", "I", "R")
+  sir <- c("S", "SDD", "I", "R", "NI")
   e2 <- sir[sir != e2]
   structure(all_any_ab_selector(type = type, e1, e2),
     class = c("ab_selector_any_all", "logical")

R/antibiogram.R

@@ -294,7 +294,7 @@ antibiogram <- function(x,
   } else if (mo_transform == "name") {
     x$`.mo` <- mo_name(x$`.mo`, language = language)
   } else {
-    x$`.mo` <- mo_property(x$`.mo`, language = language)
+    x$`.mo` <- mo_property(x$`.mo`, property = mo_transform, language = language)
   }
   x$`.mo`[is.na(x$`.mo`)] <- "(??)"
 
@@ -348,11 +348,11 @@ antibiogram <- function(x,
       } else {
         # determine whether this new column should contain S, I, R, or NA
         if (isTRUE(combine_SI)) {
-          S_values <- c("S", "I")
+          S_values <- c("S", "SDD", "I")
         } else {
           S_values <- "S"
         }
-        other_values <- setdiff(c("S", "I", "R"), S_values)
+        other_values <- setdiff(c("S", "SDD", "I", "R", "NI"), S_values)
         x_transposed <- as.list(as.data.frame(t(x[, abx, drop = FALSE]), stringsAsFactors = FALSE))
         if (isTRUE(only_all_tested)) {
           x[new_colname] <- as.sir(vapply(FUN.VALUE = character(1), x_transposed, function(x) ifelse(anyNA(x), NA_character_, ifelse(any(x %in% S_values), "S", "R")), USE.NAMES = FALSE))

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/bug_drug_combinations.R

@@ -42,7 +42,7 @@
 #' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
 #' @export
 #' @rdname bug_drug_combinations
-#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "I", "R" and "total".
+#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", and "total".
 #' @examples
 #' # example_isolates is a data set available in the AMR package.
 #' # run ?example_isolates for more info.
@@ -105,8 +105,10 @@ bug_drug_combinations <- function(x,
       mo = character(0),
       ab = character(0),
       S = integer(0),
+      SDD = integer(0),
       I = integer(0),
       R = integer(0),
+      N = integer(0),
       total = integer(0),
       stringsAsFactors = FALSE
     )
@@ -121,17 +123,19 @@ bug_drug_combinations <- function(x,
       x_mo_filter <- x[which(x[, col_mo, drop = TRUE] == unique_mo[i]), names(which(vapply(FUN.VALUE = logical(1), x, is.sir))), drop = FALSE]
       # turn and merge everything
       pivot <- lapply(x_mo_filter, function(x) {
-        m <- as.matrix(table(x))
-        data.frame(S = m["S", ], I = m["I", ], R = m["R", ], stringsAsFactors = FALSE)
+        m <- as.matrix(table(as.sir(x)))
+        data.frame(S = m["S", ], SDD = m["SDD", ], I = m["I", ], R = m["R", ], NI = m["NI", ], stringsAsFactors = FALSE)
       })
       merged <- do.call(rbind_AMR, pivot)
       out_group <- data.frame(
         mo = rep(unique_mo[i], NROW(merged)),
         ab = rownames(merged),
         S = merged$S,
+        SDD = merged$SDD,
         I = merged$I,
         R = merged$R,
-        total = merged$S + merged$I + merged$R,
+        NI = merged$NI,
+        total = merged$S + merged$SDD + merged$I + merged$R + merged$NI,
         stringsAsFactors = FALSE
       )
       if (data_has_groups) {
@@ -203,12 +207,16 @@ format.bug_drug_combinations <- function(x,
       mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
       ab = gsub("(.*)%%(.*)", "\\2", names(idx)),
       S = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$S[i], na.rm = TRUE)),
+      SDD = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$SDD[i], na.rm = TRUE)),
       I = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$I[i], na.rm = TRUE)),
       R = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$R[i], na.rm = TRUE)),
+      NI = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NI[i], na.rm = TRUE)),
       total = vapply(FUN.VALUE = double(1), idx, function(i) {
         sum(x$S[i], na.rm = TRUE) +
+          sum(x$SDD[i], na.rm = TRUE) +
           sum(x$I[i], na.rm = TRUE) +
-          sum(x$R[i], na.rm = TRUE)
+          sum(x$R[i], na.rm = TRUE) +
+          sum(x$NI[i], na.rm = TRUE)
       }),
       stringsAsFactors = FALSE
     )
@@ -223,7 +231,7 @@ format.bug_drug_combinations <- function(x,
   if (combine_SI == TRUE) {
     x$isolates <- x$R
   } else {
-    x$isolates <- x$R + x$I
+    x$isolates <- x$R + x$I + x$SDD
   }
 
   give_ab_name <- function(ab, format, language) {

R/count.R

@@ -135,62 +135,7 @@ count_resistant <- function(..., only_all_tested = FALSE) {
 count_susceptible <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I"),
-      only_all_tested = only_all_tested,
-      only_count = TRUE
-    ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
-  )
-}
-
-#' @rdname count
-#' @export
-count_R <- function(..., only_all_tested = FALSE) {
-  tryCatch(
-    sir_calc(...,
-      ab_result = "R",
-      only_all_tested = only_all_tested,
-      only_count = TRUE
-    ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
-  )
-}
-
-#' @rdname count
-#' @export
-count_IR <- function(..., only_all_tested = FALSE) {
-  if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
-    message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" being resistant. This note will be shown once for this session.", as_note = FALSE)
-  }
-  tryCatch(
-    sir_calc(...,
-      ab_result = c("I", "R"),
-      only_all_tested = only_all_tested,
-      only_count = TRUE
-    ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
-  )
-}
-
-#' @rdname count
-#' @export
-count_I <- function(..., only_all_tested = FALSE) {
-  tryCatch(
-    sir_calc(...,
-      ab_result = "I",
-      only_all_tested = only_all_tested,
-      only_count = TRUE
-    ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
-  )
-}
-
-#' @rdname count
-#' @export
-count_SI <- function(..., only_all_tested = FALSE) {
-  tryCatch(
-    sir_calc(...,
-      ab_result = c("S", "I"),
+      ab_result = c("S", "SDD", "I"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -202,7 +147,7 @@ count_SI <- function(..., only_all_tested = FALSE) {
 #' @export
 count_S <- function(..., only_all_tested = FALSE) {
   if (message_not_thrown_before("count_S", entire_session = TRUE)) {
-    message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
+    message_("Using `count_S()` is discouraged; use `count_susceptible()` instead to also consider \"I\" and \"SDD\" being susceptible. This note will be shown once for this session.", as_note = FALSE)
   }
   tryCatch(
     sir_calc(...,
@@ -214,12 +159,73 @@ count_S <- function(..., only_all_tested = FALSE) {
   )
 }
 
+#' @rdname count
+#' @export
+count_SI <- function(..., only_all_tested = FALSE) {
+  if (message_not_thrown_before("count_SI", entire_session = TRUE)) {
+    message_("Note that `count_SI()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+  }
+  tryCatch(
+    sir_calc(...,
+             ab_result = c("S", "SDD", "I"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE
+    ),
+    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+  )
+}
+
+#' @rdname count
+#' @export
+count_I <- function(..., only_all_tested = FALSE) {
+  if (message_not_thrown_before("count_I", entire_session = TRUE)) {
+    message_("Note that `count_I()` will also count dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+  }
+  tryCatch(
+    sir_calc(...,
+             ab_result = c("I", "SDD"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE
+    ),
+    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+  )
+}
+
+#' @rdname count
+#' @export
+count_IR <- function(..., only_all_tested = FALSE) {
+  if (message_not_thrown_before("count_IR", entire_session = TRUE)) {
+    message_("Using `count_IR()` is discouraged; use `count_resistant()` instead to not consider \"I\" and \"SDD\" being resistant. This note will be shown once for this session.", as_note = FALSE)
+  }
+  tryCatch(
+    sir_calc(...,
+             ab_result = c("I", "SDD", "R"),
+             only_all_tested = only_all_tested,
+             only_count = TRUE
+    ),
+    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+  )
+}
+
+#' @rdname count
+#' @export
+count_R <- function(..., only_all_tested = FALSE) {
+  tryCatch(
+    sir_calc(...,
+             ab_result = "R",
+             only_all_tested = only_all_tested,
+             only_count = TRUE
+    ),
+    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+  )
+}
+
 #' @rdname count
 #' @export
 count_all <- function(..., only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I", "R"),
+      ab_result = c("S", "SDD", "I", "R", "NI"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),

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/custom_eucast_rules.R

@@ -30,7 +30,7 @@
 #' Define Custom EUCAST Rules
 #'
 #' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
-#' @param ... rules in [formula][base::tilde] notation, see *Examples*
+#' @param ... rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*
 #' @details
 #' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
 #' @section How it works:
@@ -89,11 +89,24 @@
 #' #> 2 Klebsiella pneumoniae   R    R     S
 #' ```
 #'
-#' ### Usage of antibiotic group names
+#' ### Usage of multiple antibiotics and antibiotic group names
+#' 
+#' You can define antibiotic groups instead of single antibiotics for the rule consequence, which is the part *after* the tilde (~). In the examples above, the antibiotic group `aminopenicillins` includes both ampicillin and amoxicillin.
+#' 
+#' Rules can also be applied to multiple antibiotics and antibiotic groups simultaneously. Use the `c()` function to combine multiple antibiotics. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":
+#' 
+#' ```r
+#' x <- custom_eucast_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R")
+#' x
+#' #> A set of custom EUCAST rules:
+#' #> 
+#' #>   1. If TZP is "R" then set to "R":
+#' #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
+#' ```
 #'
-#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.
+#' These `r length(DEFINED_AB_GROUPS)` antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
 #'
-#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
+#' `r paste0("  * ", sapply(DEFINED_AB_GROUPS, function(x) paste0(tolower(gsub("^AB_", "", x)), "\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
 #' @returns A [list] containing the custom rules
 #' @export
 #' @examples
@@ -156,24 +169,34 @@ custom_eucast_rules <- function(...) {
       "the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`"
     )
     result_group <- as.character(result)[[2]]
-    if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
-      # support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
-      result_group <- paste0(result_group, "s")
+    result_group<- as.character(str2lang(result_group))
+    result_group <- result_group[result_group != "c"]
+    result_group_agents <- character(0)
+    for (j in seq_len(length(result_group))) {
+      if (paste0("AB_", toupper(result_group[j]), "S") %in% DEFINED_AB_GROUPS) {
+        # support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
+        result_group[j] <- paste0(result_group[j], "s")
+      }
+      if (paste0("AB_", toupper(result_group[j])) %in% DEFINED_AB_GROUPS) {
+        result_group_agents <- c(result_group_agents,
+                                 eval(parse(text = paste0("AB_", toupper(result_group[j]))), envir = asNamespace("AMR")))
+      } else {
+        out_group <- tryCatch(
+          suppressWarnings(as.ab(result_group[j],
+                                 fast_mode = TRUE,
+                                 flag_multiple_results = FALSE
+          )),
+          error = function(e) NA_character_
+        )
+        if (!all(is.na(out_group))) {
+          result_group_agents <- c(result_group_agents, out_group)
+        }
+      }
     }
-    if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) {
-      result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR"))
-    } else {
-      result_group <- tryCatch(
-        suppressWarnings(as.ab(result_group,
-          fast_mode = TRUE,
-          flag_multiple_results = FALSE
-        )),
-        error = function(e) NA_character_
-      )
-    }
-
+    result_group_agents <- result_group_agents[!is.na(result_group_agents)]
+    
     stop_if(
-      any(is.na(result_group)),
+      length(result_group_agents) == 0,
       "this result of rule ", i, " could not be translated to a single antimicrobial drug/group: \"",
       as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial drug, or be one of: ",
       vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), "."
@@ -181,12 +204,12 @@ custom_eucast_rules <- function(...) {
     result_value <- as.character(result)[[3]]
     result_value[result_value == "NA"] <- NA
     stop_ifnot(
-      result_value %in% c("S", "I", "R", NA),
-      "the resulting value of rule ", i, " must be either \"S\", \"I\", \"R\" or NA"
+      result_value %in% c("S", "SDD", "I", "R", "NI", NA),
+      "the resulting value of rule ", i, " must be either \"S\", \"SDD\", \"I\", \"R\", \"NI\" or NA"
     )
     result_value <- as.sir(result_value)
 
-    out[[i]]$result_group <- result_group
+    out[[i]]$result_group <- result_group_agents
     out[[i]]$result_value <- result_value
   }
 

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()]
@@ -291,7 +298,7 @@
 #' ### Download
 #' Like all data sets in this package, this data set is 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). They allow for machine reading EUCAST and CLSI guidelines, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI, though initiatives have started to overcome these burdens.
 #' 
-#' **NOTE:** this `AMR` package (and the WHONET software as well) contains internal methods to apply the guidelines, which is rather complex. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the [microorganisms.groups] data set). It is important that this is considered when using the breakpoints for own use.
+#' **NOTE:** this `AMR` package (and the WHONET software as well) contains rather complex internal methods to apply the guidelines. For example, some breakpoints must be applied on certain species groups (which are in case of this package available through the [microorganisms.groups] data set). It is important that this is considered when using the breakpoints for own use.
 #' @seealso [intrinsic_resistant]
 #' @examples
 #' clinical_breakpoints

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()
 
@@ -463,7 +462,7 @@ eucast_rules <- function(x,
           font_red(paste0(
             "v", utils::packageDescription("AMR")$Version, ", ",
             format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y")
-          )), "), see ?eucast_rules\n"
+          )), "), see `?eucast_rules`\n"
         ))
       ))
     }
@@ -591,7 +590,7 @@ eucast_rules <- function(x,
     # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
     eucast_rules_df <- list(...)$eucast_rules_df
   } else {
-    # otherwise internal data file, created in data-raw/_pre_commit_hook.R
+    # otherwise internal data file, created in data-raw/_pre_commit_checks.R
     eucast_rules_df <- EUCAST_RULES_DF
   }
 
@@ -890,6 +889,7 @@ eucast_rules <- function(x,
           ),
           type = "ansi"
         ))
+        cat("\n")
         warned <- FALSE
       }
       run_changes <- edit_sir(

R/export_biosample.R

@@ -0,0 +1,57 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
+# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
+# Data. Journal of Statistical Software, 104(3), 1-31.                 #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+#' Export Data Set as NCBI BioSample Antibiogram
+#'
+#' 
+#' @param x a data set 
+#' @param filename a character string specifying the file name
+#' @param type a character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see <https://www.ncbi.nlm.nih.gov/biosample/docs/>
+#' @keywords internal
+export_ncbi_biosample <- function(x,
+                                  filename = paste0("biosample_", format(Sys.time(), "%Y-%m-%d-%H%M%S"), ".xlsx"),
+                                  type = "pathogen MIC",
+                                  columns = where(is.mic),
+                                  save_as_xlsx = TRUE) {
+  meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
+  meet_criteria(filename, allow_class = "character", has_length = 1)
+  meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("pathogen MIC", "beta-lactamase MIC"))
+  meet_criteria(save_as_xlsx, allow_class = "logical", has_length = 1)
+  
+  out <- x %pm>%
+    pm_select(columns)
+  stop_if(NROW(out) == 0, "No columns found.")
+  
+  if (isTRUE(save_as_xlsx)) {
+    export <- import_fn("write.xlsx", pkg = "openxlsx", error_on_fail = TRUE)
+    export(out, file = filename, overwrite = TRUE, asTable = FALSE)
+  } else {
+    out
+  }
+}

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.
@@ -240,7 +236,7 @@ first_isolate <- function(x = NULL,
     FUN.VALUE = logical(1),
     X = x,
     # check only first 10,000 rows
-    FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "I", "R"), na.rm = TRUE),
+    FUN = function(x) any(as.character(x[1:10000]) %in% c("S", "SDD", "I", "R", "NI"), na.rm = TRUE),
     USE.NAMES = FALSE
   ))
   if (method == "phenotype-based" && !any_col_contains_sir) {
@@ -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/guess_ab_col.R

@@ -335,7 +335,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
   x_new <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `AB_CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `AB_CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AMR_env$AB_lookup$ab) {
       # separate drugs, such as `AMX`

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)
@@ -192,7 +188,7 @@ key_antimicrobials <- function(x = NULL,
           "No columns available ",
           paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")
         ),
-        "as key antimicrobials for ", name, "s. See ?key_antimicrobials."
+        "as key antimicrobials for ", name, "s. See `?key_antimicrobials`."
       )
     }
 
@@ -286,6 +282,8 @@ generate_antimcrobials_string <- function(df) {
           as.list(df),
           function(x) {
             x <- toupper(as.character(x))
+            x[x == "SDD"] <- "I"
+            # ignore "NI" here, no use for determining first isolates
             x[!x %in% c("S", "I", "R")] <- "."
             paste(x)
           }
@@ -316,7 +314,7 @@ antimicrobials_equal <- function(y,
     val <- strsplit(val, "", fixed = TRUE)[[1L]]
     val.int <- rep(NA_real_, length(val))
     val.int[val == "S"] <- 1
-    val.int[val == "I"] <- 2
+    val.int[val %in% c("I", "SDD")] <- 2
     val.int[val == "R"] <- 3
     val.int
   }

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")
   }
@@ -736,7 +732,7 @@ mdro <- function(x = NULL,
           sum(vapply(
             FUN.VALUE = logical(1),
             group_tbl,
-            function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))
+            function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "SDD", "I", "R"))
           ))
         }
       )
@@ -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 +27,25 @@
 # 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)))
+COMMON_MIC_VALUES <- c(0.001, 0.002, 0.004, 0.008, 0.016, 0.032, 0.064,
+                       0.125, 0.25, 0.5, 1, 2, 4, 8, 16, 32,
+                       64, 128, 256, 512, 1024)
 
 #' Transform Input to Minimum Inhibitory Concentrations (MIC)
 #'
@@ -76,6 +53,7 @@ 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 +93,16 @@ 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 [rescale_mic()], 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 +118,9 @@ valid_mic_levels <- c(
 #' fivenum(mic_data)
 #' quantile(mic_data)
 #' all(mic_data < 512)
+#' 
+#' # limit MICs using rescale_mic()
+#' rescale_mic(mic_data, mic_range = c(4, 16))
 #'
 #' # interpret MIC values
 #' as.sir(
@@ -161,113 +146,182 @@ 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")
+rescale_mic <- 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 <- plotrange_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 +343,7 @@ 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")
@@ -296,32 +351,50 @@ 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, ...) {
+  if(!identical(levels(x), VALID_MIC_LEVELS) && message_not_thrown_before("pillar_shaft.mic")) {
+    warning_(AMR_env$sup_1_icon, " These columns contain an outdated or altered structure - convert with `as.mic()` to update",
+             call = FALSE)
+  }
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
   operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
   out[is.na(x)] <- font_na(NA)
-  # maketrailing zeroes almost invisible
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", 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))))
 }
 
 # will be exported using s3_register() in R/zzz.R
 type_sum.mic <- function(x, ...) {
-  "mic"
+  if(!identical(levels(x), VALID_MIC_LEVELS)) {
+    paste0("mic", AMR_env$sup_1_icon)
+  } else {
+    "mic"
+  }
 }
 
 #' @method print mic
 #' @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'")
+  if(!identical(levels(x), VALID_MIC_LEVELS)) {
+    cat(font_red(" with an outdated or altered structure - convert with `as.mic()` to update"))
+  }
+  cat("\n")
   print(as.character(x), quote = FALSE)
   att <- attributes(x)
   if ("na.action" %in% names(att)) {
@@ -342,22 +415,44 @@ 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.", 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 +460,7 @@ 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 +468,7 @@ 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 +482,7 @@ c.mic <- function(...) {
 #' @noRd
 unique.mic <- function(x, incomparables = FALSE, ...) {
   y <- NextMethod()
-  attributes(y) <- attributes(x)
-  y
+  as.mic(y)
 }
 
 #' @method rep mic
@@ -398,20 +490,25 @@ 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
+  dbl <- as.double(x)
+  # make sure that e.g. '<0.001' comes before '0.001', and '>0.001' comes after
+  dbl[as.character(x) %like% "<[0-9]"] <- dbl[as.character(x) %like% "<[0-9]"] - 0.000002
+  dbl[as.character(x) %like% "<="] <- dbl[as.character(x) %like% "<="] - 0.000001
+  dbl[as.character(x) %like% ">="] <- dbl[as.character(x) %like% ">="] + 0.000001
+  dbl[as.character(x) %like% ">[0-9]"] <- dbl[as.character(x) %like% ">[0-9]"] + 0.000002
   if (decreasing == TRUE) {
-    ord <- order(-as.double(x))
+    x[order(-dbl)]
   } else {
-    ord <- order(as.double(x))
+    x[order(dbl)]
   }
-  x[ord]
 }
 
 #' @method hist mic
@@ -425,6 +522,7 @@ 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 +560,57 @@ 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 .Generic 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)
@@ -285,7 +285,9 @@ as.mo <- function(x,
       # do a pre-match on first character (and if it contains a space, first chars of first two terms)
       if (length(x_parts) %in% c(2, 3)) {
         # for genus + species + subspecies
-        if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
+        if (paste(x_parts[1:2], collapse = " ") %in% AMR_env$MO_lookup$fullname_lower) {
+          filtr <- which(AMR_env$MO_lookup$fullname_lower %like% paste(x_parts[1:2], collapse = " "))
+        } else if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
           filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) &
                            (AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
                               AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
@@ -460,7 +462,7 @@ as.mo <- function(x,
       }
     }
     
-    # 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_hook.R
+    # 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_checks.R
     out[out %in% MO_CONS] <- "B_STPHY_CONS"
     out[out %in% MO_COPS] <- "B_STPHY_COPS"
     if (Becker == "all") {

R/mo_property.R

@@ -106,7 +106,12 @@
 #' mo_rank("Klebsiella pneumoniae")
 #' mo_url("Klebsiella pneumoniae")
 #' mo_is_yeast(c("Candida", "Trichophyton", "Klebsiella"))
-#'
+#' 
+#' mo_group_members("Streptococcus group A")
+#' mo_group_members(c("Streptococcus group C",
+#'                    "Streptococcus group G",
+#'                    "Streptococcus group L"))
+#' 
 #'
 #' # scientific reference -----------------------------------------------------
 #'
@@ -245,7 +250,7 @@ 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)
@@ -796,6 +801,37 @@ mo_current <- function(x, language = get_AMR_locale(), ...) {
   mo_name(out, language = language)
 }
 
+
+#' @rdname mo_property
+#' @export
+mo_group_members <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
+  if (missing(x)) {
+    # this tries to find the data and an 'mo' column
+    x <- find_mo_col(fn = "mo_synonyms")
+  }
+  meet_criteria(x, allow_NA = TRUE)
+  language <- validate_language(language)
+  meet_criteria(keep_synonyms, allow_class = "logical", has_length = 1)
+  
+  add_MO_lookup_to_AMR_env()
+  
+  x.mo <- as.mo(x, language = language, keep_synonyms = keep_synonyms, ...)
+  metadata <- get_mo_uncertainties()
+  
+  members <- lapply(x.mo, function(y) {
+    AMR::microorganisms.groups$mo_name[which(AMR::microorganisms.groups$mo_group == y)]
+  })
+  names(members) <- mo_name(x, keep_synonyms = TRUE, language = language)
+  
+  if (length(members) == 1) {
+    members <- unname(unlist(members))
+  }
+  
+  load_mo_uncertainties(metadata)
+  members
+}
+
+
 #' @rdname mo_property
 #' @export
 mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
@@ -823,7 +859,8 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
         ref = mo_ref(y, keep_synonyms = keep_synonyms),
         snomed = unlist(mo_snomed(y, keep_synonyms = keep_synonyms)),
         lpsn = mo_lpsn(y, language = language, keep_synonyms = keep_synonyms),
-        gbif = mo_gbif(y, language = language, keep_synonyms = keep_synonyms)
+        gbif = mo_gbif(y, language = language, keep_synonyms = keep_synonyms),
+        group_members = mo_group_members(y, language = language, keep_synonyms = keep_synonyms)
       )
     )
   })

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/pca.R

@@ -113,7 +113,7 @@ pca <- function(x,
 
     x <- as.data.frame(new_list, stringsAsFactors = FALSE)
     if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
-      warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in ?pca.", call = FALSE)
+      warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in `?pca`.", call = FALSE)
     }
 
     # set column names

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$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_y_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_y_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    rescale_mic(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$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
+#' @export
+#' @inheritParams as.mic
+#' @rdname plot
+scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...) {
+  stop_ifnot_installed("ggplot2")
+  meet_criteria(drop, allow_class = "logical", has_length = 1)
+  scale <- ggplot2::scale_fill_discrete(drop = drop, ...)
+  scale$transform <- function(x, keep_ops = keep_operators, mic_rng = mic_range) {
+    rescale_mic(x = x, keep_operators = keep_ops, mic_range = mic_rng, as.mic = FALSE)
+  }
+  scale
+}
+
 #' @method plot mic
 #' @importFrom graphics barplot axis mtext legend
 #' @export
@@ -103,21 +184,18 @@ plot.mic <- function(x,
   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)
 
+  x <- as.mic(x) # make sure that currently implemented MIC levels are used
+  
   if (length(colours_SIR) == 1) {
     colours_SIR <- rep(colours_SIR, 3)
   }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
-  x <- plot_prepare_table(x, expand = expand)
-
+  x <- plotrange_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -193,15 +271,13 @@ barplot.mic <- 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)
 
   main <- gsub(" +", " ", paste0(main, collapse = " "))
+  
+  height <- as.mic(height) # make sure that currently implemented MIC levels are used
 
   plot(
     x = height,
@@ -239,10 +315,6 @@ autoplot.mic <- function(object,
   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 +326,8 @@ autoplot.mic <- function(object,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
 
-  x <- plot_prepare_table(object, expand = expand)
+  object <- as.mic(object) # make sure that currently implemented MIC levels are used
+  x <- plotrange_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -290,6 +363,7 @@ autoplot.mic <- function(object,
   if (any(colours_SIR %in% cols_sub$cols)) {
     vals <- c(
       "(S) Susceptible" = colours_SIR[1],
+      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
       "(I) Susceptible, incr. exp." = colours_SIR[2],
       "(I) Intermediate" = colours_SIR[2],
       "(R) Resistant" = colours_SIR[3]
@@ -316,12 +390,14 @@ 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(plotrange_as_table(object, expand = FALSE)),
     c("x", "y")
   )
 }
 
+
 #' @method plot disk
 #' @export
 #' @importFrom graphics barplot axis mtext legend
@@ -345,10 +421,6 @@ 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 +430,7 @@ plot.disk <- function(x,
   }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
-  x <- plot_prepare_table(x, expand = expand)
-
+  x <- plotrange_as_table(x, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -435,10 +506,6 @@ 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(...)$colours_RSI
-  }
   meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
   language <- validate_language(language)
   meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -481,10 +548,6 @@ autoplot.disk <- function(object,
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if ("colours_RSI" %in% names(list(...))) {
-    deprecation_warning(extra_msg = "The 'colours_RSI' argument has been replaced with 'colours_SIR'.")
-    colours_SIR <- list(...)$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 +559,7 @@ autoplot.disk <- function(object,
     title <- gsub(" +", " ", paste0(title, collapse = " "))
   }
 
-  x <- plot_prepare_table(object, expand = expand)
+  x <- plotrange_as_table(object, expand = expand)
   cols_sub <- plot_colours_subtitle_guideline(
     x = x,
     mo = mo,
@@ -533,6 +596,7 @@ autoplot.disk <- function(object,
   if (any(colours_SIR %in% cols_sub$cols)) {
     vals <- c(
       "(S) Susceptible" = colours_SIR[1],
+      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
       "(I) Susceptible, incr. exp." = colours_SIR[2],
       "(I) Intermediate" = colours_SIR[2],
       "(R) Resistant" = colours_SIR[3]
@@ -560,7 +624,7 @@ autoplot.disk <- function(object,
 # will be exported using s3_register() in R/zzz.R
 fortify.disk <- function(object, ...) {
   stats::setNames(
-    as.data.frame(plot_prepare_table(object, expand = FALSE)),
+    as.data.frame(plotrange_as_table(object, expand = FALSE)),
     c("x", "y")
   )
 }
@@ -586,14 +650,21 @@ plot.sir <- function(x,
   if (!"S" %in% data$x) {
     data <- rbind_AMR(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE))
   }
+  if (!"SDD" %in% data$x) {
+    data <- rbind_AMR(data, data.frame(x = "SDD", n = 0, s = 0, stringsAsFactors = FALSE))
+  }
   if (!"I" %in% data$x) {
     data <- rbind_AMR(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE))
   }
   if (!"R" %in% data$x) {
     data <- rbind_AMR(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE))
   }
-
-  data$x <- factor(data$x, levels = c("S", "I", "R"), ordered = TRUE)
+  if (!"NI" %in% data$x) {
+    data <- rbind_AMR(data, data.frame(x = "NI", n = 0, s = 0, stringsAsFactors = FALSE))
+  }
+  
+  data <- data[!(data$n == 0 & data$x %in% c("SDD", "I", "NI")), , drop = FALSE]
+  data$x <- factor(data$x, levels = intersect(unique(data$x), c("S", "SDD", "I", "R", "NI")), ordered = TRUE)
 
   ymax <- pm_if_else(max(data$s) > 95, 105, 100)
 
@@ -635,10 +706,6 @@ 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)
@@ -646,10 +713,15 @@ barplot.sir <- function(height,
   if (length(colours_SIR) == 1) {
     colours_SIR <- rep(colours_SIR, 3)
   }
+  # add SDD and N to colours
+  colours_SIR <- c(colours_SIR[1:2], colours_SIR[2], colours_SIR[3], "#888888")
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
   x <- table(height)
-  x <- x[c(1, 2, 3)]
+  # remove missing I, SDD, and N
+  colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
+  x <- x[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
+  # plot it
   barplot(x,
     col = colours_SIR,
     xlab = xlab,
@@ -688,15 +760,18 @@ autoplot.sir <- function(object,
   }
 
   df <- as.data.frame(table(object), stringsAsFactors = TRUE)
-  colnames(df) <- c("sir", "count")
+  colnames(df) <- c("x", "n")
+  df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "NI")), , drop = FALSE]
   ggplot2::ggplot(df) +
-    ggplot2::geom_col(ggplot2::aes(x = sir, y = count, fill = sir)) +
+    ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
     # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
     ggplot2::scale_fill_manual(
       values = c(
         "S" = colours_SIR[1],
+        "SDD" = colours_SIR[2],
         "I" = colours_SIR[2],
-        "R" = colours_SIR[3]
+        "R" = colours_SIR[3],
+        "NI" = "#888888"
       ),
       limits = force
     ) +
@@ -714,22 +789,20 @@ fortify.sir <- function(object, ...) {
   )
 }
 
-plot_prepare_table <- function(x, expand) {
+plotrange_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 <- c(min(extra_range) / 2, extra_range)
-      }
+      # expand range for MIC by adding common intermediate factors levels
+      extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
+      # remove the ones that are in 25% range of user values
+      extra_range <- extra_range[!vapply(FUN.VALUE = logical(1), extra_range, function(r) any(abs(r - x) / x < 0.25, na.rm = TRUE))]
       nms <- extra_range
       extra_range <- rep(0, length(extra_range))
       names(extra_range) <- nms
       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 +824,15 @@ 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 +844,8 @@ 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
@@ -804,8 +888,10 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
     cols <- character(length = length(sir))
     cols[is.na(sir)] <- "#BEBEBE"
     cols[sir == "S"] <- colours_SIR[1]
+    cols[sir == "SDD"] <- colours_SIR[2]
     cols[sir == "I"] <- colours_SIR[2]
     cols[sir == "R"] <- colours_SIR[3]
+    cols[sir == "NI"] <- "#888888"
     sub <- bquote(.(abname) ~ "-" ~ italic(.(moname)) ~ .(guideline_txt))
   } else {
     cols <- "#BEBEBE"

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
-#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
+#' **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()]. Since AMR v3.0, [proportion_SI()] and [proportion_I()] include dose-dependent susceptibility ('SDD').
 #'
 #' 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:
@@ -247,7 +247,7 @@ susceptibility <- function(...,
                            only_all_tested = FALSE) {
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I"),
+      ab_result = c("S", "SDD", "I"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -267,7 +267,7 @@ sir_confidence_interval <- function(...,
                                     confidence_level = 0.95,
                                     side = "both",
                                     collapse = FALSE) {
-  meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = c(1, 2, 3), is_in = c("S", "I", "R"))
+  meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = c(1:5), is_in = c("S", "SDD", "I", "R", "NI"))
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   meet_criteria(as_percent, allow_class = "logical", has_length = 1)
   meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@@ -285,7 +285,7 @@ sir_confidence_interval <- function(...,
   )
   n <- tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I", "R"),
+      ab_result = c("S", "SDD", "I", "R", "NI"),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -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]
@@ -351,9 +351,12 @@ proportion_IR <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
+  if (message_not_thrown_before("proportion_IR", entire_session = TRUE)) {
+    message_("Note that `proportion_IR()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("I", "R"),
+      ab_result = c("I", "SDD", "R"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -369,9 +372,12 @@ proportion_I <- function(...,
                          minimum = 30,
                          as_percent = FALSE,
                          only_all_tested = FALSE) {
+  if (message_not_thrown_before("proportion_I", entire_session = TRUE)) {
+    message_("Note that `proportion_I()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = "I",
+      ab_result = c("I", "SDD"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -387,9 +393,12 @@ proportion_SI <- function(...,
                           minimum = 30,
                           as_percent = FALSE,
                           only_all_tested = FALSE) {
+  if (message_not_thrown_before("proportion_SI", entire_session = TRUE)) {
+    message_("Note that `proportion_SI()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "I"),
+      ab_result = c("S", "I", "SDD"),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,

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/resistance_predict.R

@@ -231,7 +231,7 @@ resistance_predict <- function(x,
     prediction <- predictmodel$fit
     se <- predictmodel$se.fit
   } else {
-    stop("no valid model selected. See ?resistance_predict.")
+    stop("no valid model selected. See `?resistance_predict`.")
   }
 
   # prepare the output dataframe

R/sir_calc.R

@@ -41,7 +41,7 @@ sir_calc <- function(...,
                      as_percent = FALSE,
                      only_all_tested = FALSE,
                      only_count = FALSE) {
-  meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1, 2, 3))
+  meet_criteria(ab_result, allow_class = c("character", "numeric", "integer"), has_length = c(1:5))
   meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
   meet_criteria(as_percent, allow_class = "logical", has_length = 1)
   meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
@@ -137,11 +137,11 @@ sir_calc <- function(...,
     if (isTRUE(only_all_tested)) {
       # no NAs in any column
       y <- apply(
-        X = as.data.frame(lapply(x, as.integer), stringsAsFactors = FALSE),
+        X = as.data.frame(lapply(x, as.double), stringsAsFactors = FALSE),
         MARGIN = 1,
         FUN = min
       )
-      numerator <- sum(as.integer(y) %in% as.integer(ab_result), na.rm = TRUE)
+      numerator <- sum(!is.na(y) & y %in% as.double(ab_result), na.rm = TRUE)
       denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
     } else {
       # may contain NAs in any column
@@ -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)
@@ -249,7 +249,13 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
     for (i in seq_len(ncol(data))) {
       if (is.sir(data[, i, drop = TRUE])) {
         data[, i] <- as.character(data[, i, drop = TRUE])
-        data[, i] <- gsub("(I|S)", "SI", data[, i, drop = TRUE])
+        if ("SDD" %in% data[, i, drop = TRUE]) {
+          if (message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
+            message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
+          }
+          
+        }
+        data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
       }
     }
   }
@@ -272,9 +278,9 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
     for (i in seq_len(ncol(.data))) {
       values <- .data[, i, drop = TRUE]
       if (isTRUE(combine_SI)) {
-        values <- factor(values, levels = c("SI", "R"), ordered = TRUE)
+        values <- factor(values, levels = c("SI", "R", "NI"), ordered = TRUE)
       } else {
-        values <- factor(values, levels = c("S", "I", "R"), ordered = TRUE)
+        values <- factor(values, levels = c("S", "SDD", "I", "R", "NI"), ordered = TRUE)
       }
       col_results <- as.data.frame(as.matrix(table(values)), stringsAsFactors = FALSE)
       col_results$interpretation <- rownames(col_results)
@@ -351,8 +357,14 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
   } else {
     # don't use as.sir() here, as it would add the class 'sir' and we would like
     # the same data structure as output, regardless of input
-    out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)
+    if (out$value[out$interpretation == "SDD"] > 0) {
+      out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R"), ordered = TRUE)  
+    } else {
+      out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)
+    }
   }
+  
+  out <- out[!is.na(out$interpretation), , drop = FALSE]
 
   if (data_has_groups) {
     # ordering by the groups and two more: "antibiotic" and "interpretation"
@@ -373,5 +385,5 @@ 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 +101,21 @@ 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, ...) {
-  x
+# S3: disk ----
+vec_ptype_full.disk <- function(x, ...) {
+  "disk"
 }
-vec_ptype2.disk.integer <- function(x, y, ...) {
-  y
+vec_ptype_abbr.disk <- function(x, ...) {
+  "dsk"
+}
+vec_ptype2.disk.default <- function (x, y, ..., x_arg = "", y_arg = "") {
+  NA_disk_[0]
+}
+vec_ptype2.disk.disk <- function(x, y, ...) {
+  NA_disk_[0]
+}
+vec_cast.disk.disk <- function(x, to, ...) {
+  as.disk(x)
 }
 vec_cast.integer.disk <- function(x, to, ...) {
   unclass(x)
@@ -125,29 +136,63 @@ 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
+  NA_mic_[0]
+}
+vec_ptype2.mic.mic <- function(x, y, ...) {
+  # this will make sure that currently implemented MIC levels are returned
+  NA_mic_[0]
+}
+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), ...)
 }
-
-# S3: sir
-vec_ptype2.character.sir <- function(x, y, ...) {
-  x
+vec_arith.mic <- function(op, x, y, ...) {
+  vctrs::vec_arith(op, as.double(x), as.double(y))
 }
-vec_ptype2.sir.character <- function(x, y, ...) {
-  y
+
+# S3: sir ----
+vec_ptype2.sir.default <- function (x, y, ..., x_arg = "", y_arg = "") {
+  NA_sir_[0]
+}
+vec_ptype2.sir.sir <- function(x, y, ...) {
+  NA_sir_[0]
+}
+vec_ptype2.character.sir <- function(x, y, ...) {
+  NA_sir_[0]
+}
+vec_cast.sir.sir <- function(x, to, ...) {
+  # this makes sure that old SIR objects (with S/I/R) are converted to the current structure (S/SDD/I/R/NI)
+  as.sir(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

@@ -62,12 +62,15 @@ AMR_env$sir_interpretation_history <- data.frame(
   mo_user = character(0),
   ab = set_clean_class(character(0), c("ab", "character")),
   mo = set_clean_class(character(0), c("mo", "character")),
+  method = character(0),
   input = double(0),
   outcome = NA_sir_[0],
-  method = character(0),
-  breakpoint_S_R = character(0),
+  host = character(0),
+  notes = character(0),
   guideline = character(0),
   ref_table = character(0),
+  uti = logical(0),
+  breakpoint_S_R = character(0),
   stringsAsFactors = FALSE
 )
 
@@ -77,17 +80,11 @@ AMR_env$is_dark_theme <- NULL
 AMR_env$chmatch <- import_fn("chmatch", "data.table", error_on_fail = FALSE)
 AMR_env$chin <- import_fn("%chin%", "data.table", error_on_fail = FALSE)
 
-# determine info icon for messages
-if (pkg_is_available("cli")) {
-  # let cli do the determination of supported symbols
-  AMR_env$info_icon <- import_fn("symbol", "cli")$info
-  AMR_env$bullet_icon <- import_fn("symbol", "cli")$bullet
-  AMR_env$dots <- import_fn("symbol", "cli")$ellipsis
-} else {
-  AMR_env$info_icon <- "i"
-  AMR_env$bullet_icon <- "*"
-  AMR_env$dots <- "..."
-}
+# take cli symbols if available
+AMR_env$info_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$info %or% "i"
+AMR_env$bullet_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$bullet %or% "*"
+AMR_env$dots <- import_fn("symbol", "cli", error_on_fail = FALSE)$ellipsis %or% "..."
+AMR_env$sup_1_icon <- import_fn("symbol", "cli", error_on_fail = FALSE)$sup_1 %or% "*"
 
 .onLoad <- function(lib, pkg) {
   # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
@@ -98,16 +95,14 @@ 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")
+  # no type_sum of disk, that's now in vctrs::vec_ptype_full
   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 +127,7 @@ 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 +137,26 @@ 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", "disk.disk")
   s3_register("vctrs::vec_cast", "integer.disk")
   s3_register("vctrs::vec_cast", "disk.integer")
   s3_register("vctrs::vec_cast", "double.disk")
@@ -165,16 +164,26 @@ 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", "sir.default")
+  s3_register("vctrs::vec_ptype2", "sir.sir")
   s3_register("vctrs::vec_ptype2", "character.sir")
-  s3_register("vctrs::vec_ptype2", "sir.character")
   s3_register("vctrs::vec_cast", "character.sir")
   s3_register("vctrs::vec_cast", "sir.character")
+  s3_register("vctrs::vec_cast", "sir.sir")
 
   # if mo source exists, fire it up (see mo_source())
   if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
@@ -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)
+      )
+    }
   }
 }

README.md

@@ -4,9 +4,7 @@
 
 ----
 
-This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
-
-`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 175 countries.
+`AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 175 countries. This work was published in the Journal of Statistical Software (2022, Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
  
 After installing this package, R knows ~52,000 distinct microbial species and all ~600 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish, and Ukrainian.
 

_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: antimicrobial results"
     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
@@ -196,15 +198,26 @@ reference:
     - "`key_antimicrobials`"
     - "`mdro`"
     - "`count`"
-    - "`plot`"
-    - "`ggplot_sir`"
     - "`bug_drug_combinations`"
     - "`antibiotic_class_selectors`"
     - "`mean_amr_distance`"
     - "`resistance_predict`"
     - "`guess_ab_col`"
     
-  - title: "Other: AMR-specific options"
+  - 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: "AMR-specific options"
     desc: >
       The AMR package is customisable, by providing settings that can be set per user or per team. For
       example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported
@@ -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`"
@@ -250,9 +262,9 @@ reference:
     contents:
     - "`age_groups`"
     - "`age`"
+    - "`export_ncbi_biosample`"
     - "`availability`"
     - "`get_AMR_locale`"
-    - "`ggplot_pca`"
     - "`italicise_taxonomy`"
     - "`join`"
     - "`like`"
@@ -268,10 +280,10 @@ 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_checks.R

@@ -28,7 +28,7 @@
 # ==================================================================== #
 
 # Run this file to update the package using:
-# source("data-raw/_pre_commit_hook.R")
+# source("data-raw/_pre_commit_checks.R")
 
 library(dplyr, warn.conflicts = FALSE)
 try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like
@@ -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
@@ -180,10 +181,10 @@ AB_AMINOGLYCOSIDES <- antibiotics %>%
   filter(group %like% "aminoglycoside") %>%
   pull(ab)
 AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
-AB_ANTIFUNGALS <- AMR_env$AB_lookup %>%
+AB_ANTIFUNGALS <- antibiotics %>%
   filter(group %like% "antifungal") %>%
   pull(ab)
-AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>%
+AB_ANTIMYCOBACTERIALS <- antibiotics %>%
   filter(group %like% "antimycobacterial") %>%
   pull(ab)
 AB_CARBAPENEMS <- antibiotics %>%
@@ -220,7 +221,10 @@ AB_LINCOSAMIDES <- antibiotics %>%
   filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
   pull(ab)
 AB_MACROLIDES <- antibiotics %>%
-  filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>%
+  filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
+  pull(ab)
+AB_NITROFURANS <- antibiotics %>%
+  filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
   pull(ab)
 AB_OXAZOLIDINONES <- antibiotics %>%
   filter(group %like% "oxazolidinone") %>%
@@ -234,6 +238,9 @@ AB_POLYMYXINS <- antibiotics %>%
 AB_QUINOLONES <- antibiotics %>%
   filter(group %like% "quinolone") %>%
   pull(ab)
+AB_RIFAMYCINS <- antibiotics %>%
+  filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
+  pull(ab)
 AB_STREPTOGRAMINS <- antibiotics %>%
   filter(atc_group2 %like% "streptogramin") %>%
   pull(ab)
@@ -309,10 +316,12 @@ suppressMessages(usethis::use_data(EUCAST_RULES_DF,
   AB_GLYCOPEPTIDES_EXCEPT_LIPO,
   AB_LINCOSAMIDES,
   AB_MACROLIDES,
+  AB_NITROFURANS,
   AB_OXAZOLIDINONES,
   AB_PENICILLINS,
   AB_POLYMYXINS,
   AB_QUINOLONES,
+  AB_RIFAMYCINS,
   AB_STREPTOGRAMINS,
   AB_TETRACYCLINES,
   AB_TETRACYCLINES_EXCEPT_TGC,

data-raw/ab.md5

@@ -1 +1 @@
-8bf97fd5f1d8d82486902d05916ebca0
+92d3e2f8deac335c92841d2ded974dee

data-raw/antibiotics.txt

@@ -3,256 +3,258 @@
 "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"
+"AMO"	54260	"Amorolfine"	"Antifungals/antimycotics"	"D01AE16"	"Antifungals for topical use"	"Other antifungals for topical use"	"amor"	"amorolfina,amorolfine,amorolfinum,loceryl"					""
+"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"
-"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"
+"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"	"Antifungals/antimycotics"	"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"	"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"
-"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"
+"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"	"Quinolones"	"J01RA10"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
+"CIO"		"Ciprofloxacin/ornidazole"	"Quinolones"	"J01RA12"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
+"CIT"		"Ciprofloxacin/tinidazole"	"Quinolones"	"J01RA11"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
+"CLR"	84029	"Clarithromycin"	"Macrolides/lincosamides"	"J01FA09"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"ch,cla,clar,clm,clr"	"abbotic,astromen,biaxin,biaxin filmtab,biaxin hp,biaxin xl,biaxin xl filmtab,bicrolid,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycin,clarithromycine,clarithromycinum,claritromicina,clathromycin,crixan,cyllid,cyllind,fromilid,heliclar,klabax,klacid,klaciped,klaricid,klaricid h.p,klaricid h.p.,klaricid pediatric,klaricid xl,klarid,klarin,kofron,mabicrol,macladin,maclar,prevpac,veclam,vikrol,zeclar"	0.5	"g"	1	"g"	"100048-8,16619-9,16620-7,188-3,189-1,18907-6,190-9,191-7,20375-2,23619-0,25190-0,25191-8,25192-6,25253-6,34638-7,43987-7,43990-1,43991-9,7003-7,80559-8,89485-7"
 "CLA1"	5280980	"Clavulanic acid"	"Other antibacterials"	"NA"			""	"acide clavulanique,acido clavulanico,acidum clavulanicum,clavulanate,clavulanate acid,clavulanate lithium,clavulanateacid,clavulanic acid,clavulansaeure,clavulansaure,clavulinic acid,clavulox,serdaxin,sodium clavulanate"					""
-"CLX"	60063	"Clinafloxacin"	"Quinolones"	"NA"			""	"clinafloxacin"					""
-"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"
+"CLI1"		"Clindamycin inducible screening"	"Macrolides/lincosamides"	"NA"			"clin inducible,clinda inducible,clindamycin inducible"	""					""
+"CLF"	2794	"Clofazimine"	"Antimycobacterials"	"J04BA01"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"clof"	"chlofazimine,clofazimin,clofazimina,clofazimine,clofaziminum,colfazimine,lampren,lamprene,riminophenazine"	0.1	"g"			"16623-1,20376-0,23620-8,23627-3,43986-9,43988-5,43989-3,55661-3,55662-1,96108-6"
 "CLF1"	2799	"Clofoctol"	"Other antibacterials"	"J01XX03"	"Other antibacterials"	"Other antibacterials"	""	"clofoctol,clofoctolo,clofoctolum,gramplus,octofene"					""
 "CLM"	71807	"Clometocillin"	"Beta-lactams/penicillins"	"J01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	""	"chlomethocillin,clometacillin,clometocilina,clometocillin,clometocilline,clometocillinum,rixapen"	1	"g"			""
 "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 +262,63 @@
 "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 +328,80 @@
 "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 +412,7 @@
 "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 +424,63 @@
 "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
+5d90ad7fe89682bfc58700682c562207

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/microorganisms.codes.md5

@@ -1 +1 @@
-684dc6117966c478ecc7f5c87e0964d0
+89e85bfa66228cfba526e375dad7ff37