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compare: P281424/AMR:sir-s3-update
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P281424/AMR:gh-pages P281424/AMR:python-wrapper P281424/AMR:main P281424/AMR:sir-s3-update
P281424/AMR:v3.0.1 P281424/AMR:v3.0.0 P281424/AMR:v2.1.1 P281424/AMR:v2.1.0 P281424/AMR:v2.0.0 P281424/AMR:v1.8.2 P281424/AMR:v1.8.1 P281424/AMR:v1.8.0 P281424/AMR:v1.7.1 P281424/AMR:v1.7.0 P281424/AMR:v1.6.0 P281424/AMR:v1.5.0 P281424/AMR:v1.4.0 P281424/AMR:v1.3.0 P281424/AMR:v1.2.0 P281424/AMR:v1.1.0 P281424/AMR:v1.0.1 P281424/AMR:v1.0.0 P281424/AMR:v0.9.0 P281424/AMR:v0.8.0 P281424/AMR:v0.7.1 P281424/AMR:v0.7.0 P281424/AMR:v0.6.1 P281424/AMR:v0.6.0 P281424/AMR:v0.5.0 P281424/AMR:v0.4.0 P281424/AMR:v0.3.0 P281424/AMR:v0.2.0 P281424/AMR:v0.1.1 P281424/AMR:v0.1.0
1 Commits
eae14d44bf .. sir-s3-update
Author SHA1 Message Date
dr. M.S. (Matthijs) Berends d232666e49 update sir to include interpretation details 2025-08-01 15:15:49 +02:00
139 changed files with 13246 additions and 11764 deletions
Expand all files Collapse all files
.Rbuildignore
-2
View File
@@ -9,7 +9,6 @@
^_pkgdown\.yml$
^appveyor\.yml$
^codecov\.yml$
^CLAUDE\.md$
^cran-comments\.md$
^CRAN-RELEASE$
^\.github$
@@ -41,4 +40,3 @@
^CRAN-SUBMISSION$
^PythonPackage$
^README\.Rmd$
\.no_include$
.github/ISSUE_TEMPLATE/1-bug-report.yml
+5 -5
View File
@@ -22,9 +22,9 @@ body:
label: Minimal Reproducible Example (optional)
description: Please include a short R code snippet that reproduces the problem, if possible.
placeholder:
e.g.
```r
ab_name("amoxicillin/clavulanic acid", language = "es")
e.g.
```r
ab_name("amoxicillin/clavulanic acid", language = "es")
```
validations:
required: false
@@ -42,7 +42,7 @@ body:
multiple: false
options:
- ''
- Latest CRAN version (3.0.1)
- One of the latest GitHub versions (3.0.1.9xxx)
- Latest CRAN version (3.0.0)
- One of the latest GitHub versions (3.0.0.9xxx)
validations:
required: true
.github/prehooks/pre-commit
+8 -2
View File
@@ -48,6 +48,7 @@ echo "Running prehook..."
if command -v Rscript > /dev/null; then
if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
Rscript -e "source('data-raw/_pre_commit_checks.R')"
currentpkg=$(Rscript -e "cat(pkgload::pkg_name())")
echo "- Adding changed files in ./data-raw and ./man to this commit"
git add data-raw/*
git add data/*
@@ -56,9 +57,11 @@ if command -v Rscript > /dev/null; then
git add NAMESPACE
else
echo "- R package 'pkgload', 'devtools', or 'dplyr' not installed!"
currentpkg="your"
fi
else
echo "- R is not available on your system!"
currentpkg="your"
fi
echo ""
@@ -89,7 +92,7 @@ else
# Combine tag and commit number
currentversion="$currenttag.$((currentcommit + 9001))"
echo "- AMR pkg version set to ${currentversion}"
echo "- ${currentpkg} pkg version set to ${currentversion}"
# Update version number and date in DESCRIPTION
sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
@@ -100,7 +103,10 @@ else
# Update version number in NEWS.md
if [ -e "NEWS.md" ]; then
sed -i -- "1s/.*/# AMR ${currentversion}/" NEWS.md
if [ "$currentpkg" = "your" ]; then
currentpkg=""
fi
sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
echo "- Updated version number in ./NEWS.md"
rm -f NEWS.md--
git add NEWS.md
.github/workflows/check-current-testthat.yaml
+17 -16
View File
@@ -41,22 +41,7 @@ on:
name: check-recent
jobs:
setup:
runs-on: ubuntu-latest
outputs:
matrix: ${{ steps.set-matrix.outputs.matrix }}
steps:
- id: set-matrix
shell: bash
run: |
if [ "${{ github.event_name }}" = "pull_request" ]; then
echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release","allowfail":false}]}' >> "$GITHUB_OUTPUT"
else
echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false}]}' >> "$GITHUB_OUTPUT"
fi
R-code-check:
needs: setup
runs-on: ${{ matrix.config.os }}
continue-on-error: ${{ matrix.config.allowfail }}
@@ -65,7 +50,23 @@ jobs:
strategy:
fail-fast: false
matrix: ${{ fromJSON(needs.setup.outputs.matrix) }}
matrix:
config:
# current development version, check all major OSes:
# - {os: macOS-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: 'devel', allowfail: false}
- {os: ubuntu-latest, r: 'devel', allowfail: false, http-user-agent: 'release'}
# current 'release' version, check all major OSes:
- {os: macOS-latest, r: 'release', allowfail: true}
- {os: windows-latest, r: 'release', allowfail: false}
- {os: ubuntu-latest, r: 'release', allowfail: false}
# older versions (see also check-old-tinytest.yaml for even older versions):
- {os: ubuntu-latest, r: 'oldrel-1', allowfail: false}
- {os: ubuntu-latest, r: 'oldrel-2', allowfail: false}
- {os: ubuntu-latest, r: 'oldrel-3', allowfail: false}
- {os: ubuntu-latest, r: 'oldrel-4', allowfail: false}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
.github/workflows/check-old-tinytest.yaml
+9 -14
View File
@@ -29,8 +29,8 @@
on:
push:
# only run after a git push on the main branch
branches: [main]
# only run after a git push on any branch in this repo
branches: '**'
name: check-old
@@ -50,11 +50,11 @@ jobs:
# 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: false} # always fails, horrible with UTF-8
# - {os: ubuntu-latest, r: '3.4', allowfail: false} # 3.1-3.4 now always fails with Error in grep(warn_re, lines, invert = TRUE, value = TRUE) attempt to set index 46/46 in SET_STRING_ELT
# - {os: ubuntu-latest, r: '3.3', allowfail: false}
# - {os: ubuntu-latest, r: '3.2', allowfail: false}
# - {os: ubuntu-latest, r: '3.1', 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}
- {os: ubuntu-latest, r: '3.2', allowfail: false}
- {os: ubuntu-latest, r: '3.1', allowfail: false}
- {os: ubuntu-latest, r: '3.0', allowfail: false}
env:
@@ -76,14 +76,9 @@ jobs:
- uses: r-lib/actions/setup-pandoc@v2
- name: Install suggested pkgs (and tinytest) from CRAN
- name: Install tinytest from CRAN
run: |
desc_lines <- readLines('DESCRIPTION')
suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:| )", readLines('DESCRIPTION'))]
suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
suggests <- gsub("[ ,]", "", suggests)
pkgs <- unique(c(suggests, "tinytest"))
for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
install.packages("tinytest", repos = "https://cran.r-project.org")
shell: Rscript {0}
- name: Show session info
.github/workflows/check-current-testthat-dev-versions.yaml → .github/workflows/lintr.yaml
+40 -38
View File
@@ -18,7 +18,7 @@
# 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. #
# 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. #
@@ -29,33 +29,17 @@
on:
push:
branches: [main]
schedule:
# also run a schedule everyday at 1 AM.
# this is to check that all dependencies are still available (see R/zzz.R)
- cron: '0 1 * * *'
branches: '**'
pull_request:
branches: '**'
name: check-recent-dev-pkgs
name: lintr
jobs:
R-code-check:
runs-on: ${{ matrix.config.os }}
continue-on-error: ${{ matrix.config.allowfail }}
name: ${{ matrix.config.os }} (dev-pkgs)
strategy:
fail-fast: false
matrix:
config:
# current 'release' version on Ubuntu
- {os: ubuntu-latest, r: 'release', allowfail: false}
lintr:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
steps:
- uses: actions/checkout@v4
@@ -63,21 +47,39 @@ jobs:
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
use-public-rspm: false
extra-repositories: >
https://tidyverse.r-universe.dev
https://r-lib.r-universe.dev
https://tidymodels.r-universe.dev
https://yihui.r-universe.dev
r-version: release
# use RStudio Package Manager to quickly install packages
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check
upgrade: 'TRUE'
- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
extra-packages: |
any::lintr
any::cyclocomp
any::roxygen2
any::devtools
any::usethis
- name: Remove unneeded folders
run: |
# do not check these folders
rm -rf data-raw
rm -rf tests
rm -rf vignettes
- name: Lint
run: |
# get ALL linters, not just default ones
linters <- getNamespaceExports(asNamespace("lintr"))
linters <- sort(linters[grepl("_linter$", linters)])
# lose deprecated
linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)]
linters <- linters[linters != "linter"]
# and the ones we find unnnecessary
linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)]
# put the functions in a list
linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
names(linters_list) <- linters
# run them all!
lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R"))
shell: Rscript {0}
.github/workflows/publish-to-pypi.yml
+3 -4
View File
@@ -39,7 +39,7 @@ jobs:
runs-on: ubuntu-latest
env:
GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
PYPI_PAT: ${{ secrets.PYPI_PAT }}
steps:
- name: Checkout code
@@ -78,7 +78,6 @@ jobs:
cd PythonPackage/AMR
python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*
# TODO - Support Miniconda and Anaconda too
# - name: Set up Miniconda
# continue-on-error: true
# uses: conda-incubator/setup-miniconda@v2
@@ -118,7 +117,7 @@ jobs:
rm -rf PythonPackage
git init
git remote add origin https://$GH_REPO_SCOPE@github.com/msberends/AMR
git remote add origin https://$PYPI_PAT@github.com/msberends/AMR
git checkout --orphan python-wrapper
git config user.name "github-actions[bot]"
git config user.email "github-actions[bot]@users.noreply.github.com"
@@ -126,4 +125,4 @@ jobs:
git rm -rf . || true
git add .
git commit -m "Python wrapper update"
git push https://$GH_REPO_SCOPE@github.com/msberends/AMR.git python-wrapper --force
git push https://$PYPI_PAT@github.com/msberends/AMR.git python-wrapper --force
.github/workflows/renew-gpt-training-data.yml
+2 -2
View File
@@ -39,7 +39,7 @@ jobs:
runs-on: ubuntu-latest
env:
GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
PYPI_PAT: ${{ secrets.PYPI_PAT }}
steps:
- name: Checkout code
@@ -63,4 +63,4 @@ jobs:
git config user.email "github-actions[bot]@users.noreply.github.com"
git add latest_training_data.txt
git commit -m "GPT training data update"
git push https://$GH_REPO_SCOPE@github.com/msberends/amr-for-r-assistant.git main --force
git push https://$PYPI_PAT@github.com/msberends/amr-for-r-assistant.git main --force
.github/workflows/todo-tracker.yml
-84
View File
@@ -1,84 +0,0 @@
# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
on:
push:
# only on main
branches: "main"
name: Update TODO Tracker
jobs:
update-todo:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Generate TODO list from R/
run: |
export TZ=Europe/Amsterdam
last_updated=$(date +"%e %B %Y %H:%M:%S %Z" | sed 's/^ *//')
echo "## \`TODO\` Report" > todo.md
echo "" >> todo.md
echo "**Last Updated: ${last_updated}**" >> todo.md
echo "" >> todo.md
echo "_This overview is automatically updated on each push to \`main\`. It provides an automated overview of all mentions of the text \`TODO\`._" >> todo.md
echo "" >> todo.md
todos=$(grep -rn --include=\*.{R,Rmd,yaml,yml,md,css,js} --exclude={todo-tracker.yml,todo.md} "TODO" . || true)
if [ -z "$todos" ]; then
echo "✅ No TODOs found." >> todo.md
else
echo "$todos" | awk -F: -v repo="https://github.com/msberends/AMR/blob/main/" '
{
file = $1
gsub("^\\./", "", file) # remove leading ./ if present
line = $2
text = substr($0, index($0,$3))
if (file != last_file) {
if (last_file != "") print "```"
print ""
print "### [`" file "`](" repo file ")"
print "```r"
last_file = file
}
printf "L%s: %s\n", line, text
}
' >> todo.md
echo "\`\`\`" >> todo.md
fi
- name: Update GitHub issue
uses: peter-evans/create-or-update-comment@v4
with:
token: ${{ secrets.GH_REPO_SCOPE }}
issue-number: 231
comment-id: 3253439219
body-file: todo.md
edit-mode: replace
.github/workflows/website.yaml
+5 -4
View File
@@ -42,15 +42,16 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: checkout
uses: actions/checkout@v4
- uses: actions/checkout@v4
with:
# this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
# we need this for the download page on our website - dates must be of the files, not of the latest git push
fetch-depth: 0
- name: restore timestamps
uses: chetan/git-restore-mtime-action@v2
- name: Preserve timestamps
run: |
sudo apt install git-restore-mtime
git restore-mtime
- uses: r-lib/actions/setup-pandoc@v2
.gitignore
-1
View File
@@ -1,6 +1,5 @@
Meta
doc
docs
.Renviron
.Rproj.user
.Rhistory
CLAUDE.md
-183
View File
@@ -1,183 +0,0 @@
# CLAUDE.md — AMR R Package
This file provides context for Claude Code when working in this repository.
## Project Overview
**AMR** is a zero-dependency R package for antimicrobial resistance (AMR) data analysis using a One Health approach. It is peer-reviewed, used in 175+ countries, and supports 28 languages.
Key capabilities:
- SIR (Susceptible/Intermediate/Resistant) classification using EUCAST 2011–2025 and CLSI 2011–2025 breakpoints
- Antibiogram generation: traditional, combined, syndromic, and WISCA
- Microorganism taxonomy database (~79,000 species)
- Antimicrobial drug database (~620 drugs)
- Multi-drug resistant organism (MDRO) classification
- First-isolate identification
- Minimum Inhibitory Concentration (MIC) and disk diffusion handling
- Multilingual output (28 languages)
## Common Commands
All commands run inside an R session:
```r
# Rebuild documentation (roxygen2 → .Rd files + NAMESPACE)
devtools::document()
# Run all tests
devtools::test()
# Full package check (CRAN-level: docs + tests + checks)
devtools::check()
# Build pkgdown website locally
pkgdown::build_site()
# Code coverage report
covr::package_coverage()
```
From the shell:
```bash
# CRAN check from parent directory
R CMD check AMR
```
## Repository Structure
```
R/ # All R source files (62 files, ~28,000 lines)
man/ # Auto-generated .Rd documentation (do not edit manually)
tests/testthat/ # testthat test files (test-*.R) and helper-functions.R
data/ # Pre-compiled .rda datasets
data-raw/ # Scripts used to generate data/ files
vignettes/ # Rmd vignette articles
inst/ # Installed files (translations, etc.)
_pkgdown.yml # pkgdown website configuration
```
## R Source File Conventions
**Naming conventions in `R/`:**
| Prefix/Name | Purpose |
|---|---|
| `aa_*.R` | Loaded first (helpers, globals, options, package docs) |
| `zz_deprecated.R` | Deprecated function wrappers |
| `zzz.R` | `.onLoad` / `.onAttach` initialization |
**Key source files:**
- `aa_helper_functions.R` / `aa_helper_pm_functions.R` — internal utility functions (large; ~63 KB and ~37 KB)
- `aa_globals.R` — global constants and breakpoint lookup structures
- `aa_options.R` — `amr_options()` / `get_AMR_option()` system
- `mo.R` / `mo_property.R` — microorganism lookup and properties
- `ab.R` / `ab_property.R` — antimicrobial drug functions
- `av.R` / `av_property.R` — antiviral drug functions
- `sir.R` / `sir_calc.R` / `sir_df.R` — SIR classification engine
- `mic.R` / `disk.R` — MIC and disk diffusion classes
- `antibiogram.R` — antibiogram generation (traditional, combined, syndromic, WISCA)
- `first_isolate.R` — first-isolate identification algorithms
- `mdro.R` — MDRO classification (EUCAST, CLSI, CDC, custom guidelines)
- `amr_selectors.R` — tidyselect helpers for selecting AMR columns
- `interpretive_rules.R` / `custom_eucast_rules.R` — clinical interpretation rules
- `translate.R` — 28-language translation system
- `ggplot_sir.R` / `ggplot_pca.R` / `plotting.R` — visualisation functions
## Custom S3 Classes
The package defines five S3 classes with full print/format/plot/vctrs support:
| Class | Created by | Represents |
|---|---|---|
| `<mo>` | `as.mo()` | Microorganism code |
| `<ab>` | `as.ab()` | Antimicrobial drug code |
| `<av>` | `as.av()` | Antiviral drug code |
| `<sir>` | `as.sir()` | SIR value (S/I/R/SDD) |
| `<mic>` | `as.mic()` | Minimum inhibitory concentration |
| `<disk>` | `as.disk()` | Disk diffusion diameter |
## Data Files
Pre-compiled in `data/` (do not edit directly; regenerate via `data-raw/` scripts):
| File | Contents |
|---|---|
| `microorganisms.rda` | ~79,000 microbial species with full taxonomy |
| `antimicrobials.rda` | ~620 antimicrobial drugs with ATC codes |
| `antivirals.rda` | Antiviral drugs |
| `clinical_breakpoints.rda` | EUCAST + CLSI breakpoints (2011–2025) |
| `intrinsic_resistant.rda` | Intrinsic resistance patterns |
| `example_isolates.rda` | Example AMR dataset for documentation/testing |
| `WHONET.rda` | Example WHONET-format dataset |
## Zero-Dependency Design
The package has **no `Imports`** in `DESCRIPTION`. All optional integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.) are listed in `Suggests` and guarded with:
```r
if (requireNamespace("pkg", quietly = TRUE)) { ... }
```
Never add packages to `Imports`. If new functionality requires an external package, add it to `Suggests` and guard usage appropriately.
## Testing
- **Framework:** `testthat` (R ≥ 3.1); legacy `tinytest` used for R 3.0–3.6 CI
- **Test files:** `tests/testthat/test-*.R`
- **Helpers:** `tests/testthat/helper-functions.R`
- **CI matrix:** GitHub Actions across Windows / macOS / Linux × R devel / release / oldrel-1 through oldrel-4
- **Coverage:** `covr` (some files excluded: `atc_online.R`, `mo_source.R`, `translate.R`, `resistance_predict.R`, `zz_deprecated.R`, helper files, `zzz.R`)
## Documentation
- All exported functions use **roxygen2** blocks (`RoxygenNote: 7.3.3`, markdown enabled)
- Run `devtools::document()` after any change to roxygen comments
- Never edit files in `man/` directly — they are auto-generated
- Vignettes live in `vignettes/` as `.Rmd` files
- The pkgdown website is configured in `_pkgdown.yml`
## Versioning
Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
- Development versions use a `.9xxx` suffix
- Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
- `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub issue references (`#NNN`)
### Version and date bump required for every PR
All PRs are **squash-merged**, so each PR lands as exactly **one commit** on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore **exactly one version bump is allowed per PR**, regardless of how many intermediate commits are made on the branch.
#### Computing the correct version number
Run the following from the repo root to determine the version string to use:
```bash
currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
currenttagfull=$(git describe --tags --abbrev=0)
defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
echo "$currentversion"
```
The `+ 1` accounts for the fact that this PR's squash commit is not yet on the default branch. Set **both** of these files to the resulting version string (and only once per PR, even across multiple commits):
1. **`DESCRIPTION`** — the `Version:` field
2. **`NEWS.md`** — the top-level heading `# AMR <version>`
If `git describe` fails (e.g. no tags exist in the environment), fall back to reading the current version from `DESCRIPTION` and adding 1 to the last numeric component — but only if no bump has already been made in this PR.
#### Date field
The `Date:` field in `DESCRIPTION` must reflect the date of the **last commit to the PR** (not the first), in ISO format. Update it with every commit so it is always current:
```
Date: 2026-03-07
```
## Internal State
The package uses a private `AMR_env` environment (created in `aa_globals.R`) for caching expensive lookups (e.g., microorganism matching scores, breakpoint tables). This avoids re-computation within a session.
CRAN-SUBMISSION
+3 -3
View File
@@ -1,3 +1,3 @@
Version: 3.0.1
Date: 2025-09-20 10:56:46 UTC
SHA: 33fb1849eb5aa6d33828e643c8f5047dd93447e3
Version: 3.0.0
Date: 2025-06-01 16:52:53 UTC
SHA: 79038fed2169a25a7fc067c80bb25d9d78be21d9
DESCRIPTION
+5 -5
View File
@@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.1.9036
Date: 2026-03-18
Version: 3.0.0.9017
Date: 2025-07-28
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
@@ -27,10 +27,10 @@ Authors@R: c(
person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
person(given = c("Matthew"), family = "Saab", role = "ctb"),
person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
person(given = c("Rogier", "P."), family = "Schade", role = "ctb"),
person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
@@ -70,5 +70,5 @@ BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE, old_usage = TRUE)
NAMESPACE
+3 -14
View File
@@ -12,6 +12,7 @@ S3method("[",deprecated_amr_dataset)
S3method("[",disk)
S3method("[",mic)
S3method("[",mo)
S3method("[",sir)
S3method("[<-",ab)
S3method("[<-",av)
S3method("[<-",disk)
@@ -24,6 +25,7 @@ S3method("[[",deprecated_amr_dataset)
S3method("[[",disk)
S3method("[[",mic)
S3method("[[",mo)
S3method("[[",sir)
S3method("[[<-",ab)
S3method("[[<-",av)
S3method("[[<-",disk)
@@ -99,6 +101,7 @@ S3method(print,custom_eucast_rules)
S3method(print,custom_mdro_guideline)
S3method(print,deprecated_amr_dataset)
S3method(print,disk)
S3method(print,interpreted_sir)
S3method(print,mic)
S3method(print,mo)
S3method(print,mo_renamed)
@@ -133,10 +136,8 @@ export("%like%")
export("%like_case%")
export("%unlike%")
export("%unlike_case%")
export(NA_ab_)
export(NA_disk_)
export(NA_mic_)
export(NA_mo_)
export(NA_sir_)
export(ab_atc)
export(ab_atc_group1)
@@ -163,8 +164,6 @@ export(administrable_per_os)
export(age)
export(age_groups)
export(all_antimicrobials)
export(all_disk)
export(all_disk_predictors)
export(all_mic)
export(all_mic_predictors)
export(all_sir)
@@ -172,7 +171,6 @@ export(all_sir_predictors)
export(aminoglycosides)
export(aminopenicillins)
export(amr_class)
export(amr_course)
export(amr_distance_from_row)
export(amr_selector)
export(anti_join_microorganisms)
@@ -217,7 +215,6 @@ export(cephalosporins_4th)
export(cephalosporins_5th)
export(clear_custom_antimicrobials)
export(clear_custom_microorganisms)
export(clsi_rules)
export(count_I)
export(count_IR)
export(count_R)
@@ -248,8 +245,6 @@ export(ggplot_sir_predict)
export(glycopeptides)
export(guess_ab_col)
export(inner_join_microorganisms)
export(interpretive_rules)
export(ionophores)
export(is.ab)
export(is.av)
export(is.disk)
@@ -326,9 +321,7 @@ export(not_intrinsic_resistant)
export(oxazolidinones)
export(pca)
export(penicillins)
export(peptides)
export(phenicols)
export(phosphonics)
export(polymyxins)
export(proportion_I)
export(proportion_IR)
@@ -368,7 +361,6 @@ export(sir_df)
export(sir_interpretation_history)
export(sir_predict)
export(skewness)
export(spiropyrimidinetriones)
export(step_mic_log2)
export(step_sir_numeric)
export(streptogramins)
@@ -392,8 +384,6 @@ if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, disk)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, mic)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, resistance_predict)
if(getRversion() >= "3.0.0") S3method(ggplot2::fortify, sir)
if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, mic)
if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, sir)
if(getRversion() >= "3.0.0") S3method(knitr::knit_print, antibiogram)
if(getRversion() >= "3.0.0") S3method(knitr::knit_print, formatted_bug_drug_combinations)
if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
@@ -415,7 +405,6 @@ if(getRversion() >= "3.0.0") S3method(recipes::prep, step_mic_log2)
if(getRversion() >= "3.0.0") S3method(recipes::prep, step_sir_numeric)
if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
NEWS.md
+6 -69
View File
@@ -1,67 +1,13 @@
# AMR 3.0.1.9036
# AMR 3.0.0.9017
### Updates
* Modernised messaging infrastructure: `message_()`, `warning_()`, and `stop_()` now use `cli` for rich formatting (colours, inline markup, hyperlinks) when the `cli` package is installed, with a fully functional plain-text fallback when `cli` is absent
* Removed `add_fn` parameter from `message_()`, `warning_()`, and `word_wrap()` — styling is now handled by `cli` markup or dropped from the plain-text path
* New internal helper `cli_to_plain()` converts cli inline markup (`{.fun}`, `{.arg}`, `{.val}`, etc.) to plain-text equivalents for the non-cli fallback path
* Call sites across all R source files updated from `paste0()`-based string construction to cli glue syntax (e.g. `{.fun as.mo}`, `{.arg col_mo}`, `{n} results`)
# AMR 3.0.1.9035
This is primarily a bugfix release, though we added one nice feature too.
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
* Integration with the **tidymodels** framework to allow seamless use of MIC and SIR data in modelling pipelines via `recipes`
- `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
- New `tidyselect` helpers:
- `all_sir()`, `all_sir_predictors()`
- `all_mic()`, `all_mic_predictors()`
- `all_disk()`, `all_disk_predictors()`
* Data set `esbl_isolates` to practise with AMR modelling
* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
* Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
- `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
- This transforms the output from S/R to WT/NWT
- Functions such as `susceptibility()` count WT as S and NWT as R
* Function `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
- `eucast_rules()` has become a wrapper around that function
* Function `amr_course()`, which allows for automated download and unpacking of a GitHub repository for e.g. webinar use
### Fixes
* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
* Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Fixed a bug in `as.sir()` where for numeric input the arguments `S`, `I`, and `R` would not be considered (#244)
* Fixed some foreign translations of antimicrobial drugs
* Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
* Fixed a bug to disregard `NI` for susceptibility proportion functions
* Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
* Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
### Updates
* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
* `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
* `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
* `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
* Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
* Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
* Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`
* Interpretation of capped MIC values now consistently returns `"NI"` (non-interpretable) when the true MIC could be at either side of a breakpoint, depending on the selected handling mode
* This results in more reliable behaviour compared to previous versions for capped MIC values
* Removed the `"inverse"` option, which has now become redundant
* `ab_group()` now returns values consist with the AMR selectors (#246)
* Added two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
# AMR 3.0.1
This is a bugfix release following the release of v3.0.0 in June 2025.
- New `tidyselect` helpers: `all_mic()`, `all_mic_predictors()`, `all_sir()`, `all_sir_predictors()`
### Changed
* Fixed bugs introduced by `ggplot2` v4.0.0 (#236)
* MIC scale functions (such as `scale_y_mic()`) will now be applied automatically when plotting values of class `mic`
* SIR scale functions (such as `scale_x_sir()`) will now be applied automatically when plotting values of class `sir`
* Fixed a bug in `antibiogram()` for when no antimicrobials are set
* Fixed a bug in `antibiogram()` to allow column names containing the `+` character (#222)
* Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space
@@ -69,19 +15,10 @@ This is a bugfix release following the release of v3.0.0 in June 2025.
* Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
* Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
* Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
* Fixed a bug in `mdro()` to make sure all genes specified in arguments are acknowledged
* Fixed a bug the `antimicrobials` data set to remove statins (#229)
* Fixed a bug the `microorganisms` data set for MycoBank IDs and synonyms (#233)
* Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
* Fixed skimmers (`skimr` package) of class `ab`, `sir`, and `disk` (#234)
* Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
* Fixed some specific Dutch translations for antimicrobials
* Added a warning to `as.ab()` if input resembles antiviral codes or names (#232)
* Added all reasons in verbose output of `mdro()` (#227)
* Added `names` to `age_groups()` so that custom names can be given (#215)
* Added note to `as.sir()` to make it explicit when higher-level taxonomic breakpoints are used (#218)
* Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the `antimicrobials` data set (#225)
* Updated Fosfomycin to be of antibiotic class Phosphonics (#225)
* Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms
@@ -90,7 +27,7 @@ This is a bugfix release following the release of v3.0.0 in June 2025.
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's Atlantic Veterinary College](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
* Data set `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
* Dataset `antibiotics` has been renamed to `antimicrobials` as the data set contains more than just antibiotics. Using `antibiotics` will still work, but now returns a warning.
* Removed all functions and references that used the deprecated `rsi` class, which were all replaced with their `sir` equivalents over two years ago.
* Functions `resistance_predict()` and `sir_predict()` are now deprecated and will be removed in a future version. Use the `tidymodels` framework instead, for which we [wrote a basic introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
@@ -102,7 +39,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* `ab_atc()` now supports ATC codes of veterinary antimicrobials (that all start with "Q")
* `ab_url()` now supports retrieving the WHOCC url of their ATCvet pages
* **Support for WISCA antibiograms**
* The `antibiogram()` function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in data sets with sparse data. A dedicated `wisca()` function is also available for easy usage.
* The `antibiogram()` function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated `wisca()` function is also available for easy usage.
* **More global coverage of languages**
* Added full support for 8 new languages: Arabic, Bengali, Hindi, Indonesian, Korean, Swahili, Urdu, and Vietnamese. The `AMR` package is now available in 28 languages.
* **Major update to fungal taxonomy and tools for mycologists**
R/aa_globals.R
+10 -11
View File
@@ -34,37 +34,37 @@ EUCAST_VERSION_BREAKPOINTS <- list(
version_txt = "v15.0",
year = 2025,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
url = "https://www.eucast.org/clinical_breakpoints/"
),
"14.0" = list(
version_txt = "v14.0",
year = 2024,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
url = "https://www.eucast.org/clinical_breakpoints/"
),
"13.1" = list(
version_txt = "v13.1",
year = 2023,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
url = "https://www.eucast.org/clinical_breakpoints/"
),
"12.0" = list(
version_txt = "v12.0",
year = 2022,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
url = "https://www.eucast.org/clinical_breakpoints/"
),
"11.0" = list(
version_txt = "v11.0",
year = 2021,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
url = "https://www.eucast.org/clinical_breakpoints/"
),
"10.0" = list(
version_txt = "v10.0",
year = 2020,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/bacteria/document-archive/"
url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"
)
)
EUCAST_VERSION_EXPERT_RULES <- list(
@@ -72,19 +72,19 @@ EUCAST_VERSION_EXPERT_RULES <- list(
version_txt = "v3.3",
year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
),
"3.2" = list(
version_txt = "v3.2",
year = 2020,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
),
"3.1" = list(
version_txt = "v3.1",
year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
)
)
EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
@@ -92,7 +92,7 @@ EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
version_txt = "v1.2",
year = 2023,
title = "'EUCAST Expected Resistant Phenotypes'",
url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes"
)
)
@@ -233,7 +233,6 @@ globalVariables(c(
"uti_index",
"value",
"varname",
"where",
"x",
"xvar",
"y",
R/aa_helper_functions.R
+174 -198
View File
@@ -305,7 +305,8 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
# this column should contain logicals
if (!is.logical(x[, found, drop = TRUE])) {
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."
"`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.",
add_fn = font_red
)
found <- NULL
}
@@ -382,30 +383,17 @@ pkg_is_available <- function(pkg, also_load = FALSE, min_version = NULL) {
isTRUE(out)
}
highlight_code <- function(code) {
if (pkg_is_available("cli", min_version = "3.0.0")) {
cli::code_highlight(code)
} else {
code
}
}
import_fn <- function(name, pkg, error_on_fail = TRUE) {
if (isTRUE(error_on_fail)) {
stop_ifnot_installed(pkg)
}
if (pkg == "rstudioapi" && !in_rstudio()) {
# only allow rstudioapi to be imported if we're in RStudio
return(NULL)
}
tryCatch(
# don't use get() to avoid fetching non-API functions
getExportedValue(name = name, ns = asNamespace(pkg)),
error = function(e) {
if (isTRUE(error_on_fail)) {
stop_("function {.code ", name, "()} is not an exported object from package '", pkg,
"'. Please create an issue at https://github.com/msberends/AMR/issues. Many thanks!",
stop_("function `", name, "()` is not an exported object from package '", pkg,
"'. Please create an issue at ", font_url("https://github.com/msberends/AMR/issues"), ". Many thanks!",
call = FALSE
)
} else {
@@ -415,108 +403,30 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
)
}
# Convert cli glue markup to plain text for the non-cli fallback path.
# Called by message_(), warning_(), and stop_() when cli is not available.
cli_to_plain <- function(msg, envir = parent.frame()) {
resolve <- function(x) {
# If x looks like {expr}, evaluate the inner expression
if (grepl("^\\{.+\\}$", x)) {
inner <- substring(x, 2L, nchar(x) - 1L)
tryCatch(
paste0(as.character(eval(parse(text = inner), envir = envir)), collapse = ", "),
error = function(e) x
)
} else {
x
}
}
apply_sub <- function(msg, pattern, formatter) {
while (grepl(pattern, msg, perl = TRUE)) {
m <- regexec(pattern, msg)
matches <- regmatches(msg, m)[[1]]
if (length(matches) < 2L) break
full_match <- matches[1L]
content <- matches[2L]
replacement <- formatter(content)
idx <- regexpr(full_match, msg, fixed = TRUE)
if (idx == -1L) break
msg <- paste0(
substr(msg, 1L, idx - 1L),
replacement,
substr(msg, idx + nchar(full_match), nchar(msg))
)
}
msg
}
# cli inline markup -> plain-text equivalents (one level of glue nesting allowed)
msg <- apply_sub(msg, "\\{\\.fun (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "()`"))
msg <- apply_sub(msg, "\\{\\.arg (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`"))
msg <- apply_sub(msg, "\\{\\.code (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("`", resolve(c), "`"))
msg <- apply_sub(msg, "\\{\\.val (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0('"', resolve(c), '"'))
msg <- apply_sub(msg, "\\{\\.field (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0('"', resolve(c), '"'))
msg <- apply_sub(msg, "\\{\\.cls (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("<", resolve(c), ">"))
msg <- apply_sub(msg, "\\{\\.pkg (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
msg <- apply_sub(msg, "\\{\\.strong (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
msg <- apply_sub(msg, "\\{\\.emph (\\{[^}]+\\}|[^}]+)\\}", function(c) paste0("*", resolve(c), "*"))
msg <- apply_sub(msg, "\\{\\.help ([^}]+)\\}", function(c) {
# Handle [display text](topic) markdown link format: extract just the display text
m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
if (length(m) >= 2L) m[2L] else paste0("`", resolve(c), "`")
})
msg <- apply_sub(msg, "\\{\\.topic ([^}]+)\\}", function(c) {
# Handle [display text](topic) markdown link format: extract just the display text
m <- regmatches(c, regexec("^\\[(.*)\\]\\([^)]*\\)$", c))[[1L]]
if (length(m) >= 2L) m[2L] else paste0("?", resolve(c))
})
msg <- apply_sub(msg, "\\{\\.url (\\{[^}]+\\}|[^}]+)\\}", function(c) resolve(c))
msg <- apply_sub(msg, "\\{\\.href ([^}]+)\\}", function(c) strsplit(resolve(c), " ", fixed = TRUE)[[1L]][1L])
# bare {variable} or {expression} -> evaluate in caller's environment
while (grepl("\\{[^{}]+\\}", msg)) {
m <- regexec("\\{([^{}]+)\\}", msg)
matches <- regmatches(msg, m)[[1]]
if (length(matches) < 2L) break
full_match <- matches[1L]
inner <- matches[2L]
replacement <- tryCatch(
paste0(as.character(eval(parse(text = inner), envir = envir)), collapse = ", "),
error = function(e) full_match
)
idx <- regexpr(full_match, msg, fixed = TRUE)
if (idx == -1L) break
msg <- paste0(
substr(msg, 1L, idx - 1L),
replacement,
substr(msg, idx + nchar(full_match), nchar(msg))
)
}
msg
}
# this alternative wrapper to the message(), warning() and stop() functions:
# - wraps text to never break lines within words (plain-text fallback only)
# - adds indentation for note-style messages (plain-text fallback only)
# When cli is available this just returns the pasted input; cli handles formatting.
# - wraps text to never break lines within words
# - ignores formatted text while wrapping
# - adds indentation dependent on the type of message (such as NOTE)
# - can add additional formatting functions like blue or bold text
word_wrap <- function(...,
add_fn = list(),
as_note = FALSE,
width = 0.95 * getOption("width"),
extra_indent = 0) {
if (pkg_is_available("cli", min_version = "3.0.0")) {
return(paste0(c(...), collapse = ""))
}
msg <- paste0(c(...), collapse = "")
if (isTRUE(as_note)) {
msg <- paste0(AMR_env$info_icon, " ", gsub("^note:? ?", "", msg, ignore.case = TRUE))
}
if (grepl("\n", msg, fixed = TRUE)) {
if (msg %like% "\n") {
# run word_wraps() over every line here, bind them and return again
return(paste0(
vapply(
FUN.VALUE = character(1),
trimws(unlist(strsplit(msg, "\n", fixed = TRUE)), which = "right"),
word_wrap,
add_fn = add_fn,
as_note = FALSE,
width = width,
extra_indent = extra_indent
@@ -524,75 +434,155 @@ word_wrap <- function(...,
collapse = "\n"
))
}
wrapped <- paste0(strwrap(msg, width = width), collapse = "\n")
if (grepl("\u2139 ", msg, fixed = TRUE)) {
indentation <- 2L + extra_indent
} else if (grepl("^=> ", msg)) {
indentation <- 3L + extra_indent
# correct for operators (will add the space later on)
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 <- 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,
simplify = TRUE,
width = width
),
collapse = "\n"
)
msg_stripped_wrapped <- paste0(unlist(strsplit(msg_stripped_wrapped, "(\n|\\*\\|\\*)")),
collapse = "\n"
)
msg_stripped_spaces <- which(unlist(strsplit(msg_stripped, "", fixed = TRUE)) == " ")
msg_stripped_wrapped_spaces <- which(unlist(strsplit(msg_stripped_wrapped, "", fixed = TRUE)) != "\n")
# so these are the indices of spaces that need to be replaced
replace_spaces <- which(!msg_stripped_spaces %in% msg_stripped_wrapped_spaces)
# put it together
msg <- unlist(strsplit(msg, " ", fixed = TRUE))
msg[replace_spaces] <- paste0(msg[replace_spaces], "\n")
# add space around operators again
msg <- gsub(paste0(ops, ops), "\\1 \\2", msg, perl = TRUE)
msg <- paste0(msg, collapse = " ")
msg <- gsub("\n ", "\n", msg, fixed = TRUE)
if (msg_stripped %like% "\u2139 ") {
indentation <- 2 + extra_indent
} else if (msg_stripped %like% "^=> ") {
indentation <- 3 + extra_indent
} else {
indentation <- 0L + extra_indent
indentation <- 0 + extra_indent
}
if (indentation > 0L) {
wrapped <- gsub("\n", paste0("\n", strrep(" ", indentation)), wrapped, fixed = TRUE)
msg <- gsub("\n", paste0("\n", strrep(" ", indentation)), msg, fixed = TRUE)
# remove trailing empty characters
msg <- gsub("(\n| )+$", "", msg)
if (length(add_fn) > 0) {
if (!is.list(add_fn)) {
add_fn <- list(add_fn)
}
for (i in seq_len(length(add_fn))) {
msg <- add_fn[[i]](msg)
}
}
gsub("(\n| )+$", "", wrapped)
# format backticks
if (pkg_is_available("cli") &&
tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE) &&
tryCatch(getExportedValue("isAvailable", ns = asNamespace("rstudioapi"))(), error = function(e) {
return(FALSE)
}) &&
tryCatch(getExportedValue("versionInfo", ns = asNamespace("rstudioapi"))()$version > "2023.6.0.0", error = function(e) {
return(FALSE)
})) {
# we are in a recent version of RStudio, so do something nice: add links to our help pages in the console.
parts <- strsplit(msg, "`", fixed = TRUE)[[1]]
cmds <- parts %in% paste0(ls(envir = asNamespace("AMR")), "()")
# functions with a dot are not allowed: https://github.com/rstudio/rstudio/issues/11273#issuecomment-1156193252
# lead them to the help page of our package
parts[cmds & parts %like% "[.]"] <- font_url(
url = paste0("ide:help:AMR::", gsub("()", "", parts[cmds & parts %like% "[.]"], fixed = TRUE)),
txt = parts[cmds & parts %like% "[.]"]
)
# 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% "[.]"]
)
# datasets should give help page as well
parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")] <- font_url(
url = paste0("ide:help:AMR::", gsub("()", "", parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")], fixed = TRUE)),
txt = parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")]
)
# text starting with `?` must also lead to the help page
parts[parts %like% "^[?].+"] <- font_url(
url = paste0("ide:help:AMR::", gsub("?", "", parts[parts %like% "^[?].+"], fixed = TRUE)),
txt = parts[parts %like% "^[?].+"]
)
msg <- paste0(parts, collapse = "`")
}
msg <- gsub("`(.+?)`", font_grey_bg("`\\1`"), msg)
# clean introduced whitespace in between fullstops
msg <- gsub("[.] +[.]", "..", msg)
# remove extra space that was introduced (e.g. "Smith et al. , 2022")
msg <- gsub(". ,", ".,", msg, fixed = TRUE)
msg <- gsub("[ ,", "[,", msg, fixed = TRUE)
msg <- gsub("/ /", "//", msg, fixed = TRUE)
msg
}
message_ <- function(...,
appendLF = TRUE,
add_fn = list(font_blue),
as_note = TRUE) {
if (pkg_is_available("cli", min_version = "3.0.0")) {
msg <- paste0(c(...), collapse = "")
if (isTRUE(as_note)) {
cli::cli_inform(c("i" = msg), .envir = parent.frame())
} else {
cli::cli_inform(msg, .envir = parent.frame())
}
} else {
plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
message(word_wrap(plain_msg, as_note = as_note), appendLF = appendLF)
}
message(
word_wrap(...,
add_fn = add_fn,
as_note = as_note
),
appendLF = appendLF
)
}
warning_ <- function(...,
add_fn = list(),
immediate = FALSE,
call = FALSE) {
if (pkg_is_available("cli", min_version = "3.0.0")) {
msg <- paste0(c(...), collapse = "")
cli::cli_warn(msg, .envir = parent.frame())
} else {
plain_msg <- cli_to_plain(paste0(c(...), collapse = ""), envir = parent.frame())
warning(trimws2(word_wrap(plain_msg, as_note = FALSE)), immediate. = immediate, call. = call)
}
warning(
trimws2(word_wrap(...,
add_fn = add_fn,
as_note = FALSE
)),
immediate. = immediate,
call. = call
)
}
# this alternative to the stop() function:
# - adds the function name where the error was thrown (plain-text fallback)
# - wraps text to never break lines within words (plain-text fallback)
# - adds the function name where the error was thrown
# - wraps text to never break lines within words
stop_ <- function(..., call = TRUE) {
msg <- paste0(c(...), collapse = "")
if (pkg_is_available("cli", min_version = "3.0.0")) {
msg_call <- ""
if (!isFALSE(call)) {
if (isTRUE(call)) {
call_obj <- sys.call(-1)
} else if (!isFALSE(call)) {
call_obj <- sys.call(call)
call <- as.character(sys.call(-1)[1])
} else {
call_obj <- NULL
# so you can go back more than 1 call, as used in sir_calc(), that now throws a reference to e.g. n_sir()
call <- as.character(sys.call(call)[1])
}
cli::cli_abort(msg, call = call_obj, .envir = parent.frame())
msg_call <- paste0("in ", call, "():")
}
msg <- trimws2(word_wrap(msg, add_fn = list(), as_note = FALSE))
if (!is.null(AMR_env$cli_abort) && length(unlist(strsplit(msg, "\n", fixed = TRUE))) <= 1) {
if (is.character(call)) {
call <- as.call(str2lang(paste0(call, "()")))
} else {
call <- NULL
}
AMR_env$cli_abort(msg, call = call)
} else {
msg_call <- ""
if (!isFALSE(call)) {
if (isTRUE(call)) {
call_name <- as.character(sys.call(-1)[1])
} else {
# go back more than 1 call, as used in sir_calc() to reference e.g. n_sir()
call_name <- as.character(sys.call(call)[1])
}
msg_call <- paste0("in ", call_name, "():")
}
plain_msg <- cli_to_plain(trimws2(word_wrap(msg, as_note = FALSE)), envir = parent.frame())
stop(paste(msg_call, plain_msg), call. = FALSE)
stop(paste(msg_call, msg), call. = FALSE)
}
}
@@ -635,7 +625,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
return_after_integrity_check <- function(value, type, check_vector) {
if (!all(value[!is.na(value)] %in% check_vector)) {
warning_("invalid ", type, ", NA generated")
warning_(paste0("invalid ", type, ", NA generated"))
value[!value %in% check_vector] <- NA
}
value
@@ -699,12 +689,8 @@ format_included_data_number <- function(data) {
vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
# makes unique and sorts, and this also removed NAs
v <- unique(v)
has_na <- anyNA(v)
if (isTRUE(sort)) {
v <- sort(v)
if (has_na) {
v <- c(v, NA)
}
}
if (isTRUE(reverse)) {
v <- rev(v)
@@ -726,25 +712,18 @@ 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, sort(VALID_SIR_LEVELS))) {
if (identical(v, c("I", "NI", "R", "S", "SDD"))) {
# class 'sir' should be sorted like this
v <- VALID_SIR_LEVELS
v <- c("S", "SDD", "I", "R", "NI")
}
# oxford comma
if (last_sep %in% c(" or ", " and ") && length(v) > 2) {
last_sep <- paste0(",", last_sep)
}
NAs <- which(is.na(v))
if (is.numeric(v)) {
v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE))
}
quoted <- paste0(quotes, v, quotes)
quoted[NAs] <- "NA"
# all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
paste0(
paste(quoted[seq_len(length(quoted) - 1)], collapse = ", "),
last_sep, quoted[length(quoted)]
paste0(quotes, v[seq_len(length(v) - 1)], quotes, collapse = ", "),
last_sep, paste0(quotes, v[length(v)], quotes)
)
}
@@ -945,7 +924,7 @@ ascertain_sir_classes <- function(x, obj_name) {
warning_(
"the data provided in argument `", obj_name,
"` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
"See {.help [{.fun as.sir}](AMR::as.sir)}.",
"See `?as.sir`.",
immediate = TRUE
)
sirs_eligible <- is_sir_eligible(x)
@@ -991,13 +970,8 @@ get_current_data <- function(arg_name, call) {
# an element `.data` will be in the environment when using dplyr::select()
return(env$`.data`)
} else if (valid_df(env$training)) {
if (!is.null(env$x) && valid_df(env$x$template)) {
# an element `x$template` will be in the environment when using some tidymodels functions such as `prep()`
return(env$x$template)
} else {
# this is a fallback for some tidymodels functions such as `prep()`
return(env$training)
}
# an element `training` will be in the environment when using some tidymodels functions such as `prep()`
return(env$training)
} else if (valid_df(env$data)) {
# an element `data` will be in the environment when using older dplyr versions, or some tidymodels functions such as `fit()`
return(env$data)
@@ -1067,8 +1041,24 @@ get_current_column <- function() {
# cur_column() doesn't always work (only allowed for certain conditions set by dplyr), but it's probably still possible:
frms <- lapply(sys.frames(), function(env) {
if (all(c("dots", "i") %in% names(env))) {
names(env$dots)[env$i]
if (tryCatch(!is.null(env$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$i]
} else {
# for mutate(across())
if (!is.null(env$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$i]
} else {
env$i
}
}
} else {
NULL
}
@@ -1122,14 +1112,11 @@ format_custom_query_rule <- function(query, colours = has_colour()) {
query <- gsub("any\\((.*)\\)$", paste0(font_black("any of "), "\\1"), query)
query <- gsub("all\\((.*)\\)$", paste0(font_black("all of "), "\\1"), query)
if (colours == TRUE) {
query <- gsub("[\"']S[\"']", font_green_bg(" S "), query)
query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
query <- gsub("[\"']I[\"']", font_orange_bg(" I "), query)
query <- gsub("[\"']R[\"']", font_rose_bg(" R "), query)
query <- gsub("[\"']SDD[\"']", font_orange_bg(" SDD "), query)
query <- gsub("[\"']S[\"']", font_green_bg(" S "), query)
query <- gsub("[\"']NI[\"']", font_grey_bg(font_black(" NI ")), query)
query <- gsub("[\"']WT[\"']", font_green_bg(" SDD "), query)
query <- gsub("[\"']NWT[\"']", font_rose_bg(" I "), query)
query <- gsub("[\"']NS[\"']", font_rose_bg(" R "), query)
query <- gsub("[\"']I[\"']", font_orange_bg(" I "), query)
}
# replace the black colour 'stops' with blue colour 'starts'
query <- gsub("\033[39m", "\033[34m", as.character(query), fixed = TRUE)
@@ -1201,13 +1188,6 @@ reset_all_thrown_messages <- function() {
)
}
in_rstudio <- function() {
identical(Sys.getenv("RSTUDIO"), "1")
}
in_positron <- function() {
identical(Sys.getenv("POSITRON"), "1")
}
has_colour <- function() {
if (is.null(AMR_env$supports_colour)) {
if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
@@ -1239,14 +1219,10 @@ try_colour <- function(..., before, after, collapse = " ") {
}
}
is_dark <- function() {
AMR_env$current_theme <- NULL
current_theme_fn <- import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)
if (!is.null(current_theme_fn)) {
AMR_env$current_theme <- current_theme_fn()$editor
}
AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
AMR_env$former_theme <- AMR_env$current_theme
AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(current_theme_fn()$dark), error = function(e) TRUE)
AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
}
isTRUE(AMR_env$is_dark_theme)
}
@@ -1641,8 +1617,8 @@ get_n_cores <- function(max_cores = Inf) {
# Support `where()` if tidyselect not installed ----
if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
# tidyselect::where() exists, retrieve from their namespace to make `where()`s work across the package in default arguments
where <- tidyselect::where
# tidyselect::where() exists, load the namespace to make `where()`s work across the package in default arguments
loadNamespace("tidyselect")
} else {
where <- function(fn) {
# based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
R/aa_options.R
+5 -17
View File
@@ -29,27 +29,15 @@
#' Options for the AMR package
#'
#' @description
#' This is an overview of all the package-specific options you can set in the `AMR` package. Set them using the [options()] function, e.g.:
#'
#' `options(AMR_guideline = "CLSI")`
#' @section Options (alphabetical order):
#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
#' @section Options:
#' * `AMR_antibiogram_formatting_type` \cr A [numeric] (1-22) to use in [antibiogram()], to indicate which formatting type to use.
#' * `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$type)`.
#' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"none"`, `"conservative"`, `"standard"`, or `"lenient"` - the default is `"conservative"`.
#' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"standard"`, `"strict"`, `"relaxed"`, or `"inverse"` - the default is `"standard"`.
#' * `AMR_cleaning_regex` \cr A [regular expression][base::regex] (case-insensitive) to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to clean the user input. The default is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
#' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
#' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
#' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
#' * `AMR_guideline` \cr A [character] to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. [as.sir()], [resistance()], [susceptibility()], [interpretive_rules()] and many plotting functions. **While unset**, the AMR package uses the latest implemented EUCAST guideline (currently `r AMR::clinical_breakpoints$guideline[1]`).
#'
#' - For [as.sir()], this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`.
#'
#' - For [resistance()] and [susceptibility()], this setting determines how the `"I"` (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, `"I"` is considered *resistant* in susceptibility calculations; under EUCAST, `"I"` is considered *susceptible* in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
#'
#' - For [interpretive_rules()], this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
#'
#' - For many plotting functions (e.g., for MIC or disk diffusion values), supplying `mo` and `ab` enables automatic SIR-based interpretative colouring. These colours are derived from [as.sir()] in the background and therefore depend on the active `guideline` setting, which again uses `r AMR::clinical_breakpoints$guideline[1]` if not set explicitly.
#' * `AMR_guideline` \cr A [character] to set the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$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`.
@@ -75,9 +63,9 @@
#'
#' ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with [as.sir()].
#'
#' ## Share Options Within Team
#' ### Share Options Within Team
#'
#' For a more collaborative 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:
#' 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
+3 -35
View File
@@ -54,7 +54,7 @@
#' @section Source:
#' 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://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases ab
#' @return A [character] [vector] with additional class [`ab`]
#' @seealso
@@ -119,14 +119,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
x_bak_clean <- x
if (already_regex == FALSE) {
x_bak_clean_before_gen <- x_bak_clean
x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
# generalise_antibiotic_name() rewrites "PH"->"F" and "TH"->"T", which
# mangles short valid AB codes (e.g. "ETH"->"ET", "PHN"->"FN", "STH"->"ST")
# making them unrecognisable in the lookup. Restore any values that were
# already valid AB codes before generalisation (#245).
is_valid_ab_code <- x_bak_clean_before_gen %in% AMR_env$AB_lookup$ab
x_bak_clean[is_valid_ab_code] <- x_bak_clean_before_gen[is_valid_ab_code]
}
x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
@@ -209,9 +202,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
if (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))
if (any(x_new[!already_known & !is.na(x_new)] %in% unlist(AMR_env$AV_lookup$generalised_all, use.names = FALSE), na.rm = TRUE)) {
warning_("in {.help [{.fun as.ab}](AMR::as.ab)}: some input seems to resemble antiviral drugs - use {.help [{.fun as.av}](AMR::as.av)} or e.g. {.help [{.fun av_name}](AMR::av_name)} for these, not {.help [{.fun as.ab}](AMR::as.ab)} or e.g. {.help [{.fun ab_name}](AMR::ab_name)}.")
}
}
for (i in which(!already_known)) {
@@ -458,7 +448,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
x_unknown <- x_unknown[!x_unknown %in% c("", NA)]
if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_(
"in `as.ab()`: ", ifelse(length(unique(x_unknown)) == 1, "this value", "these values"), " could not be coerced to a valid antimicrobial ID: ",
"in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
vector_and(x_unknown), "."
)
}
@@ -514,14 +504,6 @@ ab_reset_session <- function() {
}
}
#' @rdname as.ab
#' @details `NA_ab_` is a missing value of the new `ab` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
#' @format NULL
#' @export
NA_ab_ <- set_clean_class(NA_character_,
new_class = c("ab", "character")
)
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
pillar_shaft.ab <- function(x, ...) {
@@ -529,7 +511,7 @@ pillar_shaft.ab <- function(x, ...) {
out[is.na(x)] <- font_na(NA)
# add the names to the drugs as mouse-over!
if (in_rstudio()) {
if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
out[!is.na(x)] <- font_url(
url = paste0(x[!is.na(x)], ": ", ab_name(x[!is.na(x)])),
txt = out[!is.na(x)]
@@ -645,20 +627,6 @@ rep.ab <- function(x, ...) {
out
}
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, ab)
get_skimmers.ab <- function(column) {
ab <- as.ab(column, info = FALSE)
ab <- ab[!is.na(ab)]
skimr::sfl(
skim_type = "ab",
n_unique = ~ length(unique(ab)),
top_ab = ~ names(sort(-table(ab)))[1L],
top_ab_name = ~ names(sort(-table(ab_name(ab, info = FALSE))))[1L],
top_group = ~ names(sort(-table(ab_group(ab, info = FALSE))))[1L]
)
}
generalise_antibiotic_name <- function(x) {
x <- toupper(x)
# remove suffices
R/ab_from_text.R
+1 -1
View File
@@ -212,7 +212,7 @@ ab_from_text <- function(text,
}
})
} else {
stop_("{.arg type} must be either 'drug', 'dose' or 'administration'")
stop_("`type` must be either 'drug', 'dose' or 'administration'")
}
# collapse text if needed
R/ab_property.R
+3 -25
View File
@@ -65,7 +65,6 @@
#' ab_synonyms("AMX")
#' ab_tradenames("AMX")
#' ab_group("AMX")
#' ab_group("AMX", all_groups = TRUE) # most specific to most general
#' ab_atc_group1("AMX")
#' ab_atc_group2("AMX")
#' ab_url("AMX")
@@ -164,32 +163,11 @@ ab_tradenames <- function(x, ...) {
}
#' @rdname ab_property
#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most specific group name.
#' @export
ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
ab_group <- function(x, language = get_AMR_locale(), ...) {
meet_criteria(x, allow_NA = TRUE)
language <- validate_language(language)
meet_criteria(all_groups, allow_class = "logical", has_length = 1)
grps <- ab_validate(x = x, property = "group", ...)
for (i in seq_along(grps)) {
if (is.null(grps[[i]]) || all(is.na(grps[[i]]))) {
grps[[i]] <- NA_character_
}
if (all_groups == FALSE) {
# take the first match based on ABX_PRIORITY_LIST
grps[[i]] <- grps[[i]][1]
}
if (language != "en") {
grps[[i]] <- translate_into_language(grps[[i]], language = language, only_affect_ab_names = TRUE)
}
}
names(grps) <- x
if (length(grps) == 1 || all_groups == FALSE) {
unname(unlist(grps))
} else {
grps
}
translate_into_language(ab_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
}
#' @rdname ab_property
@@ -304,7 +282,7 @@ ab_info <- function(x, language = get_AMR_locale(), ...) {
ab = as.character(x),
cid = ab_cid(x),
name = ab_name(x, language = language),
group = ab_group(x, language = language, all_groups = TRUE),
group = ab_group(x, language = language),
atc = ab_atc(x),
atc_group1 = ab_atc_group1(x, language = language),
atc_group2 = ab_atc_group2(x, language = language),
R/amr_course.R
-62
View File
@@ -1,62 +0,0 @@
# ==================================================================== #
# 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, et al. (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://amr-for-r.org #
# ==================================================================== #
#' Download and Unpack an AMR Course Repository
#'
#' Downloads and unpacks a GitHub repository containing course materials, using [usethis::use_course()]. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
#' @param github_repo A character string specifying the GitHub repository with username and repo name, e.g. `"https://github.com/username/repo"`.
#' @param branch A character string specifying the branch to download. Defaults to `"main"`.
#' @param ... Additional arguments passed on to [usethis::use_course()].
#' @details
#' This function constructs a ZIP archive URL from the provided `github_repo` and `branch`, then delegates to [usethis::use_course()] to handle the download and extraction.
#'
#' The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
#' @return
#' Called for its side effect. [usethis::use_course()] will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever [usethis::use_course()] returns.
#' @seealso [usethis::use_course()]
#' @export
#' @examples
#' \dontrun{
#'
#' # Let this run by users, e.g., webinar participants
#' amr_course("https://github.com/my_user_name/our_AMR_course")
#' }
amr_course <- function(github_repo, branch = "main", ...) {
if (!"usethis" %in% rownames(utils::installed.packages())) {
if ("rlang" %in% rownames(utils::installed.packages())) {
rlang::check_installed("usethis")
} else {
stop("Package usethis is not installed. Please run: install.packages(\"usethis\")", call. = FALSE)
}
}
url <- paste0(github_repo, "/archive/refs/heads/", branch, ".zip")
use_course <- import_fn("use_course", "usethis")
message("This will download and unpack the contents of a repository.\n")
use_course(url, ...)
}
R/amr_selectors.R
+11 -47
View File
@@ -352,14 +352,6 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
ionophores <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("ionophores", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
isoxazolylpenicillins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
@@ -425,14 +417,6 @@ penicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("penicillins", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
peptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("peptides", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
@@ -441,14 +425,6 @@ phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("phenicols", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
phosphonics <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("phosphonics", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
@@ -474,14 +450,6 @@ rifamycins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
amr_select_exec("rifamycins", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
spiropyrimidinetriones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(return_all, allow_class = "logical", has_length = 1)
amr_select_exec("spiropyrimidinetriones", only_sir_columns = only_sir_columns, return_all = return_all)
}
#' @rdname antimicrobial_selectors
#' @export
streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
@@ -717,7 +685,7 @@ amr_select_exec <- function(function_name,
}
# untreatable drugs
untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam|inducible)")]
untreatable <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$name %like% "(-high|EDTA|polysorbate|macromethod|screening|nacubactam)")]
if (!is.null(vars_df) && only_treatable == TRUE) {
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "amr_class", "untreatable")) {
@@ -745,9 +713,9 @@ amr_select_exec <- function(function_name,
if (is.null(amr_class_args) || isTRUE(function_name %in% c("antifungals", "antimycobacterials"))) {
ab_group <- NULL
if (isTRUE(function_name == "antifungals")) {
abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antifungals" %in% x))]
abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antifungals")]
} else if (isTRUE(function_name == "antimycobacterials")) {
abx <- AMR_env$AB_lookup$ab[which(vapply(FUN.VALUE = logical(1), AMR_env$AB_lookup$group, function(x) "Antimycobacterials" %in% x))]
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_checks.R
# carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
@@ -755,11 +723,7 @@ amr_select_exec <- function(function_name,
# manually added codes from add_custom_antimicrobials() must also be supported
if (length(AMR_env$custom_ab_codes) > 0) {
custom_ab <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$ab %in% AMR_env$custom_ab_codes), ]
check_string <- paste0(
vapply(FUN.VALUE = character(1), custom_ab$group, function(x) paste(x, collapse = " ")),
custom_ab$atc_group1,
custom_ab$atc_group2
)
check_string <- paste0(custom_ab$group, custom_ab$atc_group1, custom_ab$atc_group2)
if (function_name == "betalactams") {
find_group <- "beta[-]?lactams"
} else if (function_name %like% "cephalosporins_") {
@@ -837,7 +801,7 @@ amr_select_exec <- function(function_name,
#' @export
#' @noRd
print.amr_selector <- function(x, ...) {
warning_("It should never be needed to print an antimicrobial selector class. Are you using {.pkg data.table}? Then add the argument {.code with = FALSE}, see our examples at {.help [{.fun amr_selector}](AMR::amr_selector)}.",
warning_("It should never be needed to print an antimicrobial selector class. Are you using data.table? Then add the argument `with = FALSE`, see our examples at `?amr_selector`.",
immediate = TRUE
)
cat("Class 'amr_selector'\n")
@@ -855,10 +819,10 @@ c.amr_selector <- function(...) {
all_any_amr_selector <- function(type, ..., na.rm = TRUE) {
cols_ab <- c(...)
result <- cols_ab[toupper(cols_ab) %in% VALID_SIR_LEVELS]
result <- cols_ab[toupper(cols_ab) %in% c("S", "SDD", "I", "R", "NI")]
if (length(result) == 0) {
message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
result <- VALID_SIR_LEVELS
result <- c("S", "SDD", "I", "R", "NI")
}
cols_ab <- cols_ab[!cols_ab %in% result]
df <- get_current_data(arg_name = NA, call = -3)
@@ -967,7 +931,7 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
}
}
# this is `!=`, so turn around the values
sir <- VALID_SIR_LEVELS
sir <- c("S", "SDD", "I", "R", "NI")
e2 <- sir[sir != e2]
structure(all_any_amr_selector(type = type, e1, e2),
class = c("amr_selector_any_all", "logical")
@@ -1037,11 +1001,11 @@ find_ab_names <- function(ab_group, n = 3) {
# try popular first, they have DDDs
drugs <- AMR_env$AB_lookup[which((!is.na(AMR_env$AB_lookup$iv_ddd) | !is.na(AMR_env$AB_lookup$oral_ddd)) &
AMR_env$AB_lookup$name %unlike% " " &
vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group &
AMR_env$AB_lookup$group %like% ab_group &
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
if (length(drugs) < n) {
# now try it all
drugs <- AMR_env$AB_lookup[which((vapply(FUN.VALUE = character(1), AMR_env$AB_lookup$group, function(x) paste(x, collapse = " ")) %like% ab_group |
drugs <- AMR_env$AB_lookup[which((AMR_env$AB_lookup$group %like% ab_group |
AMR_env$AB_lookup$atc_group1 %like% ab_group |
AMR_env$AB_lookup$atc_group2 %like% ab_group) &
AMR_env$AB_lookup$ab %unlike% "[0-9]$"), ]$name
@@ -1062,7 +1026,7 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
if (message_not_thrown_before(function_name, sort(agents))) {
if (length(agents) == 0) {
if (is.null(ab_group)) {
message_("For {.help [{.fun ", function_name, "}](AMR::", function_name, ")} no antimicrobial drugs found", examples, ".")
message_("For `", function_name, "()` no antimicrobial drugs found", examples, ".")
} else if (ab_group == "administrable_per_os") {
message_("No orally administrable drugs found", examples, ".")
} else if (ab_group == "administrable_iv") {
R/antibiogram.R
+19 -21
View File
@@ -163,7 +163,7 @@
#' antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
#' ```
#'
#' WISCA uses a sophisticated Bayesian decision model to combine both local and pooled antimicrobial resistance data. This approach not only evaluates local patterns but can also draw on multi-centre data sets to improve regimen accuracy, even in low-incidence infections like paediatric bloodstream infections (BSIs).
#' WISCA uses a sophisticated Bayesian decision model to combine both local and pooled antimicrobial resistance data. This approach not only evaluates local patterns but can also draw on multi-centre datasets to improve regimen accuracy, even in low-incidence infections like paediatric bloodstream infections (BSIs).
#'
#' ### Grouped tibbles
#'
@@ -445,7 +445,7 @@ antibiogram.default <- function(x,
meet_criteria(wisca, allow_class = "logical", has_length = 1)
if (isTRUE(wisca)) {
if (!is.null(mo_transform) && !missing(mo_transform)) {
warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, {.arg mo_transform} will be ignored.")
warning_("WISCA must be based on the species level as WISCA parameters are based on this. For that reason, `mo_transform` will be ignored.")
}
mo_transform <- function(x) suppressMessages(suppressWarnings(paste(mo_genus(x, keep_synonyms = TRUE, language = NULL), mo_species(x, keep_synonyms = TRUE, language = NULL))))
}
@@ -453,7 +453,7 @@ antibiogram.default <- function(x,
deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
antimicrobials <- list(...)$antibiotics
}
meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer", "function"), allow_NA = FALSE, allow_NULL = FALSE)
meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
if (!is.function(mo_transform)) {
meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
}
@@ -482,7 +482,7 @@ antibiogram.default <- function(x,
# try to find columns based on type
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
stop_if(is.null(col_mo), "`col_mo` must be set")
}
# transform MOs
x$`.mo` <- x[, col_mo, drop = TRUE]
@@ -519,11 +519,7 @@ antibiogram.default <- function(x,
# get antimicrobials
ab_trycatch <- tryCatch(colnames(suppressWarnings(x[, antimicrobials, drop = FALSE])), error = function(e) NULL)
if (is.null(ab_trycatch)) {
# try with tidyverse
ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
}
if (is.null(ab_trycatch)) {
stop_ifnot(is.character(suppressMessages(antimicrobials)), "{.arg antimicrobials} must be an antimicrobial selector, or a character vector.")
stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
antimicrobials.bak <- antimicrobials
# split antimicrobials on separator and make it a list
antimicrobials <- strsplit(gsub(" ", "", antimicrobials), "+", fixed = TRUE)
@@ -560,11 +556,12 @@ antibiogram.default <- function(x,
next
} else {
# determine whether this new column should contain S, I, R, or NA
S_values <- c("S", "WT")
if (isTRUE(combine_SI)) {
S_values <- c(S_values, "SDD", "I")
S_values <- c("S", "SDD", "I")
} else {
S_values <- "S"
}
other_values <- setdiff(c("S", "SDD", "I", "R", "WT", "NWT", "NS"), S_values)
other_values <- setdiff(c("S", "SDD", "I", "R"), 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))
@@ -583,7 +580,7 @@ antibiogram.default <- function(x,
if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
ab_transform <- NULL
warning_(
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial drug columns (e.g., \"AMP+GEN\").\n\n",
"Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial agent columns (e.g., \"AMP+GEN\").\n\n",
"To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
"If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
)
@@ -614,12 +611,13 @@ antibiogram.default <- function(x,
counts <- out
out$n_susceptible <- out$S + out$WT
if (isTRUE(combine_SI)) {
out$n_susceptible <- out$n_susceptible + out$I + out$SDD
out$n_susceptible <- out$S + out$I + out$SDD
} else {
out$n_susceptible <- out$S
}
if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
warning_("All combinations had less than {.arg minimum} = {minimum} results, returning an empty antibiogram")
warning_("All combinations had less than `minimum = ", minimum, "` results, returning an empty antibiogram")
return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
} else if (any(out$n_tested < minimum, na.rm = TRUE)) {
mins <- sum(out$n_tested < minimum, na.rm = TRUE)
@@ -627,7 +625,7 @@ antibiogram.default <- function(x,
out <- out %pm>%
subset(n_tested >= minimum)
if (isTRUE(info) && mins > 0) {
message_("NOTE: {mins} combinations had less than {.arg minimum} = {minimum} results and were ignored")
message_("NOTE: ", mins, " combinations had less than `minimum = ", minimum, "` results and were ignored", add_fn = font_red)
}
}
}
@@ -812,7 +810,7 @@ antibiogram.default <- function(x,
# 21. 5 (4-6,N=15/300)
# 22. 5% (4-6%,N=15/300)
if (wisca == TRUE && !formatting_type %in% c(1, 2, 13, 14) && info == TRUE && message_not_thrown_before("antibiogram", wisca, formatting_type)) {
message_("Using WISCA with a {.arg formatting_type} that includes the denominator is not useful")
message_("Using WISCA with a `formatting_type` that includes the denominator is not useful")
}
out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
if (formatting_type == 1) out <- out %pm>% pm_summarise(out_value = round(coverage * 100, digits = digits))
@@ -998,8 +996,8 @@ antibiogram.grouped_df <- function(x,
interval_side = "two-tailed",
info = interactive(),
...) {
stop_ifnot(is.null(mo_transform), "{.arg mo_transform} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes {.arg mo_transform} redundant.", call = FALSE)
stop_ifnot(is.null(syndromic_group), "{.arg syndromic_group} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making {.arg syndromic_group} redundant.", call = FALSE)
stop_ifnot(is.null(mo_transform), "`mo_transform` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes `mo_transform` redundant.", call = FALSE)
stop_ifnot(is.null(syndromic_group), "`syndromic_group` must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making `syndromic_groups` redundant.", call = FALSE)
groups <- attributes(x)$groups
n_groups <- NROW(groups)
progress <- progress_ticker(
@@ -1198,7 +1196,7 @@ simulate_coverage <- function(params) {
#' @param wisca_model The outcome of [wisca()] or [`antibiogram(..., wisca = TRUE)`][antibiogram()].
#' @rdname antibiogram
retrieve_wisca_parameters <- function(wisca_model, ...) {
stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use {.help [{.fun wisca}](AMR::wisca)} or {.help [{.fun antibiogram}](AMR::antibiogram)} (with {.code wisca = TRUE}) to create a WISCA model.")
stop_ifnot(isTRUE(attributes(wisca_model)$wisca), "This function only applies to WISCA models. Use `wisca()` or `antibiogram(..., wisca = TRUE)` to create a WISCA model.")
attributes(wisca_model)$wisca_parameters
}
R/atc_online.R
+3 -3
View File
@@ -99,12 +99,12 @@ atc_online_property <- function(atc_code,
read_html <- import_fn("read_html", "xml2")
if (!all(atc_code %in% unlist(AMR::antimicrobials$atc))) {
missing <- atc_code %unlike% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"
atc_code[missing] <- as.character(ab_atc(atc_code[missing], only_first = TRUE))
atc_code <- as.character(ab_atc(atc_code, only_first = TRUE))
}
if (!has_internet()) {
message_("There appears to be no internet connection, returning NA.",
add_fn = font_red,
as_note = FALSE
)
return(rep(NA, length(atc_code)))
@@ -180,7 +180,7 @@ atc_online_property <- function(atc_code,
colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
if (length(out) == 0) {
message_("in {.help [{.fun atc_online_property}](AMR::atc_online_property)}: no properties found for ATC ", atc_code[i], ". Please check {.href {atc_url} this WHOCC webpage}.")
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
}
R/av.R
+1 -1
View File
@@ -51,7 +51,7 @@
#' @section Source:
#' 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://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
#' @aliases av
#' @return A [character] [vector] with additional class [`ab`]
#' @seealso
R/av_from_text.R
+1 -1
View File
@@ -168,7 +168,7 @@ av_from_text <- function(text,
}
})
} else {
stop_("{.arg type} must be either 'drug', 'dose' or 'administration'")
stop_("`type` must be either 'drug', 'dose' or 'administration'")
}
# collapse text if needed
R/bug_drug_combinations.R
+7 -20
View File
@@ -43,7 +43,7 @@
#' @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", "SDD", "I", "R", "WT, "NWT", 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.
@@ -111,8 +111,6 @@ bug_drug_combinations <- function(x,
SDD = integer(0),
I = integer(0),
R = integer(0),
WT = integer(0),
NWT = integer(0),
total = integer(0),
total_rows = integer(0),
stringsAsFactors = FALSE
@@ -135,9 +133,6 @@ bug_drug_combinations <- function(x,
I = m["I", ],
R = m["R", ],
NI = m["NI", ],
WT = m["WT", ],
NWT = m["NWT", ],
NS = m["NS", ],
na = m[which(is.na(rownames(m))), ],
stringsAsFactors = FALSE
)
@@ -151,11 +146,8 @@ bug_drug_combinations <- function(x,
I = merged$I,
R = merged$R,
NI = merged$NI,
WT = merged$WT,
NWT = merged$NWT,
NS = merged$NS,
total = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS,
total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$WT + merged$NWT + merged$NS + merged$na,
total = merged$S + merged$SDD + merged$I + merged$R + merged$NI,
total_rows = merged$S + merged$SDD + merged$I + merged$R + merged$NI + merged$na,
stringsAsFactors = FALSE
)
if (data_has_groups) {
@@ -237,17 +229,12 @@ format.bug_drug_combinations <- function(x,
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$NI[i], na.rm = TRUE)),
WT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$WT[i], na.rm = TRUE)),
NWT = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NWT[i], na.rm = TRUE)),
NS = vapply(FUN.VALUE = double(1), idx, function(i) sum(x$NS[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$WT[i], na.rm = TRUE) +
sum(x$NWT[i], na.rm = TRUE) +
sum(x$NS[i], na.rm = TRUE)
sum(x$NI[i], na.rm = TRUE)
}),
stringsAsFactors = FALSE
)
@@ -259,10 +246,10 @@ format.bug_drug_combinations <- function(x,
if (remove_intrinsic_resistant == TRUE) {
x <- subset(x, R != total)
}
x$isolates <- x$R + x$NWT
if (combine_SI == TRUE) {
x$isolates <- x$isolates + x$I + x$SDD
x$isolates <- x$R
} else {
x$isolates <- x$R + x$I + x$SDD
}
give_ab_name <- function(ab, format, language) {
R/count.R
+11 -36
View File
@@ -33,16 +33,13 @@
#'
#' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
#' @param ... One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.sir()] if needed.
#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
#' * EUCAST: [count_susceptible()] \eqn{= N_{S} + N_{I}}, [count_resistant()] \eqn{= N_{R}}
#' * CLSI: [count_susceptible()] \eqn{= N_{S} + N_{SDD}}, [count_resistant()] \eqn{= N_{I} + N_{R}}
#'
#' You can also use e.g. [count_R()] or [count_S()] instead, to be explicit.
#' @inheritParams proportion
#' @inheritSection as.sir Interpretation of SIR
#' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
#'
#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `dplyr`'s `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
#' The function [count_resistant()] is equal to the function [count_R()]. The function [count_susceptible()] is equal to the function [count_SI()].
#'
#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
#'
#' The function [count_df()] takes any variable from `data` that has an [`sir`] class (created with [as.sir()]) and counts the number of S's, I's and R's. It also supports grouped variables. The function [sir_df()] works exactly like [count_df()], but adds the percentage of S, I and R.
#' @inheritSection proportion Combination Therapy
@@ -122,21 +119,10 @@
#' count_df(translate = FALSE)
#' }
#' }
count_resistant <- function(...,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.")
}
count_resistant <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c(
"R", "NWT", "NS",
if (identical(guideline, "CLSI")) "I"
),
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -146,21 +132,10 @@ count_resistant <- function(...,
#' @rdname count
#' @export
count_susceptible <- function(...,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.")
}
count_susceptible <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c(
"S", "SDD", "WT",
if (identical(guideline, "EUCAST")) "I"
),
ab_result = c("S", "SDD", "I"),
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -186,7 +161,7 @@ count_S <- function(..., only_all_tested = FALSE) {
count_SI <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("S", "SDD", "I", "WT"),
ab_result = c("S", "SDD", "I"),
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -212,7 +187,7 @@ count_I <- function(..., only_all_tested = FALSE) {
count_IR <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD", "R", "NWT"),
ab_result = c("I", "SDD", "R"),
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -225,7 +200,7 @@ count_IR <- function(..., only_all_tested = FALSE) {
count_R <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("R", "NWT", "NS"),
ab_result = "R",
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -238,7 +213,7 @@ count_R <- function(..., only_all_tested = FALSE) {
count_all <- function(..., only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = VALID_SIR_LEVELS,
ab_result = c("S", "SDD", "I", "R", "NI"),
only_all_tested = only_all_tested,
only_count = TRUE
),
R/custom_antimicrobials.R
+1 -1
View File
@@ -155,7 +155,7 @@ add_custom_antimicrobials <- function(x) {
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE]
class(AMR_env$AB_lookup$ab) <- c("ab", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal {.code antimicrobials} data set.")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antimicrobials` data set.")
}
#' @rdname add_custom_antimicrobials
R/custom_eucast_rules.R
+6 -6
View File
@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
)
stop_if(
identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
"rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}.")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(
inherits(dots[[i]], "formula"),
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
"rule ", i, " must be a valid formula input (e.g., using '~'), see `?custom_eucast_rules`"
)
# Query
@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
result <- dots[[i]][[3]]
stop_ifnot(
deparse(result) %like% "==",
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help [{.fun custom_eucast_rules}](AMR::custom_eucast_rules)}"
"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]]
result_group <- as.character(str2lang(result_group))
@@ -220,8 +220,8 @@ custom_eucast_rules <- function(...) {
result_value <- as.character(result)[[3]]
result_value[result_value == "NA"] <- NA
stop_ifnot(
result_value %in% c(VALID_SIR_LEVELS, NA),
paste0("the resulting value of rule ", i, " must be either ", vector_or(c(VALID_SIR_LEVELS, NA), sort = FALSE))
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)
R/custom_mdro_guideline.R
+9 -8
View File
@@ -145,15 +145,15 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
)
stop_if(
identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see {.help [{.fun mdro}](AMR::mdro)}"
"rules must be a valid formula inputs (e.g., using '~'), see `?mdro`"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help [{.fun mdro}](AMR::mdro)}.")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?mdro`.")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(
inherits(dots[[i]], "formula"),
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help [{.fun mdro}](AMR::mdro)}"
"rule ", i, " must be a valid formula input (e.g., using '~'), see `?mdro`"
)
# Query
@@ -202,7 +202,7 @@ c.custom_mdro_guideline <- function(x, ..., as_factor = NULL) {
}
for (g in list(...)) {
stop_ifnot(inherits(g, "custom_mdro_guideline"),
"for combining custom MDRO guidelines, all rules must be created with {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}",
"for combining custom MDRO guidelines, all rules must be created with `custom_mdro_guideline()`",
call = FALSE
)
vals <- attributes(x)$values
@@ -259,15 +259,16 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
}
)
if (identical(qry, "error")) {
warning_("in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i,
warning_("in `custom_mdro_guideline()`: rule ", i,
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
AMR_env$err_msg,
call = FALSE
call = FALSE,
add_fn = font_red
)
next
}
stop_ifnot(is.logical(qry), "in {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)}: rule ", i, " (`", guideline[[i]]$query,
"`) must return {.code TRUE} or {.code FALSE}, not ",
stop_ifnot(is.logical(qry), "in custom_mdro_guideline(): rule ", i, " (`", guideline[[i]]$query,
"`) must return `TRUE` or `FALSE`, not ",
format_class(class(qry), plural = FALSE),
call = FALSE
)
R/custom_microorganisms.R
+3 -3
View File
@@ -281,9 +281,9 @@ add_custom_microorganisms <- function(x) {
AMR_env$MO_lookup <- unique(rbind_AMR(AMR_env$MO_lookup, new_df))
class(AMR_env$MO_lookup$mo) <- c("mo", "character")
if (nrow(x) <= 3) {
message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal {.code microorganisms} data set.")
message_("Added ", vector_and(italicise(x$fullname), quotes = FALSE), " to the internal `microorganisms` data set.")
} else {
message_("Added ", nr2char(nrow(x)), " records to the internal {.code microorganisms} data set.")
message_("Added ", nr2char(nrow(x)), " records to the internal `microorganisms` data set.")
}
}
@@ -303,7 +303,7 @@ clear_custom_microorganisms <- function() {
AMR_env$custom_mo_codes <- character(0)
AMR_env$mo_previously_coerced <- AMR_env$mo_previously_coerced[which(AMR_env$mo_previously_coerced$mo %in% AMR_env$MO_lookup$mo), , drop = FALSE]
AMR_env$mo_uncertainties <- AMR_env$mo_uncertainties[0, , drop = FALSE]
message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal {.code microorganisms} data set.")
message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `microorganisms` data set.")
}
abbreviate_mo <- function(x, minlength = 5, prefix = "", hyphen_as_space = FALSE, ...) {
R/data.R
+3 -3
View File
@@ -38,7 +38,7 @@
#' - `ab`\cr antimicrobial ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. ***This is a unique identifier.***
#' - `cid`\cr Compound ID as found in PubChem. ***This is a unique identifier.***
#' - `name`\cr Official name as used by WHONET/EARS-Net or the WHO. ***This is a unique identifier.***
#' - `group`\cr One or more short and concise group names, based on WHONET and WHOCC definitions
#' - `group`\cr A short and concise group name, based on WHONET and WHOCC definitions
#' - `atc`\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02` (last updated `r documentation_date(TAXONOMY_VERSION$ATC_DDD$accessed_date)`):
#' - `atc_group1`\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like `"Macrolides, lincosamides and streptogramins"`
#' - `atc_group2`\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like `"Macrolides"`
@@ -282,7 +282,7 @@
#' Data Set with Clinical Breakpoints for SIR Interpretation
#'
#' @description Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, `r length(unique(clinical_breakpoints$host[!clinical_breakpoints$host %in% clinical_breakpoints$type]))` different animal groups, and ECOFFs.
#' @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$type]))` different animal groups, and ECOFFs.
#'
#' These breakpoints are currently implemented:
#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
@@ -368,7 +368,7 @@
#' @format A [tibble][tibble::tibble] with `r format(nrow(esbl_isolates), big.mark = " ")` observations and `r ncol(esbl_isolates)` variables:
#' - `esbl`\cr Logical indicator if the isolate is ESBL-producing
#' - `genus`\cr Genus of the microorganism
#' - `AMC:COL`\cr MIC values for 17 antimicrobial drugs, transformed to class [`mic`] (see [as.mic()])
#' - `AMC:COL`\cr MIC values for 17 antimicrobial agents, transformed to class [`mic`] (see [as.mic()])
#' @details See our [tidymodels integration][amr-tidymodels] for an example using this data set.
#' @examples
#' esbl_isolates
R/disk.R
+6 -8
View File
@@ -121,7 +121,7 @@ as.disk <- function(x, na.rm = FALSE) {
cur_col <- get_current_column()
warning_("in `as.disk()`: ", na_after - na_before, " result",
ifelse(na_after - na_before > 1, "s", ""),
ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
@@ -236,14 +236,12 @@ rep.disk <- function(x, ...) {
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
get_skimmers.disk <- function(column) {
column <- as.integer(column)
skimr::sfl(
skim_type = "disk",
p0 = ~ stats::quantile(column, probs = 0, na.rm = TRUE, names = FALSE),
p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
hist = ~ skimr::inline_hist(stats::na.omit(column), 10)
min = ~ min(as.double(.), na.rm = TRUE),
max = ~ max(as.double(.), na.rm = TRUE),
median = ~ stats::median(as.double(.), na.rm = TRUE),
n_unique = ~ length(unique(stats::na.omit(.))),
hist = ~ skimr::inline_hist(stats::na.omit(as.double(.)))
)
}
R/interpretive_rules.R → R/eucast_rules.R
+53 -73
View File
@@ -53,16 +53,15 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
vector_and(txt, quotes = FALSE)
}
#' Apply Interpretive Rules
#' Apply EUCAST Rules
#'
#' @description
#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
#' Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://www.eucast.org>), see *Source*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
#'
#' To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see *Details*.
#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
#' @param x A data set with antimicrobials columns, such as `amox`, `AMX` and `AMC`.
#' @param info A [logical] to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.
#' @param guideline A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option [`AMR_guideline`][AMR-options].
#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_interpretive_rules`][AMR-options]: `options(AMR_interpretive_rules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
#' @param rules A [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expected_phenotypes"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expected_phenotypes")`. The default value can be set to another value using the package option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
#' @param version_breakpoints The version number to use for the EUCAST Clinical Breakpoints guideline. Can be `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
#' @param version_expected_phenotypes The version number to use for the EUCAST Expected Phenotypes. Can be `r vector_or(names(EUCAST_VERSION_EXPECTED_PHENOTYPES), reverse = TRUE)`.
@@ -101,9 +100,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#'
#' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
#'
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_interpretive_rules`][AMR-options], i.e. run `options(AMR_interpretive_rules = "all")`.
#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
#' @aliases EUCAST
#' @rdname interpretive_rules
#' @rdname eucast_rules
#' @export
#' @return The input of `x`, possibly with edited values of antimicrobials. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations.
#' @source
@@ -157,23 +156,21 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
#'
#' eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
interpretive_rules <- function(x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE,
version_breakpoints = 15.0,
version_expected_phenotypes = 1.2,
version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA,
only_sir_columns = any(is.sir(x)),
custom_rules = NULL,
overwrite = FALSE,
...) {
eucast_rules <- function(x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
verbose = FALSE,
version_breakpoints = 15.0,
version_expected_phenotypes = 1.2,
version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA,
only_sir_columns = any(is.sir(x)),
custom_rules = NULL,
overwrite = FALSE,
...) {
meet_criteria(x, allow_class = "data.frame")
meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1, is_in = c("EUCAST", "CLSI"))
meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5, 6), is_in = c("breakpoints", "expected_phenotypes", "expert", "other", "all", "custom"))
meet_criteria(verbose, allow_class = "logical", has_length = 1)
@@ -185,26 +182,21 @@ interpretive_rules <- function(x,
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
meet_criteria(overwrite, allow_class = "logical", has_length = 1)
stop_if(
guideline == "CLSI",
"CLSI guideline is not yet supported."
)
stop_if(
!is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
"For the {.arg ampc_cephalosporin_resistance} argument to work, the {.arg rules} argument must contain {.code \"expert\"} or {.code \"all\"}."
"For the `ampc_cephalosporin_resistance` argument to work, the `rules` argument must contain `\"expert\"` or `\"all\"`."
)
add_MO_lookup_to_AMR_env()
if ("custom" %in% rules && is.null(custom_rules)) {
warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: no custom rules were set with the {.arg custom_rules} argument",
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
immediate = TRUE
)
rules <- rules[rules != "custom"]
if (length(rules) == 0) {
if (isTRUE(info)) {
message_("No other rules were set, returning original data", as_note = FALSE)
message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
}
return(x)
}
@@ -232,7 +224,7 @@ interpretive_rules <- function(x,
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
}
if (q_continue %in% c(FALSE, 2)) {
message_("Cancelled, returning original data", as_note = FALSE)
message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
return(x)
}
}
@@ -241,7 +233,7 @@ interpretive_rules <- function(x,
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
stop_if(is.null(col_mo), "`col_mo` must be set")
}
decimal.mark <- getOption("OutDec")
@@ -459,7 +451,7 @@ interpretive_rules <- function(x,
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
x$genus_species <- trimws(paste(x$genus, x$species))
if (isTRUE(info) && NROW(x.bak) > 10000) {
message_("OK.", as_note = FALSE)
message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
}
n_added <- 0
@@ -481,7 +473,7 @@ interpretive_rules <- function(x,
"Rules by the ",
font_bold(paste0("AMR package v", utils::packageDescription("AMR")$Version)),
" (", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"),
"), see {.help [{.fun eucast_rules}](AMR::eucast_rules)}\n"
"), see `?eucast_rules`\n"
)
))
cat("\n\n")
@@ -595,13 +587,23 @@ interpretive_rules <- function(x,
} else {
if (isTRUE(info)) {
cat("\n")
message_("Skipping inhibitor-inheritance rules defined by this AMR package: setting S to drug+inhibitor where drug is S, and setting R to drug where drug+inhibitor is R. Add \"other\" or \"all\" to the {.arg rules} argument to apply those rules.")
message_(paste0(
font_red("Skipping inhibitor-inheritance rules defined by this AMR package: setting "),
font_green_bg(" S "),
font_red(" to drug+inhibitor where drug is "),
font_green_bg(" S "),
font_red(", and setting "),
font_rose_bg(" R "),
font_red(" to drug where drug+inhibitor is "),
font_rose_bg(" R "),
font_red(". Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
))
}
}
if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) {
if (isTRUE(info)) {
message_("Skipping custom EUCAST rules, since the {.arg rules} argument does not contain {.code \"custom\"}.")
message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
}
custom_rules <- NULL
}
@@ -663,7 +665,8 @@ interpretive_rules <- function(x,
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == ab],
"' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
" since a column '", ab_s, "' is missing but required for the chosen rules"
" since a column '", ab_s, "' is missing but required for the chosen rules",
add_fn = font_red
)
}
cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -887,7 +890,7 @@ interpretive_rules <- function(x,
for (i in seq_len(length(custom_rules))) {
rule <- custom_rules[[i]]
rows <- tryCatch(which(eval(parse(text = rule$query), envir = x)),
error = function(e) stop_(conditionMessage(e), " (check available data and compare with the custom rules set)", call = FALSE)
error = function(e) stop_(paste0(conditionMessage(e), font_red(" (check available data and compare with the custom rules set)")), call = FALSE)
)
cols <- as.character(rule$result_group)
cols <- c(
@@ -1050,9 +1053,9 @@ interpretive_rules <- function(x,
cat(paste0(font_grey(strrep("-", 0.95 * getOption("width", 100))), "\n"))
if (isFALSE(verbose) && total_n_added + total_n_changed > 0) {
cat("\n", word_wrap("Use ", highlight_code("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
cat("\n", word_wrap("Use `eucast_rules(..., verbose = TRUE)` (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "")
} else if (isTRUE(verbose)) {
cat("\n", word_wrap("Used 'Verbose mode' ({.code verbose = TRUE}), which returns a data.frame with all specified edits.\nUse {.code verbose = FALSE} to apply the rules on your data."), "\n\n", sep = "")
cat("\n", word_wrap("Used 'Verbose mode' (`verbose = TRUE`), which returns a data.frame with all specified edits.\nUse `verbose = FALSE` to apply the rules on your data."), "\n\n", sep = "")
}
}
@@ -1062,13 +1065,13 @@ interpretive_rules <- function(x,
warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_(
"in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", highlight_code(paste0(x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
"in `eucast_rules()`: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
), ")")), "\n",
" - ", highlight_code(paste0(x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)")), "\n",
" - ", highlight_code(paste0(x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"))
), ")\n",
" - ", x_deparsed, " %>% mutate_if(is_sir_eligible, as.sir)\n",
" - ", x_deparsed, " %>% mutate(across(where(is_sir_eligible), as.sir))"
)
}
@@ -1089,29 +1092,6 @@ interpretive_rules <- function(x,
}
}
#' @rdname interpretive_rules
#' @export
eucast_rules <- function(x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
...) {
if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.topic [AMR-options](AMR::AMR-options)}.")
}
interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
}
#' @rdname interpretive_rules
#' @export
clsi_rules <- function(x,
col_mo = NULL,
info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
...) {
interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "CLSI", ...)
}
# helper function for editing the table ----
edit_sir <- function(x,
to,
@@ -1151,10 +1131,10 @@ edit_sir <- function(x,
track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
}
isNA <- is.na(new_edits[rows, cols])
isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI" | new_edits[rows, cols] == "WT" | new_edits[rows, cols] == "NWT" | new_edits[rows, cols] == "NS")
isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
non_SIR <- !isSIR
if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
warning_("Some values had SIR values and were not overwritten, since {.code overwrite = FALSE}.")
warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
}
tryCatch(
# insert into original table
@@ -1178,7 +1158,7 @@ edit_sir <- function(x,
suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
}
warning_(
"in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: value \"", to, "\" added to the factor levels of column",
"in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level."
@@ -1186,7 +1166,7 @@ edit_sir <- function(x,
txt_warning()
warned <- FALSE
} else {
warning_("in {.help [{.fun eucast_rules}](AMR::eucast_rules)}: ", w$message)
warning_("in `eucast_rules()`: ", w$message)
txt_warning()
}
},
@@ -1250,7 +1230,7 @@ edit_sir <- function(x,
return(track_changes)
}
#' @rdname interpretive_rules
#' @rdname eucast_rules
#' @export
eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor"))
R/first_isolate.R
+41 -33
View File
@@ -61,7 +61,7 @@
#'
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
#'
#' ## Different methods
#' ### Different methods
#'
#' According to previously-mentioned sources, there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).
#'
@@ -89,29 +89,21 @@
#' | - Major difference in any antimicrobial result | - `first_isolate(x, type = "points")` |
#' | - Any difference in key antimicrobial results | - `first_isolate(x, type = "keyantimicrobials")` |
#'
#' **Isolate-based**
#'
#' _Minimum variables required: Microorganism identifier_
#' ### Isolate-based
#'
#' This method does not require any selection, as all isolates should be included. It does, however, respect all arguments set in the [first_isolate()] function. For example, the default setting for `include_unknown` (`FALSE`) will omit selection of rows without a microbial ID.
#'
#' **Patient-based**
#' ### Patient-based
#'
#' _Minimum variables required: Microorganism identifier, Patient identifier_
#' To include every genus-species combination per patient once, set the `episode_days` to `Inf`. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
#'
#' This method includes every genus-species combination per patient once. This method makes sure that no duplicate isolates are selected from the same patient. This method is preferred to e.g. identify the first MRSA finding of each patient to determine the incidence. Conversely, in a large longitudinal data set, this could mean that isolates are *excluded* that were found years after the initial isolate.
#' ### Episode-based
#'
#' **Episode-based**
#'
#' _Minimum variables required: Microorganism identifier, Patient identifier, Date_
#'
#' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be e.g., 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
#' To include every genus-species combination per patient episode once, set the `episode_days` to a sensible number of days. Depending on the type of analysis, this could be 14, 30, 60 or 365. Short episodes are common for analysing specific hospital or ward data or ICU cases, long episodes are common for analysing regional and national data.
#'
#' This is the most common method to correct for duplicate isolates. Patients are categorised into episodes based on their ID and dates (e.g., the date of specimen receipt or laboratory result). While this is a common method, it does not take into account antimicrobial test results. This means that e.g. a methicillin-resistant *Staphylococcus aureus* (MRSA) isolate cannot be differentiated from a wildtype *Staphylococcus aureus* isolate.
#'
#' **Phenotype-based**
#'
#' _Minimum variables required: Microorganism identifier, Patient identifier, Date, Antimicrobial test results_
#' ### Phenotype-based
#'
#' This is a more reliable method, since it also *weighs* the antibiogram (antimicrobial test results) yielding so-called 'first weighted isolates'. There are two different methods to weigh the antibiogram:
#'
@@ -246,7 +238,7 @@ 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% VALID_SIR_LEVELS, 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) {
@@ -263,7 +255,8 @@ first_isolate <- function(x = NULL,
),
""
)
)
),
add_fn = font_red
)
}
@@ -271,7 +264,7 @@ first_isolate <- function(x = NULL,
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
stop_if(is.null(col_mo), "`col_mo` must be set")
}
# methods ----
@@ -308,7 +301,7 @@ first_isolate <- function(x = NULL,
# -- date
if (is.null(col_date)) {
col_date <- search_type_in_df(x = x, type = "date", info = info)
stop_if(is.null(col_date), "{.arg col_date} must be set")
stop_if(is.null(col_date), "`col_date` must be set")
}
# -- patient id
@@ -317,11 +310,11 @@ first_isolate <- function(x = NULL,
# WHONET support
x$patient_id <- paste(x$`First name`, x$`Last name`, x$Sex)
col_patient_id <- "patient_id"
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for {.arg col_patient_id}")
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
}
stop_if(is.null(col_patient_id), "{.arg col_patient_id} must be set")
stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
}
# -- specimen
@@ -333,7 +326,7 @@ first_isolate <- function(x = NULL,
check_columns_existance <- function(column, tblname = x) {
if (!is.null(column)) {
stop_ifnot(column %in% colnames(tblname),
"Column '{column}' not found.",
"Column '", column, "' not found.",
call = FALSE
)
}
@@ -362,7 +355,9 @@ first_isolate <- function(x = NULL,
}
# remove testcodes
if (!is.null(testcodes_exclude) && isTRUE(info) && message_not_thrown_before("first_isolate", "excludingtestcodes")) {
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE))
message_("Excluding test codes: ", vector_and(testcodes_exclude, quotes = TRUE),
add_fn = font_red
)
}
if (is.null(col_specimen)) {
@@ -373,7 +368,9 @@ first_isolate <- function(x = NULL,
if (!is.null(specimen_group)) {
check_columns_existance(col_specimen, x)
if (isTRUE(info) && message_not_thrown_before("first_isolate", "excludingspecimen")) {
message_("Excluding other than specimen group '{specimen_group}'")
message_("Excluding other than specimen group '", specimen_group, "'",
add_fn = font_red
)
}
}
if (!is.null(col_keyantimicrobials)) {
@@ -415,6 +412,7 @@ first_isolate <- function(x = NULL,
if (abs(row.start) == Inf || abs(row.end) == Inf) {
if (isTRUE(info)) {
message_("=> Found ", font_bold("no isolates"),
add_fn = font_black,
as_note = FALSE
)
}
@@ -423,6 +421,7 @@ first_isolate <- function(x = NULL,
if (row.start == row.end) {
if (isTRUE(info)) {
message_("=> Found ", font_bold("1 first isolate"), ", as the data only contained 1 row",
add_fn = font_black,
as_note = FALSE
)
}
@@ -430,7 +429,9 @@ first_isolate <- function(x = NULL,
}
if (length(c(row.start:row.end)) == pm_n_distinct(x[c(row.start:row.end), col_mo, drop = TRUE])) {
if (isTRUE(info)) {
message_("=> Found {.strong {length(c(row.start:row.end))} first isolates}, as all isolates were different microbial species",
message_("=> Found ", font_bold(paste(length(c(row.start:row.end)), "first isolates")),
", as all isolates were different microbial species",
add_fn = font_black,
as_note = FALSE
)
}
@@ -449,12 +450,14 @@ first_isolate <- function(x = NULL,
if (type == "keyantimicrobials") {
message_("Basing inclusion on key antimicrobials, ",
ifelse(ignore_I == FALSE, "not ", ""),
"ignoring I"
"ignoring I",
add_fn = font_red
)
}
if (type == "points") {
message_("Basing inclusion on all antimicrobial results, using a points threshold of ",
points_threshold
points_threshold,
add_fn = font_red
)
}
}
@@ -513,7 +516,9 @@ first_isolate <- function(x = NULL,
if (any(!is.na(x$newvar_is_icu)) && any(x$newvar_is_icu == TRUE, na.rm = TRUE)) {
if (icu_exclude == TRUE) {
if (isTRUE(info)) {
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.")
message_("Excluding ", format(sum(x$newvar_is_icu, na.rm = TRUE), decimal.mark = decimal.mark, big.mark = big.mark), " isolates from ICU.",
add_fn = font_red
)
}
x[which(x$newvar_is_icu), "newvar_first_isolate"] <- FALSE
} else if (isTRUE(info)) {
@@ -537,8 +542,9 @@ first_isolate <- function(x = NULL,
paste0('"', x, '"')
}
})
message_("\nGroup: {toString(paste0(names(group), ' = ', group))}\n",
as_note = FALSE
message_("\nGroup: ", paste0(names(group), " = ", group, collapse = ", "), "\n",
as_note = FALSE,
add_fn = font_red
)
}
}
@@ -551,7 +557,8 @@ first_isolate <- function(x = NULL,
format(sum(x$newvar_mo == "UNKNOWN", na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark
),
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')"
" isolates with a microbial ID 'UNKNOWN' (in column '", font_bold(col_mo), "')",
add_fn = font_red
)
}
x[which(x$newvar_mo == "UNKNOWN"), "newvar_first_isolate"] <- include_unknown
@@ -562,7 +569,8 @@ first_isolate <- function(x = NULL,
"Excluding ", format(sum(is.na(x$newvar_mo), na.rm = TRUE),
decimal.mark = decimal.mark, big.mark = big.mark
),
" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')"
" isolates with a microbial ID `NA` (in column '", font_bold(col_mo), "')",
add_fn = font_red
)
}
x[which(is.na(x$newvar_mo)), "newvar_first_isolate"] <- FALSE
@@ -608,7 +616,7 @@ first_isolate <- function(x = NULL,
),
p_found_total, " of total where a microbial ID was available)"
),
as_note = FALSE
add_fn = font_black, as_note = FALSE
)
}
R/guess_ab_col.R
+8 -6
View File
@@ -79,6 +79,7 @@ guess_ab_col <- function(x = NULL, search_string = NULL, verbose = FALSE, only_s
if (isTRUE(verbose)) {
message_("No column found as input for ", search_string,
" (", ab_name(search_string, language = NULL, tolower = TRUE), ").",
add_fn = font_black,
as_note = FALSE
)
}
@@ -210,7 +211,7 @@ get_column_abx <- function(x,
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (anyNA(newnames)) {
if (isTRUE(info)) {
message_("WARNING: some columns returned NA for {.help [{.fun as.ab}](AMR::as.ab)}", as_note = FALSE)
message_(paste0(font_yellow(font_bold(" WARNING: ")), "some columns returned `NA` for `as.ab()`"), as_note = FALSE)
}
warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
call = FALSE,
@@ -221,7 +222,7 @@ get_column_abx <- function(x,
unexisting_cols <- which(!vapply(FUN.VALUE = logical(1), dots, function(col) all(col %in% x_columns)))
if (length(unexisting_cols) > 0) {
if (isTRUE(info)) {
message_(" ERROR", as_note = FALSE)
message_(" ERROR", add_fn = list(font_red, font_bold), as_note = FALSE)
}
stop_("Column(s) not found: ", vector_and(unlist(dots[[unexisting_cols]]), quotes = FALSE),
call = FALSE
@@ -265,11 +266,11 @@ get_column_abx <- function(x,
if (isTRUE(info)) {
if (all_okay == TRUE) {
message_(" OK.", as_note = FALSE)
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else if (!isFALSE(dups)) {
message_("WARNING: some results from {.help [{.fun as.ab}](AMR::as.ab)} are duplicated: ", vector_and(dups, quotes = "`"), as_note = FALSE)
message_(paste0(font_yellow(font_bold(" WARNING: ")), "some results from `as.ab()` are duplicated: ", vector_and(dups, quotes = "`")), as_note = FALSE)
} else {
message_(" WARNING.", as_note = FALSE)
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
}
for (i in seq_len(length(out))) {
@@ -287,7 +288,8 @@ get_column_abx <- function(x,
"Column '", font_bold(out[i]), "' will not be used for ",
names(out)[i], " (", suppressMessages(ab_name(names(out)[i], tolower = TRUE, language = NULL, fast_mode = TRUE)), ")",
", as this antimicrobial has already been set."
)
),
add_fn = font_red
)
}
}
R/join_microorganisms.R
+3 -3
View File
@@ -143,9 +143,9 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
if (is.null(by) && NCOL(x) == 1) {
by <- colnames(x)[1L]
} else {
stop_if(is.null(by), "no column with microorganism names or codes found, set this column with {.arg by}", call = -2)
stop_if(is.null(by), "no column with microorganism names or codes found, set this column with `by`", call = -2)
}
message_('Joining, by = "{by}"', as_note = FALSE) # message same as dplyr::join functions
message_('Joining, by = "', by, '"', add_fn = font_black, as_note = FALSE) # message same as dplyr::join functions
}
if (!all(x[, by, drop = TRUE] %in% AMR_env$MO_lookup$mo, na.rm = TRUE)) {
x$join.mo <- as.mo(x[, by, drop = TRUE])
@@ -185,7 +185,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
}
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
warning_("in `{type}_microorganisms()`: the newly joined data set contains {nrow(joined) - nrow(x)} rows more than the number of rows of {.arg x}.")
warning_("in `", type, "_microorganisms()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
as_original_data_class(joined, class(x.bak)) # will remove tibble groups
R/key_antimicrobials.R
+4 -5
View File
@@ -187,7 +187,7 @@ 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 {.help [{.fun key_antimicrobials}](AMR::key_antimicrobials)}."
"as key antimicrobials for ", name, "s. See `?key_antimicrobials`."
)
}
@@ -282,9 +282,6 @@ generate_antimicrobials_string <- function(df) {
function(x) {
x <- toupper(as.character(x))
x[x == "SDD"] <- "I"
x[x == "WT"] <- "S"
x[x == "NWT"] <- "R"
x[x == "NS"] <- "R"
# ignore "NI" here, no use for determining first isolates
x[!x %in% c("S", "I", "R")] <- "."
paste(x)
@@ -315,7 +312,9 @@ antimicrobials_equal <- function(y,
key2sir <- function(val) {
val <- strsplit(val, "", fixed = TRUE)[[1L]]
val.int <- rep(NA_real_, length(val))
val.int[val %in% VALID_SIR_LEVELS] <- as.double(as.sir(val[val %in% VALID_SIR_LEVELS]))
val.int[val == "S"] <- 1
val.int[val %in% c("I", "SDD")] <- 2
val.int[val == "R"] <- 3
val.int
}
# only run on uniques
R/mdro.R
+69 -109
View File
@@ -31,7 +31,7 @@
#'
#' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
#' @param x A [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank for automatic determination.
#' @param guideline A specific guideline to follow, see sections *Supported International / National Guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
#' @param guideline A specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
#' @param esbl [logical] values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).
#' @param carbapenemase [logical] values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).
#' @param mecA [logical] values, or a column name containing logical values, indicating the presence of a *mecA* gene (or production of its proteins).
@@ -41,8 +41,7 @@
#' @inheritParams eucast_rules
#' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
#' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @param infer_from_combinations A [logical] to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does **not** imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to `TRUE`.
#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @details
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#'
@@ -144,7 +143,6 @@ mdro <- function(x = NULL,
combine_SI = TRUE,
verbose = FALSE,
only_sir_columns = any(is.sir(x)),
infer_from_combinations = TRUE,
...) {
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@@ -167,32 +165,57 @@ mdro <- function(x = NULL,
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
meet_criteria(verbose, allow_class = "logical", has_length = 1)
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
stop_("There were no SIR columns found in the data set, despite {.arg only_sir_columns} being {.code TRUE}. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
stop_("There were no SIR columns found in the data set, despite `only_sir_columns` being `TRUE`. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
stop_("There were no eligible SIR columns found in the data set. Transform columns with {.help [{.fun as.sir}](AMR::as.sir)} for valid antimicrobial interpretations.")
stop_("There were no eligible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
}
# get gene values as TRUE/FALSE
resolve_gene_var <- function(x, gene, varname) {
if (is.character(gene)) {
meet_criteria(gene, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
gene <- x[[gene]]
meet_criteria(gene, allow_class = "logical", allow_NA = TRUE)
} else if (length(gene) == 1) {
gene <- rep(gene, NROW(x))
}
x[[varname]] <- gene
x
if (is.character(esbl)) {
meet_criteria(esbl, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
esbl <- x[[esbl]]
meet_criteria(esbl, allow_class = "logical", allow_NA = TRUE)
} else if (length(esbl) == 1) {
esbl <- rep(esbl, NROW(x))
}
if (is.character(carbapenemase)) {
meet_criteria(carbapenemase, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
carbapenemase <- x[[carbapenemase]]
meet_criteria(carbapenemase, allow_class = "logical", allow_NA = TRUE)
} else if (length(carbapenemase) == 1) {
carbapenemase <- rep(carbapenemase, NROW(x))
}
if (is.character(mecA)) {
meet_criteria(mecA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
mecA <- x[[mecA]]
meet_criteria(mecA, allow_class = "logical", allow_NA = TRUE)
} else if (length(mecA) == 1) {
mecA <- rep(mecA, NROW(x))
}
if (is.character(mecC)) {
meet_criteria(mecC, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
mecC <- x[[mecC]]
meet_criteria(mecC, allow_class = "logical", allow_NA = TRUE)
} else if (length(mecC) == 1) {
mecC <- rep(mecC, NROW(x))
}
if (is.character(vanA)) {
meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
vanA <- x[[vanA]]
meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
} else if (length(vanA) == 1) {
vanA <- rep(vanA, NROW(x))
}
if (is.character(vanB)) {
meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
vanB <- x[[vanB]]
meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
} else if (length(vanB) == 1) {
vanB <- rep(vanB, NROW(x))
}
x <- resolve_gene_var(x, esbl, "esbl")
x <- resolve_gene_var(x, carbapenemase, "carbapenemase")
x <- resolve_gene_var(x, mecA, "mecA")
x <- resolve_gene_var(x, mecC, "mecC")
x <- resolve_gene_var(x, vanA, "vanA")
x <- resolve_gene_var(x, vanB, "vanB")
info.bak <- info
# don't throw info's more than once per call
@@ -213,7 +236,7 @@ mdro <- function(x = NULL,
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
}
if (q_continue %in% c(FALSE, 2)) {
message_("Cancelled, returning original data", as_note = FALSE)
message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
return(x)
}
}
@@ -251,7 +274,7 @@ mdro <- function(x = NULL,
guideline.bak <- guideline
if (is.list(guideline)) {
# Custom MDRO guideline ---------------------------------------------------
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use {.help [{.fun custom_mdro_guideline}](AMR::custom_mdro_guideline)} to create custom guidelines")
stop_ifnot(inherits(guideline, "custom_mdro_guideline"), "use `custom_mdro_guideline()` to create custom guidelines")
if (isTRUE(info)) {
txt <- paste0(
"Determining MDROs based on custom rules",
@@ -328,13 +351,13 @@ mdro <- function(x = NULL,
}
if (is.null(col_mo) && guideline$code == "tb") {
message_(
"No column found as input for {.arg col_mo}, ",
"No column found as input for `col_mo`, ",
font_bold(paste0("assuming all rows contain ", font_italic("Mycobacterium tuberculosis"), "."))
)
x$mo <- as.mo("Mycobacterium tuberculosis", keep_synonyms = TRUE)
col_mo <- "mo"
}
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
stop_if(is.null(col_mo), "`col_mo` must be set")
if (guideline$code == "cmi2012") {
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
@@ -476,58 +499,12 @@ mdro <- function(x = NULL,
if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
# ampicillin column is missing, but amoxicillin is available
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.")
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.", add_fn = font_red)
}
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
}
cols_ab <- cols_ab[!duplicated(cols_ab)]
# Infer resistance for missing base drugs ----
if (isTRUE(infer_from_combinations)) {
.combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
if (length(.combos_in_data) > 0) {
.base_drugs <- suppressMessages(
as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
)
.unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
for (.base in .unique_bases) {
.base_code <- as.character(.base)
if (!.base_code %in% names(cols_ab)) {
# Base drug column absent; find all available combo columns for this base drug
.combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
.combo_cols <- unname(cols_ab[as.character(.combos)])
.combo_cols <- .combo_cols[!is.na(.combo_cols)]
if (length(.combo_cols) > 0) {
# Vectorised: if ANY combination is R, infer base drug as R; otherwise NA
.sir_chars <- as.data.frame(
lapply(x[, .combo_cols, drop = FALSE], function(col) as.character(as.sir(col))),
stringsAsFactors = FALSE
)
.new_col <- paste0(.base_code, ".inferred_sir_proxy_from#", paste0(.combos, collapse = "/"), "#")
x[[.new_col]] <- ifelse(rowSums(.sir_chars == "R", na.rm = TRUE) > 0L, "R", NA_character_)
cols_ab <- c(cols_ab, stats::setNames(.new_col, .base_code))
if (isTRUE(info.bak)) {
message_(
"Inferring resistance for ",
ab_name(.base_code, language = NULL, tolower = TRUE),
" (", font_bold(.base_code, collapse = NULL), ", ", font_italic("missing"), ") from ",
vector_or(
quotes = FALSE,
last_sep = " and/or ",
paste0(
ab_name(.combos, language = NULL, tolower = TRUE),
" (", font_bold(.combos, collapse = NULL), ", ", font_italic("available"), ")"
)
)
)
}
}
}
}
cols_ab <- cols_ab[!duplicated(names(cols_ab))]
}
}
# nolint start
AMC <- cols_ab["AMC"]
AMK <- cols_ab["AMK"]
@@ -722,16 +699,6 @@ mdro <- function(x = NULL,
x
}
ab_without_inhibitor <- function(ab_codes) {
# Get the base drug AB code from a drug+inhibitor combination.
# e.g., AMC (amoxicillin/clavulanic acid) -> AMX (amoxicillin)
# TZP (piperacillin/tazobactam) -> PIP (piperacillin)
# SAM (ampicillin/sulbactam) -> AMP (ampicillin)
combo_names <- ab_name(ab_codes, language = NULL)
base_names <- gsub("/.*", "", combo_names)
suppressMessages(as.ab(base_names))
}
# antimicrobial classes
# nolint start
aminoglycosides <- c(TOB, GEN)
@@ -805,7 +772,7 @@ mdro <- function(x = NULL,
)
}
x[rows_to_change, "MDRO"] <<- to
x[rows_to_change, "reason"] <<- paste0(x[rows_to_change, "reason", drop = TRUE], "; ", reason)
x[rows_to_change, "reason"] <<- reason
x[rows_not_to_change, "reason"] <<- "guideline criteria not met"
}
}
@@ -835,7 +802,7 @@ 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% VALID_SIR_LEVELS[VALID_SIR_LEVELS != "NI"])
function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "SDD", "I", "R"))
))
}
)
@@ -875,7 +842,7 @@ mdro <- function(x = NULL,
}
if (isTRUE(info)) {
message_(" OK.", as_note = FALSE)
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
}
}
@@ -887,7 +854,7 @@ mdro <- function(x = NULL,
x <- left_join_microorganisms(x, by = col_mo)
x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
x$row_number <- seq_len(nrow(x))
x$reason <- ""
x$reason <- NA_character_
x$all_nonsusceptible_columns <- ""
if (guideline$code == "cmi2012") {
@@ -1531,7 +1498,7 @@ mdro <- function(x = NULL,
}
trans_tbl(
3, # positive
rows = which(x$order == "Enterobacterales" & x$esbl == TRUE),
rows = which(x$order == "Enterobacterales" & esbl == TRUE),
cols = "any",
any_all = "any",
reason = "Enterobacterales: ESBL"
@@ -1552,18 +1519,17 @@ mdro <- function(x = NULL,
)
trans_tbl(
3,
rows = which(x$order == "Enterobacterales" & x$carbapenemase == TRUE),
rows = which(x$order == "Enterobacterales" & carbapenemase == TRUE),
cols = "any",
any_all = "any",
reason = "Enterobacterales: carbapenemase"
)
c.freundii_complex <- AMR::microorganisms.groups$mo_name[AMR::microorganisms.groups$mo_group_name == "Citrobacter freundii complex"]
trans_tbl(
3,
rows = which(col_values(x, SXT) == "R" &
(col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c(c.freundii_complex, "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
cols = c(SXT, aminoglycosides, fluoroquinolones),
any_all = "any",
reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"
@@ -1591,14 +1557,14 @@ mdro <- function(x = NULL,
)
trans_tbl(
2, # unconfirmed
rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(x$carbapenemase)),
rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(carbapenemase)),
cols = carbapenems,
any_all = "any",
reason = "A. baumannii-calcoaceticus complex: potential carbapenemase"
)
trans_tbl(
3,
rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & x$carbapenemase == TRUE),
rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & carbapenemase == TRUE),
cols = carbapenems,
any_all = "any",
reason = "A. baumannii-calcoaceticus complex: carbapenemase"
@@ -1608,7 +1574,6 @@ mdro <- function(x = NULL,
x$psae <- 0
x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R") | NA_as_FALSE(col_values(x, MEM) == "R"), 1, 0)
x$psae <- x$psae + ifelse(NA_as_FALSE(x$carbapenemase), 1, 0)
x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R") | NA_as_FALSE(col_values(x, CZA) == "R"), 1, 0)
x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
@@ -1637,7 +1602,7 @@ mdro <- function(x = NULL,
)
trans_tbl(
3,
rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (x$vanA == TRUE | x$vanB == TRUE)),
rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (vanA == TRUE | vanB == TRUE)),
cols = c(PEN, AMX, AMP, VAN),
any_all = "any",
reason = "E. faecium: vanA/vanB gene + penicillin group"
@@ -1646,14 +1611,14 @@ mdro <- function(x = NULL,
# Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
trans_tbl(
2,
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(x$mecA) | is.na(x$mecC))),
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
any_all = "any",
reason = "S. aureus complex: potential MRSA"
)
trans_tbl(
3,
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (x$mecA == TRUE | x$mecC == TRUE)),
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
cols = "any",
any_all = "any",
reason = "S. aureus complex: mecA/mecC gene"
@@ -1934,15 +1899,10 @@ mdro <- function(x = NULL,
# fill in empty reasons
x$reason[is.na(x$reason)] <- "not covered by guideline"
x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
# starting semicolons must be removed
x$reason <- trimws(gsub("^;", "", x$reason))
# if criteria were not met initially, but later they were, then they have a following semicolon; remove the initial lack of meeting criteria
x$reason <- trimws(gsub("guideline criteria not met;", "", x$reason, fixed = TRUE))
# format data set
colnames(x)[colnames(x) == col_mo] <- "microorganism"
x$microorganism <- mo_name(x$microorganism, language = NULL)
x$guideline <- paste0(guideline$author, " - ", guideline$name, ifelse(is.na(guideline$version), "", paste0(" (", guideline$version, ")")))
x$all_nonsusceptible_columns <- gsub(".inferred_sir_proxy_from#(.*?)#", " (inferred from \\1)", x$all_nonsusceptible_columns, perl = TRUE)
x$guideline <- paste0(guideline$author, " - ", guideline$name, ", ", guideline$version, ")")
x[, c(
"row_number",
"microorganism",
@@ -1965,7 +1925,7 @@ brmo <- function(x = NULL, only_sir_columns = any(is.sir(x)), ...) {
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
stop_if(
"guideline" %in% names(list(...)),
"argument {.arg guideline} must not be set since this is a guideline-specific function"
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, guideline = "BRMO", ...)
}
@@ -1978,7 +1938,7 @@ mrgn <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, .
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
stop_if(
"guideline" %in% names(list(...)),
"argument {.arg guideline} must not be set since this is a guideline-specific function"
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "MRGN", ...)
}
@@ -1990,7 +1950,7 @@ mdr_tb <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
stop_if(
"guideline" %in% names(list(...)),
"argument {.arg guideline} must not be set since this is a guideline-specific function"
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "TB", ...)
}
@@ -2002,7 +1962,7 @@ mdr_cmi2012 <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = F
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
stop_if(
"guideline" %in% names(list(...)),
"argument {.arg guideline} must not be set since this is a guideline-specific function"
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "CMI 2012", ...)
}
@@ -2014,7 +1974,7 @@ eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = any(is.si
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
stop_if(
"guideline" %in% names(list(...)),
"argument {.arg guideline} must not be set since this is a guideline-specific function"
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "EUCAST", ...)
}
R/mean_amr_distance.R
+1 -1
View File
@@ -118,7 +118,7 @@ mean_amr_distance.disk <- function(x, ...) {
mean_amr_distance.sir <- function(x, ..., combine_SI = TRUE) {
meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1)
if (isTRUE(combine_SI)) {
x[x %in% c("I", "SDD")] <- "S" # do not acknowledge CLSI/EUCAST guideline here to keep the numeric mean_amr_distance consistent between systems
x[x %in% c("I", "SDD")] <- "S"
}
mean_amr_distance(as.double(x))
}
R/mic.R
+12 -45
View File
@@ -63,7 +63,6 @@ COMMON_MIC_VALUES <- c(
#' @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 round_to_next_log2 A [logical] to round up all values to the next log2 level, that are not either `r vector_or(COMMON_MIC_VALUES, quotes = F)`. Values that are already in this list (with or without operators), are left unchanged (including any operators).
#' @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)))`).
#'
@@ -126,7 +125,7 @@ COMMON_MIC_VALUES <- c(
#' # this can also coerce combined MIC/SIR values:
#' as.mic("<=0.002; S")
#'
#' # mathematical processing treats MICs as, and returns, numeric values
#' # mathematical processing treats MICs as numeric values
#' fivenum(mic_data)
#' quantile(mic_data)
#' all(mic_data < 512)
@@ -134,10 +133,6 @@ COMMON_MIC_VALUES <- c(
#' # rescale MICs using rescale_mic()
#' rescale_mic(mic_data, mic_range = c(4, 16))
#'
#' # round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:
#' c(1:8)
#' as.mic(c(1:8), round_to_next_log2 = TRUE)
#'
#' # interpret MIC values
#' as.sir(
#' x = as.mic(2),
@@ -162,12 +157,10 @@ COMMON_MIC_VALUES <- c(
#' if (require("ggplot2")) {
#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
#' }
as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2 = 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)
meet_criteria(keep_operators, allow_class = c("character", "logical"), is_in = c("all", "none", "edges", FALSE, TRUE), has_length = 1)
meet_criteria(round_to_next_log2, allow_class = "logical", has_length = 1)
if (isTRUE(keep_operators)) {
keep_operators <- "all"
} else if (isFALSE(keep_operators)) {
@@ -175,9 +168,6 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
}
if (is.mic(x) && (keep_operators == "all" || !any(x %like% "[>=<]", na.rm = TRUE))) {
if (isTRUE(round_to_next_log2)) {
x <- roundup_to_nearest_log2(x)
}
if (!identical(levels(x), VALID_MIC_LEVELS)) {
# might be from an older AMR version - just update MIC factor levels
x <- set_clean_class(factor(as.character(x), levels = VALID_MIC_LEVELS, ordered = TRUE),
@@ -217,9 +207,8 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
warning_("Some MICs were combined values, only the first values are kept")
x[x %like% "[0-9]/.*[0-9]"] <- gsub("/.*", "", x[x %like% "[0-9]/.*[0-9]"])
}
x <- trimws2(gsub("[^e\\P{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
# remove other invalid characters
x <- gsub("[^0-9e.><= -]+", "", x, perl = TRUE)
x <- gsub("[^a-zA-Z0-9.><= -]+", "", x, perl = TRUE)
# transform => to >= and =< to <=
x <- gsub("=<", "<=", x, fixed = TRUE)
x <- gsub("=>", ">=", x, fixed = TRUE)
@@ -271,7 +260,7 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
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, "'")),
ifelse(is.null(cur_col), "", paste0(" in index '", cur_col, "'")),
" truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",
@@ -290,10 +279,6 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
x[!x %in% keep] <- gsub("[>=<]", "", x[!x %in% keep])
}
if (isTRUE(round_to_next_log2)) {
x <- roundup_to_nearest_log2(x)
}
set_clean_class(factor(x, levels = VALID_MIC_LEVELS, ordered = TRUE),
new_class = c("mic", "ordered", "factor")
)
@@ -320,7 +305,7 @@ NA_mic_ <- set_clean_class(factor(NA, levels = VALID_MIC_LEVELS, ordered = TRUE)
#' @rdname as.mic
#' @param mic_range A manual range to rescale the MIC values, e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling on one side, e.g., `mic_range = c(NA, 32)`.
#' @export
rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, round_to_next_log2 = FALSE) {
rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
meet_criteria(mic_range, allow_class = c("numeric", "integer", "logical", "mic"), has_length = 2, allow_NA = TRUE, allow_NULL = TRUE)
if (is.numeric(mic_range)) {
mic_range <- trimws(format(mic_range, scientific = FALSE))
@@ -351,7 +336,7 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE, r
x[x > max_mic] <- max_mic
}
x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators), round_to_next_log2 = round_to_next_log2)
x <- as.mic(x, keep_operators = ifelse(keep_operators == "edges", "none", keep_operators))
if (isTRUE(as.mic)) {
if (keep_operators == "edges" && length(unique(x)) > 1) {
@@ -611,33 +596,15 @@ 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(column, probs = 0, na.rm = TRUE, names = FALSE),
p25 = ~ stats::quantile(column, probs = 0.25, na.rm = TRUE, names = FALSE),
p50 = ~ stats::quantile(column, probs = 0.5, na.rm = TRUE, names = FALSE),
p75 = ~ stats::quantile(column, probs = 0.75, na.rm = TRUE, names = FALSE),
p100 = ~ stats::quantile(column, probs = 1, na.rm = TRUE, names = FALSE),
hist = ~ skimr::inline_hist(log2(stats::na.omit(column)), 10)
p0 = ~ stats::quantile(., probs = 0, na.rm = TRUE, names = FALSE),
p25 = ~ stats::quantile(., probs = 0.25, na.rm = TRUE, names = FALSE),
p50 = ~ stats::quantile(., probs = 0.5, na.rm = TRUE, names = FALSE),
p75 = ~ stats::quantile(., probs = 0.75, na.rm = TRUE, names = FALSE),
p100 = ~ stats::quantile(., probs = 1, na.rm = TRUE, names = FALSE),
hist = ~ skimr::inline_hist(log2(stats::na.omit(.)), 5)
)
}
roundup_to_nearest_log2 <- function(x) {
x_dbl <- suppressWarnings(as.double(gsub("[>=<]", "", x)))
x_new <- vapply(
FUN.VALUE = double(1),
x_dbl,
function(val) {
if (is.na(val)) {
NA_real_
} else {
COMMON_MIC_VALUES[which(COMMON_MIC_VALUES >= val)][1]
}
}
)
x[!x_dbl %in% COMMON_MIC_VALUES] <- x_new[!x_dbl %in% COMMON_MIC_VALUES]
x
}
# Miscellaneous mathematical functions ------------------------------------
#' @method mean mic
R/mo.R
+18 -36
View File
@@ -38,15 +38,13 @@
#'
#' This excludes enterococci at default (who are in group D), use `Lancefield = "all"` to also categorise all enterococci as group D.
#' @param minimum_matching_score A numeric value to set as the lower limit for the [MO matching score][mo_matching_score()]. When left blank, this will be determined automatically based on the character length of `x`, its [taxonomic kingdom][microorganisms] and [human pathogenicity][mo_matching_score()].
#' @param keep_synonyms A [logical] to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of *S. pyogenes*. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
#'
#' The default is `FALSE`, which will return a note if outdated taxonomic names were processed. The default can be set with the package option [`AMR_keep_synonyms`][AMR-options], i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
#' @param keep_synonyms A [logical] to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`, which will return a note if old taxonomic names were processed. The default can be set with the package option [`AMR_keep_synonyms`][AMR-options], i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
#' @param reference_df A [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ignore_pattern A Perl-compatible [regular expression][base::regex] (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the package option [`AMR_ignore_pattern`][AMR-options], e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
#' @param cleaning_regex A Perl-compatible [regular expression][base::regex] (case-insensitive) to clean the input of `x`. Every matched part in `x` will be removed. At default, this is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the package option [`AMR_cleaning_regex`][AMR-options].
#' @param only_fungi A [logical] to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for [all microorganism functions][mo_property()] with the package option [`AMR_only_fungi`][AMR-options], i.e. `options(AMR_only_fungi = TRUE)`.
#' @param language Language to translate text like "no growth", which defaults to the system language (see [get_AMR_locale()]).
#' @param info A [logical] to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with outdated taxonomic names. The default is `TRUE` only in interactive mode.
#' @param info A [logical] to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is `TRUE` only in interactive mode.
#' @param ... Other arguments passed on to functions.
#' @rdname as.mo
#' @aliases mo
@@ -84,7 +82,7 @@
#' There are three helper functions that can be run after using the [as.mo()] function:
#' - Use [mo_uncertainties()] to get a [data.frame] that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see *Matching Score for Microorganisms* below).
#' - Use [mo_failures()] to get a [character] [vector] with all values that could not be coerced to a valid value.
#' - Use [mo_renamed()] to get a [data.frame] with all values that could be coerced based on outdated, previously accepted taxonomic names.
#' - Use [mo_renamed()] to get a [data.frame] with all values that could be coerced based on old, previously accepted taxonomic names.
#'
#' ### For Mycologists
#'
@@ -402,12 +400,7 @@ as.mo <- function(x,
top_hits <- mo_to_search[order(m, decreasing = TRUE, na.last = NA)] # na.last = NA will remove the NAs
if (length(top_hits) == 0) {
warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ",
ifelse(is.null(minimum_matching_score),
paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"),
minimum_matching_score
),
". Try setting this value lower or even to 0.", call = FALSE)
warning_("No hits found for \"", x_search, "\" with minimum_matching_score = ", ifelse(is.null(minimum_matching_score), paste0("NULL (=", round(min(minimum_matching_score_current, na.rm = TRUE), 3), ")"), minimum_matching_score), ". Try setting this value lower or even to 0.", call = FALSE)
result_mo <- NA_character_
} else {
result_mo <- MO_lookup_current$mo[match(top_hits[1], MO_lookup_current$fullname)]
@@ -483,7 +476,7 @@ as.mo <- function(x,
}
} else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
# keep synonyms is TRUE, so check if any do have synonyms
warning_("{.help [{.fun as.mo}](AMR::as.mo)} returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use ", highlight_code("as.mo(..., keep_synonyms = FALSE)"), " to clean the input to currently accepted taxonomic names, or set the R option {.code AMR_keep_synonyms} to {.code FALSE}. This warning will be shown once per session.", call = FALSE)
warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " old taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
}
# Apply Becker ----
@@ -630,14 +623,6 @@ mo_cleaning_regex <- function() {
)
}
#' @rdname as.mo
#' @details `NA_mo_` is a missing value of the new `mo` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
#' @format NULL
#' @export
NA_mo_ <- set_clean_class(NA_character_,
new_class = c("mo", "character")
)
# UNDOCUMENTED METHODS ----------------------------------------------------
# this prevents the requirement for putting the dependency in Imports:
@@ -690,7 +675,7 @@ pillar_shaft.mo <- function(x, ...) {
}
# add the names to the bugs as mouse-over!
if (in_rstudio()) {
if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
out[!x %in% c("UNKNOWN", NA)] <- font_url(
url = paste0(
x[!x %in% c("UNKNOWN", NA)], ": ",
@@ -762,17 +747,13 @@ freq.mo <- function(x, ...) {
# this prevents the requirement for putting the dependency in Imports:
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
get_skimmers.mo <- function(column) {
mo <- as.mo(column, keep_synonyms = TRUE, language = NULL, info = FALSE)
mo <- mo[!is.na(mo)]
spp <- mo[mo_species(mo, keep_synonyms = TRUE, language = NULL, info = FALSE) != ""]
skimr::sfl(
skim_type = "mo",
n_unique = ~ length(unique(mo)),
gram_negative = ~ sum(mo_is_gram_negative(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
gram_positive = ~ sum(mo_is_gram_positive(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
yeast = ~ sum(mo_is_yeast(mo, keep_synonyms = TRUE, language = NULL, info = FALSE), na.rm = TRUE),
top_genus = ~ names(sort(-table(mo_genus(mo, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
top_species = ~ names(sort(-table(mo_name(spp, keep_synonyms = TRUE, language = NULL, info = FALSE))))[1L],
unique_total = ~ length(unique(stats::na.omit(.))),
gram_negative = ~ sum(mo_is_gram_negative(.), na.rm = TRUE),
gram_positive = ~ sum(mo_is_gram_positive(.), na.rm = TRUE),
top_genus = ~ names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
top_species = ~ names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
)
}
@@ -907,14 +888,14 @@ rep.mo <- function(x, ...) {
print.mo_uncertainties <- function(x, n = 10, ...) {
more_than_50 <- FALSE
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No uncertainties to show. Only uncertainties of the last call to {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n\n")))
cat(word_wrap("No uncertainties to show. Only uncertainties of the last call to `as.mo()` or any `mo_*()` function are stored.\n\n", add_fn = font_blue))
return(invisible(NULL))
} else if (NROW(x) > 50) {
more_than_50 <- TRUE
x <- x[1:50, , drop = FALSE]
}
cat(font_blue(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See {.help [{.fun mo_matching_score}](AMR::mo_matching_score)}.\n\n")))
cat(word_wrap("Matching scores are based on the resemblance between the input and the full taxonomic name, and the pathogenicity in humans. See `?mo_matching_score`.\n\n", add_fn = font_blue))
add_MO_lookup_to_AMR_env()
@@ -924,12 +905,13 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
col_green <- function(x) font_green_bg(x, collapse = NULL)
if (has_colour()) {
cat(font_blue(word_wrap("Colour keys: ",
cat(word_wrap("Colour keys: ",
col_red(" 0.000-0.549 "),
col_orange(" 0.550-0.649 "),
col_yellow(" 0.650-0.749 "),
col_green(" 0.750-1.000")
)), font_green_bg(" "), "\n", sep = "")
col_green(" 0.750-1.000"),
add_fn = font_blue
), font_green_bg(" "), "\n", sep = "")
}
score_set_colour <- function(text, scores) {
@@ -1032,7 +1014,7 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
#' @noRd
print.mo_renamed <- function(x, extra_txt = "", n = 25, ...) {
if (NROW(x) == 0) {
cat(font_blue(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of {.help [{.fun as.mo}](AMR::as.mo)} or any mo_*() function are stored.\n")))
cat(word_wrap("No renamed taxonomy to show. Only renamed taxonomy of the last call of `as.mo()` or any `mo_*()` function are stored.\n", add_fn = font_blue))
return(invisible(NULL))
}
R/mo_property.R
+2 -2
View File
@@ -1043,10 +1043,10 @@ find_mo_col <- function(fn) {
)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
if (message_not_thrown_before(fn = fn)) {
message_("Using column '", font_bold(mo), "' as input for {.help [{.fun ", fn, "}](AMR::", fn, ")}")
message_("Using column '", font_bold(mo), "' as input for `", fn, "()`")
}
return(df[, mo, drop = TRUE])
} else {
stop_("argument {.arg x} is missing and no column with info about microorganisms could be found.", call = -2)
stop_("argument `x` is missing and no column with info about microorganisms could be found.", call = -2)
}
}
R/mo_source.R
+3 -2
View File
@@ -129,7 +129,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
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$", "the {.arg destination} must be a file location with file extension .rds.")
stop_ifnot(destination %like% "[.]rds$", "the `destination` must be a file location with file extension .rds.")
mo_source_destination <- path.expand(destination)
if (is.null(path) || path %in% c(FALSE, "")) {
@@ -137,6 +137,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
if (file.exists(mo_source_destination)) {
unlink(mo_source_destination)
message_("Removed mo_source file '", font_bold(mo_source_destination), "'",
add_fn = font_red,
as_note = FALSE
)
}
@@ -249,7 +250,7 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
current_ext <- regexpr("\\.([[:alnum:]]+)$", destination)
current_ext <- ifelse(current_ext > -1L, substring(destination, current_ext + 1L), "")
vowel <- ifelse(current_ext %like% "^[AEFHILMNORSX]", "n", "")
stop_("The AMR mo source must be an RDS file, not a{vowel} {toupper(current_ext)} file. If \"{basename(destination)}\" was meant as your input file, use {.help [{.fun set_mo_source}](AMR::set_mo_source)} on this file. In any case, the option {.code AMR_mo_source} must be set to another path.")
stop_("The AMR mo source must be an RDS file, not a", vowel, " ", toupper(current_ext), " file. If `\"", basename(destination), "\"` was meant as your input file, use `set_mo_source()` on this file. In any case, the option `AMR_mo_source` must be set to another path.")
}
if (is.null(AMR_env$mo_source)) {
AMR_env$mo_source <- readRDS_AMR(path.expand(destination))
R/plotting.R
+68 -152
View File
@@ -52,19 +52,11 @@
#' @details
#' ### The `scale_*_mic()` Functions
#'
#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
#'
#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [mic][as.mic()].
#'
#' When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as `>=`). Missing intermediate log2 levels will always be plotted too.
#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as `>=`) if desired. Missing intermediate log2 levels will be plotted too.
#'
#' ### The `scale_*_sir()` Functions
#'
#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
#'
#' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [sir][as.sir()].
#'
#' At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`). At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
#'
#' ### Additional `ggplot2` Functions
#'
@@ -122,12 +114,17 @@
#' ) +
#' geom_col()
#' mic_plot +
#' labs(title = "scale_x_mic() automatically applied")
#' labs(title = "without scale_x_mic()")
#' }
#' if (require("ggplot2")) {
#' mic_plot +
#' scale_x_mic(keep_operators = "none") +
#' labs(title = "with scale_x_mic() keeping no operators")
#' 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 +
@@ -154,7 +151,7 @@
#' ) +
#' geom_boxplot() +
#' geom_violin(linetype = 2, colour = "grey30", fill = NA) +
#' labs(title = "scale_y_mic() automatically applied")
#' scale_y_mic()
#' }
#' if (require("ggplot2")) {
#' ggplot(
@@ -186,7 +183,7 @@
#'
#' # Plotting using scale_y_mic() and scale_colour_sir() ------------------
#' if (require("ggplot2")) {
#' mic_sir_plot <- ggplot(
#' plain <- ggplot(
#' data.frame(
#' mic = some_mic_values,
#' group = some_groups,
@@ -200,16 +197,21 @@
#' theme_minimal() +
#' geom_boxplot(fill = NA, colour = "grey30") +
#' geom_jitter(width = 0.25)
#' labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
#'
#' mic_sir_plot
#' plain
#' }
#' if (require("ggplot2")) {
#' mic_sir_plot +
#' # and now with our MIC and SIR scale functions:
#' plain +
#' scale_y_mic() +
#' scale_colour_sir()
#' }
#' if (require("ggplot2")) {
#' plain +
#' scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
#' scale_colour_sir(
#' language = "pt", # Portuguese
#' name = "Support in 28 languages"
#' language = "pt",
#' name = "Support in 27 languages"
#' )
#' }
#' }
@@ -227,9 +229,6 @@
#' plot(some_sir_values)
NULL
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, mic)
scale_type.mic <- function(x) c("mic", "discrete")
create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
ggplot_fn <- getExportedValue(paste0("scale_", aest, "_continuous"),
ns = asNamespace("ggplot2")
@@ -248,7 +247,6 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
as.double(rescale_mic(x = as.double(as.mic(x)), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE))
}
scale$transform_df <- function(self, df) {
out <- list()
if (!aest %in% colnames(df)) {
# support for geom_hline(), geom_vline(), etc
other_x <- c("xintercept", "xmin", "xmax", "xend", "width")
@@ -260,11 +258,11 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
} else {
stop_("No support for plotting df with `scale_", aest, "_mic()` with columns ", vector_and(colnames(df), sort = FALSE))
}
mics <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
if (!is.null(self$mic_values_rescaled) && any(mics < min(self$mic_values_rescaled, na.rm = TRUE) | mics > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
out <- rescale_mic(x = as.double(as.mic(df[[aest_val]])), keep_operators = "none", mic_range = NULL, as.mic = TRUE)
if (!is.null(self$mic_values_rescaled) && any(out < min(self$mic_values_rescaled, na.rm = TRUE) | out > max(self$mic_values_rescaled, na.rm = TRUE), na.rm = TRUE)) {
warning_("The value for `", aest_val, "` is outside the plotted MIC range, consider using/updating the `mic_range` argument in `scale_", aest, "_mic()`.")
}
out[[aest_val]] <- log2(as.double(mics))
df[[aest_val]] <- log2(as.double(out))
} else {
self$mic_values_rescaled <- rescale_mic(x = as.double(as.mic(df[[aest]])), keep_operators = keep_operators, mic_range = mic_range, as.mic = TRUE)
# create new breaks and labels here
@@ -285,18 +283,14 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
self$mic_values_levels[1] <- paste0("<=", self$mic_values_levels[1])
self$mic_values_levels[length(self$mic_values_levels)] <- paste0(">=", self$mic_values_levels[length(self$mic_values_levels)])
}
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df)) {
if (!"x" %in% colnames(df) || all(is.na(df$x))) {
out$group <- 1
} else {
out$group <- as.integer(factor(df$x))
}
self$mic_values_log <- log2(as.double(self$mic_values_rescaled))
if (aest == "y" && "group" %in% colnames(df) && "x" %in% colnames(df)) {
df$group <- as.integer(factor(df$x))
}
out[[aest]] <- self$mic_values_log
df[[aest]] <- self$mic_values_log
}
out
df
}
scale$breaks <- function(..., self) {
@@ -323,6 +317,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
}
}
}
scale$limits <- function(x, ..., self) {
if (!is.null(self$mic_limits_set)) {
if (is.function(self$mic_limits_set)) {
@@ -334,7 +329,7 @@ create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
rng <- range(log2(as.mic(self$mic_values_levels)))
# add 0.5 extra space
rng <- c(rng[1] - 0.5, rng[2] + 0.5)
if (!is.null(x) && !is.na(x[1]) && x[1] == 0) {
if (!is.na(x[1]) && x[1] == 0) {
# scale that start at 0 must remain so, e.g. in case of geom_col()
rng[1] <- 0
}
@@ -382,9 +377,6 @@ scale_fill_mic <- function(keep_operators = "edges", mic_range = NULL, ...) {
create_scale_mic("fill", keep_operators = keep_operators, mic_range = mic_range, ...)
}
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(ggplot2::scale_type, sir)
scale_type.sir <- function(x) c("sir", "discrete")
create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
args <- list(...)
args[c("value", "labels", "limits")] <- NULL
@@ -399,12 +391,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
args,
list(
aesthetics = aesthetics,
values = c(colours_SIR,
NI = "grey30",
WT = unname(colours_SIR[1]),
NWT = unname(colours_SIR[4]),
NS = unname(colours_SIR[4])
)
values = c(colours_SIR, NI = "grey30")
)
)
}
@@ -412,7 +399,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
scale$labels <- function(x) {
stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see {.help [{.fun as.sir}](AMR::as.sir)}.",
"Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see `?as.sir`.",
call = FALSE
)
x <- as.character(x)
@@ -429,9 +416,6 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
x[x == "SI"] <- "(S/I) Susceptible"
x[x == "IR"] <- "(I/R) Non-susceptible"
x[x == "NI"] <- "(NI) Non-interpretable"
x[x == "WT"] <- "(WT) Wildtype"
x[x == "NWT"] <- "(NWT) Non-wildtype"
x[x == "NS"] <- "(NS) Non-susceptible"
x <- translate_AMR(x, language = language)
}
x
@@ -545,16 +529,11 @@ plot.mic <- function(x,
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
x <- as.mic(x) # make sure that currently implemented MIC levels are used
main <- gsub(" +", " ", paste0(main, collapse = " "))
colours_SIR <- expand_SIR_colours(colours_SIR)
# wildtype/Non-wildtype
is_wt_nwt <- identical(breakpoint_type, "ECOFF")
x <- plotrange_as_table(x, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(
x = x,
@@ -585,14 +564,10 @@ plot.mic <- function(x,
if (any(colours_SIR %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- colours_SIR[1]
}
if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(WT) Wildtype")
legend_col <- colours_SIR[1]
}
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
legend_col <- c(legend_col, colours_SIR[2])
@@ -601,14 +576,10 @@ plot.mic <- function(x,
legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[3])
}
if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(R) Resistant")
legend_col <- c(legend_col, colours_SIR[4])
}
if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(NWT) Non-wildtype")
legend_col <- c(legend_col, colours_SIR[4])
}
legend("top",
x.intersp = 0.5,
@@ -701,8 +672,6 @@ autoplot.mic <- function(object,
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
if ("main" %in% names(list(...))) {
title <- list(...)$main
@@ -713,9 +682,6 @@ autoplot.mic <- function(object,
colours_SIR <- expand_SIR_colours(colours_SIR)
# wildtype/Non-wildtype
is_wt_nwt <- identical(breakpoint_type, "ECOFF")
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(
@@ -734,21 +700,17 @@ autoplot.mic <- function(object,
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(
c(
"(S) Susceptible",
"(SDD) Susceptible dose-dependent",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant",
"(WT) Wildtype",
"(NWT) Non-wildtype"
"(R) Resistant"
),
language = language
),
@@ -763,9 +725,7 @@ autoplot.mic <- function(object,
"(I) Susceptible, incr. exp." = colours_SIR[3],
"(I) Intermediate" = colours_SIR[3],
"(R) Resistant" = colours_SIR[4],
"(NI) Non-interpretable" = "grey30",
"(WT) Wildtype" = colours_SIR[1],
"(NWT) Non-wildtype" = colours_SIR[4]
"(NI) Non-interpretable" = "grey30"
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
@@ -829,15 +789,10 @@ plot.disk <- function(x,
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
main <- gsub(" +", " ", paste0(main, collapse = " "))
colours_SIR <- expand_SIR_colours(colours_SIR)
# wildtype/Non-wildtype
is_wt_nwt <- identical(breakpoint_type, "ECOFF")
x <- plotrange_as_table(x, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(
x = x,
@@ -869,14 +824,10 @@ plot.disk <- function(x,
if (any(colours_SIR %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
legend_txt <- "(R) Resistant"
legend_col <- colours_SIR[4]
}
if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
legend_txt <- "(NWT) Non-wildtype"
legend_col <- colours_SIR[4]
}
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
legend_col <- c(legend_col, colours_SIR[3])
@@ -885,14 +836,10 @@ plot.disk <- function(x,
legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
legend_col <- c(legend_col, colours_SIR[2])
}
if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(S) Susceptible")
legend_col <- c(legend_col, colours_SIR[1])
}
if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "(WT) Wildtype")
legend_col <- c(legend_col, colours_SIR[1])
}
legend("top",
x.intersp = 0.5,
legend = translate_into_language(legend_txt, language = language),
@@ -924,8 +871,6 @@ barplot.disk <- function(height,
),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...) {
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
@@ -936,8 +881,6 @@ barplot.disk <- function(height,
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)
main <- gsub(" +", " ", paste0(main, collapse = " "))
@@ -950,10 +893,6 @@ barplot.disk <- function(height,
ab = ab,
guideline = guideline,
colours_SIR = colours_SIR,
language = language,
expand = expand,
include_PKPD = include_PKPD,
breakpoint_type = breakpoint_type,
...
)
}
@@ -1000,9 +939,6 @@ autoplot.disk <- function(object,
colours_SIR <- expand_SIR_colours(colours_SIR)
# wildtype/Non-wildtype
is_wt_nwt <- identical(breakpoint_type, "ECOFF")
x <- plotrange_as_table(object, expand = expand)
cols_sub <- plot_colours_subtitle_guideline(
x = x,
@@ -1020,26 +956,23 @@ autoplot.disk <- function(object,
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(
c(
"(S) Susceptible",
paste("(I)", plot_name_of_I(cols_sub$guideline)),
"(R) Resistant",
"(WT) Wildtype",
"(NWT) Non-wildtype"
"(R) Resistant"
),
language = language
),
ordered = TRUE
)
p <- ggplot2::ggplot(df)
if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c(
"(S) Susceptible" = colours_SIR[1],
@@ -1047,9 +980,7 @@ autoplot.disk <- function(object,
"(I) Susceptible, incr. exp." = colours_SIR[3],
"(I) Intermediate" = colours_SIR[3],
"(R) Resistant" = colours_SIR[4],
"(NI) Non-interpretable" = "grey30",
"(WT) Wildtype" = colours_SIR[1],
"(NWT) Non-wildtype" = colours_SIR[4]
"(NI) Non-interpretable" = "grey30"
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
@@ -1097,25 +1028,25 @@ plot.sir <- function(x,
data <- as.data.frame(table(x), stringsAsFactors = FALSE)
colnames(data) <- c("x", "n")
data$s <- round((data$n / sum(data$n)) * 100, 1)
data <- data[which(data$n > 0), ]
if (!all(data$x %in% c("WT", "NWT"), na.rm = TRUE)) {
# # be sure to have at least S, I, and R
if (!"S" %in% data$x) {
data <- rbind_AMR(data, data.frame(x = "S", n = 0, s = 0, stringsAsFactors = FALSE))
}
if (!"I" %in% data$x) {
data <- rbind_AMR(data, data.frame(x = "I", n = 0, s = 0, stringsAsFactors = FALSE))
}
if (!"R" %in% data$x) {
data <- rbind_AMR(data, data.frame(x = "R", n = 0, s = 0, stringsAsFactors = FALSE))
}
lvls <- VALID_SIR_LEVELS[VALID_SIR_LEVELS %in% c(data$x, c("S", "I", "R"))]
} else {
lvls <- c("WT", "NWT")
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))
}
if (!"NI" %in% data$x) {
data <- rbind_AMR(data, data.frame(x = "NI", n = 0, s = 0, stringsAsFactors = FALSE))
}
data$x <- factor(data$x, levels = lvls, ordered = TRUE)
data <- data[!(data$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$s) > 95, 105, 100)
@@ -1130,7 +1061,7 @@ plot.sir <- function(x,
axes = FALSE
)
# x axis
axis(side = 1, at = seq_along(lvls), labels = lvls, lwd = 0)
axis(side = 1, at = 1:pm_n_distinct(data$x), labels = levels(data$x), lwd = 0)
# y axis, 0-100%
axis(side = 2, at = seq(0, 100, 5))
@@ -1173,14 +1104,9 @@ barplot.sir <- function(height,
main <- gsub(" +", " ", paste0(main, collapse = " "))
x <- table(height)
if (all(height %in% c("WT", "NWT"), na.rm = TRUE)) {
colours_SIR <- colours_SIR[c(1, 4)]
x <- x[names(x) %in% c("WT", "NWT")]
} else {
# remove missing I, SDD, and N
colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
x <- x[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
}
# remove missing I, SDD, and N
colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
x <- x[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
# plot it
barplot(x,
col = colours_SIR,
@@ -1226,11 +1152,6 @@ autoplot.sir <- function(object,
df <- as.data.frame(table(object), stringsAsFactors = TRUE)
colnames(df) <- c("x", "n")
df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "NI")), , drop = FALSE]
if (all(object %in% c("WT", "NWT"), na.rm = TRUE)) {
df <- df[which(df$x %in% c("WT", "NWT")), ]
} else {
df <- df[which(!df$x %in% c("WT", "NWT", "NS")), ]
}
ggplot2::ggplot(df) +
ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
@@ -1240,9 +1161,7 @@ autoplot.sir <- function(object,
"SDD" = colours_SIR[2],
"I" = colours_SIR[3],
"R" = colours_SIR[4],
"NI" = "grey30",
"WT" = colours_SIR[1],
"NWT" = colours_SIR[4]
"NI" = "grey30"
),
limits = force
) +
@@ -1371,9 +1290,6 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
cols[sir == "I"] <- colours_SIR[3]
cols[sir == "R"] <- colours_SIR[4]
cols[sir == "NI"] <- "grey30"
cols[sir == "WT"] <- colours_SIR[1]
cols[sir == "NWT"] <- colours_SIR[4]
cols[sir == "NS"] <- colours_SIR[4]
sub <- bquote(.(abname) ~ "-" ~ italic(.(moname)) ~ .(guideline_txt))
} else {
cols <- "#BEBEBE"
R/proportion.R
+10 -35
View File
@@ -38,11 +38,6 @@
#' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antimicrobials, see section *Combination Therapy* below.
#' @param data A [data.frame] containing columns with class [`sir`] (see [as.sir()]).
#' @param translate_ab A column name of the [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()].
#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
#' * EUCAST: [susceptibility()] \eqn{= \%S + \%I}, [resistance()] \eqn{= \%R}
#' * CLSI: [susceptibility()] \eqn{= \%S + \%SDD}, [resistance()] \eqn{= \%I + \%R}
#'
#' You can also use e.g. [proportion_R()] or [proportion_S()] instead, to be explicit.
#' @inheritParams ab_property
#' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is `TRUE`.
#' @param ab_result Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".
@@ -233,20 +228,10 @@
resistance <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.")
}
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c(
"R", "NWT", "NS",
if (identical(guideline, "CLSI")) "I"
),
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -261,20 +246,10 @@ resistance <- function(...,
susceptibility <- function(...,
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
guideline = getOption("AMR_guideline", "EUCAST")) {
# other arguments for meet_criteria are handled by sir_calc()
meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
message_("This message will be shown once per session.")
}
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c(
"S", "SDD", "WT",
if (identical(guideline, "EUCAST")) "I"
),
ab_result = c("S", "SDD", "I"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -294,7 +269,7 @@ sir_confidence_interval <- function(...,
confidence_level = 0.95,
side = "both",
collapse = FALSE) {
meet_criteria(ab_result, allow_class = c("character", "sir"), has_length = seq_along(VALID_SIR_LEVELS), is_in = VALID_SIR_LEVELS)
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)
@@ -312,7 +287,7 @@ sir_confidence_interval <- function(...,
)
n <- tryCatch(
sir_calc(...,
ab_result = VALID_SIR_LEVELS,
ab_result = c("S", "SDD", "I", "R", "NI"),
only_all_tested = only_all_tested,
only_count = TRUE
),
@@ -366,7 +341,7 @@ proportion_R <- function(...,
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("R", "NWT", "NS"),
ab_result = "R",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -384,7 +359,7 @@ proportion_IR <- function(...,
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("I", "SDD", "R", "NWT", "NS"),
ab_result = c("I", "SDD", "R"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -420,7 +395,7 @@ proportion_SI <- function(...,
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("S", "I", "SDD", "WT"),
ab_result = c("S", "I", "SDD"),
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
@@ -438,7 +413,7 @@ proportion_S <- function(...,
only_all_tested = FALSE) {
tryCatch(
sir_calc(...,
ab_result = c("S", "WT"),
ab_result = "S",
minimum = minimum,
as_percent = as_percent,
only_all_tested = only_all_tested,
R/resistance_predict.R
+1 -1
View File
@@ -238,7 +238,7 @@ resistance_predict <- function(x,
prediction <- predictmodel$fit
se <- predictmodel$se.fit
} else {
stop("no valid model selected. See {.help [{.fun resistance_predict}](AMR::resistance_predict)}.")
stop("no valid model selected. See `?resistance_predict`.")
}
# prepare the output dataframe
R/sir.R
+342 -296
View File
File diff suppressed because it is too large Load Diff
R/sir_calc.R
+9 -11
View File
@@ -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", "sir"), has_length = seq_along(VALID_SIR_LEVELS), is_in = VALID_SIR_LEVELS)
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)
@@ -117,8 +117,6 @@ sir_calc <- function(...,
print_warning <- FALSE
ab_result <- as.sir(ab_result)
denominator_vals <- levels(ab_result)
denominator_vals <- denominator_vals[denominator_vals != "NI"]
if (is.data.frame(x)) {
sir_integrity_check <- character(0)
@@ -150,7 +148,7 @@ sir_calc <- function(...,
denominator <- sum(vapply(FUN.VALUE = logical(1), x_transposed, function(y) !(anyNA(y))))
} else {
# may contain NAs in any column
other_values <- setdiff(c(NA, denominator_vals), ab_result)
other_values <- setdiff(c(NA, levels(ab_result)), ab_result)
if ("SDD" %in% ab_result && "SDD" %in% unlist(x_transposed) && message_not_thrown_before("sir_calc", only_count, ab_result, entire_session = TRUE)) {
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
@@ -167,13 +165,13 @@ sir_calc <- function(...,
message_("Note that `", ifelse(only_count, "count", "proportion"), "_", ifelse("S" %in% ab_result, "S", ""), "I", ifelse("R" %in% ab_result, "R", ""), "()` will also include dose-dependent susceptibility, 'SDD'. This note will be shown once for this session.", as_note = FALSE)
}
numerator <- sum(x %in% ab_result, na.rm = TRUE)
denominator <- sum(x %in% denominator_vals, na.rm = TRUE)
denominator <- sum(x %in% levels(ab_result), na.rm = TRUE)
}
if (print_warning == TRUE) {
if (message_not_thrown_before("sir_calc")) {
warning_("Increase speed by transforming to class 'sir' on beforehand:\n",
highlight_code(" your_data %>% mutate_if(is_sir_eligible, as.sir)"),
" your_data %>% mutate_if(is_sir_eligible, as.sir)",
call = FALSE
)
}
@@ -261,13 +259,13 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
for (i in seq_len(ncol(data))) {
# transform SIR columns
if (is.sir(data[, i, drop = TRUE])) {
data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
data[which(data[, i, drop = TRUE] %in% c("S", "SDD", "WT")), i] <- "S"
data[which(data[, i, drop = TRUE] %in% c("R", "NWT", "NS")), i] <- "R"
data[, i] <- as.character(data[, i, drop = TRUE])
if (isTRUE(combine_SI)) {
data[which(data[, i, drop = TRUE] %in% c("I", "S")), i] <- "SI"
if ("SDD" %in% data[, i, drop = TRUE] && 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])
}
data[which(!data[, i, drop = TRUE] %in% c("S", "SI", "I", "R")), i] <- NA_character_
}
}
R/sysdata.rda
BIN
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R/tidymodels.R
+16 -35
View File
@@ -1,21 +1,20 @@
#' AMR Extensions for Tidymodels
#'
#' This family of functions allows using AMR-specific data types such as `<sir>` and `<mic>` inside `tidymodels` pipelines.
#' This family of functions allows using AMR-specific data types such as `<mic>` and `<sir>` inside `tidymodels` pipelines.
#' @inheritParams recipes::step_center
#' @details
#' You can read more in our online [AMR with tidymodels introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
#'
#' Tidyselect helpers include:
#' - [all_sir()] and [all_sir_predictors()] to select [`<sir>`][as.sir()] columns
#' - [all_mic()] and [all_mic_predictors()] to select [`<mic>`][as.mic()] columns
#' - [all_disk()] and [all_disk_predictors()] to select [`<disk>`][as.disk()] columns
#' - [all_mic()] and [all_mic_predictors()] to select `<mic>` columns
#' - [all_sir()] and [all_sir_predictors()] to select `<sir>` columns
#'
#' Pre-processing pipeline steps include:
#' - [step_sir_numeric()] to convert SIR columns to numeric (via `as.numeric()`), to be used with [all_sir_predictors()]: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA`. Keep this in mind for further processing, especially if the model does not allow for `NA` values.
#' - [step_mic_log2()] to convert MIC columns to numeric (via `as.numeric()`) and apply a log2 transform, to be used with [all_mic_predictors()]
#' - [step_sir_numeric()] to convert SIR columns to numeric (via `as.numeric()`), to be used with [all_sir_predictors()]: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA`. Keep this in mind for further processing, especially if the model does not allow for `NA` values.
#'
#' These steps integrate with `recipes::recipe()` and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
#' @seealso [recipes::recipe()], [as.sir()], [as.mic()], [as.disk()]
#' @seealso [recipes::recipe()], [as.mic()], [as.sir()]
#' @name amr-tidymodels
#' @keywords internal
#' @export
@@ -67,55 +66,35 @@
#' bind_cols(out_testing)
#'
#' # Evaluate predictions using standard classification metrics
#' our_metrics <- metric_set(accuracy,
#' recall,
#' precision,
#' sensitivity,
#' specificity,
#' ppv,
#' npv)
#' our_metrics <- metric_set(accuracy, kap, ppv, npv)
#' metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
#'
#' # Show performance
#' metrics
#' }
all_sir <- function() {
x <- tidymodels_amr_select(class = "sir")
names(x)
}
#' @rdname amr-tidymodels
#' @export
all_sir_predictors <- function() {
x <- tidymodels_amr_select(class = "sir")
intersect(x, recipes::has_role("predictor"))
}
#' @rdname amr-tidymodels
#' @export
all_mic <- function() {
x <- tidymodels_amr_select(class = "mic")
x <- tidymodels_amr_select(levels(NA_mic_))
names(x)
}
#' @rdname amr-tidymodels
#' @export
all_mic_predictors <- function() {
x <- tidymodels_amr_select(class = "mic")
x <- tidymodels_amr_select(levels(NA_mic_))
intersect(x, recipes::has_role("predictor"))
}
#' @rdname amr-tidymodels
#' @export
all_disk <- function() {
x <- tidymodels_amr_select(class = "disk")
all_sir <- function() {
x <- tidymodels_amr_select(levels(NA_sir_))
names(x)
}
#' @rdname amr-tidymodels
#' @export
all_disk_predictors <- function() {
x <- tidymodels_amr_select(class = "disk")
all_sir_predictors <- function() {
x <- tidymodels_amr_select(levels(NA_sir_))
intersect(x, recipes::has_role("predictor"))
}
@@ -181,6 +160,7 @@ bake.step_mic_log2 <- function(object, new_data, ...) {
print.step_mic_log2 <- function(x, width = max(20, options()$width - 35), ...) {
title <- "Log2 transformation of MIC columns"
recipes::print_step(x$columns, x$terms, x$trained, title, width)
invisible(x)
}
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
@@ -256,6 +236,7 @@ bake.step_sir_numeric <- function(object, new_data, ...) {
print.step_sir_numeric <- function(x, width = max(20, options()$width - 35), ...) {
title <- "Numeric transformation of SIR columns"
recipes::print_step(x$columns, x$terms, x$trained, title, width)
invisible(x)
}
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
@@ -269,13 +250,13 @@ tidy.step_sir_numeric <- function(x, ...) {
res
}
tidymodels_amr_select <- function(class) {
tidymodels_amr_select <- function(check_vector) {
df <- get_current_data()
ind <- which(
vapply(
FUN.VALUE = logical(1),
df,
function(x) inherits(x, class),
function(x) all(x %in% c(check_vector, NA), na.rm = TRUE) & any(x %in% check_vector),
USE.NAMES = TRUE
),
useNames = TRUE
R/translate.R
+15 -23
View File
@@ -249,7 +249,7 @@ translate_into_language <- function(from,
any_form_in_patterns <- tryCatch(
any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
error = function(e) {
warning_("Translation not possible. Please create an issue at {.url https://github.com/msberends/AMR/issues}. Many thanks!")
warning_("Translation not possible. Please create an issue at ", font_url("https://github.com/msberends/AMR/issues"), ". Many thanks!")
return(FALSE)
}
)
@@ -263,27 +263,19 @@ translate_into_language <- function(from,
df_trans$pattern[df_trans$regular_expr == TRUE] <- gsub("$$", "$", df_trans$pattern[df_trans$regular_expr == TRUE], fixed = TRUE)
}
# non-regex part
translate_exec <- function(term) {
# sort trans file on length of pattern
trns <- df_trans[order(nchar(df_trans$pattern), decreasing = TRUE), ]
for (i in seq_len(nrow(trns))) {
term <- gsub(
pattern = trns$pattern[i],
replacement = trns[i, lang, drop = TRUE],
x = term,
ignore.case = !trns$case_sensitive[i] & trns$regular_expr[i],
fixed = !trns$regular_expr[i],
perl = trns$regular_expr[i],
lapply(
# starting with longest pattern, since more general translations are shorter, such as 'Group'
order(nchar(df_trans$pattern), decreasing = TRUE),
function(i) {
from_unique_translated <<- gsub(
pattern = df_trans$pattern[i],
replacement = df_trans[i, lang, drop = TRUE],
x = from_unique_translated,
ignore.case = !df_trans$case_sensitive[i] & df_trans$regular_expr[i],
fixed = !df_trans$regular_expr[i],
perl = df_trans$regular_expr[i]
)
}
term
}
from_unique_translated[order(nchar(from_unique_translated), decreasing = TRUE)] <- vapply(
FUN.VALUE = character(1),
USE.NAMES = FALSE,
from_unique_translated[order(nchar(from_unique_translated), decreasing = TRUE)],
translate_exec
)
# force UTF-8 for diacritics
@@ -293,11 +285,11 @@ translate_into_language <- function(from,
out <- from_unique_translated[match(from.bak, from_unique)]
if (!identical(from.bak, out) && get_AMR_locale() == lang && is.null(getOption("AMR_locale", default = NULL)) && message_not_thrown_before("translation", entire_session = TRUE) && interactive()) {
message(font_blue(word_wrap(
message(word_wrap(
"Assuming the ", LANGUAGES_SUPPORTED_NAMES[[lang]]$exonym, " language (",
LANGUAGES_SUPPORTED_NAMES[[lang]]$endonym, ") for the AMR package. See `set_AMR_locale()` to change this or to silence this once-per-session note.",
as_note = TRUE
)))
add_fn = list(font_blue), as_note = TRUE
))
}
out
R/zz_deprecated.R
+1 -1
View File
@@ -124,7 +124,7 @@ deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = N
". The old name will be removed in future version, so please update your code.",
ifelse(type == "argument",
". While the old argument still works, it will be removed in a future version, so please update your code.",
" and will be removed in a future version, see {.topic [AMR-deprecated](AMR::AMR-deprecated)}."
" and will be removed in a future version, see `?AMR-deprecated`."
)
),
ifelse(!is.null(extra_msg),
R/zzz.R
-8
View File
@@ -115,14 +115,6 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
}
.onAttach <- function(libname, pkgname) {
if (interactive() && is.null(getOption("AMR_guideline"))) {
packageStartupMessage(
word_wrap(
"Assuming ", AMR::clinical_breakpoints$guideline[1], " as the default AMR guideline, see `?AMR-options` to change this."
)
)
}
# if custom ab option is available, load it
if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {
README.Rmd
+1 -4
View File
@@ -49,11 +49,8 @@ To install the latest 'beta' version:
```{r, eval = FALSE}
install.packages("AMR", repos = "beta.amr-for-r.org")
```
If this does not work, try to install directly from GitHub using the `remotes` package:
```{r, eval = FALSE}
# if this does not work, try to install directly from GitHub using the 'remotes' package:
remotes::install_github("msberends/AMR")
```
README.md
+1 -5
View File
@@ -58,12 +58,8 @@ To install the latest ‘beta’ version:
``` r
install.packages("AMR", repos = "beta.amr-for-r.org")
```
If this does not work, try to install directly from GitHub using the
`remotes` package:
``` r
# if this does not work, try to install directly from GitHub using the 'remotes' package:
remotes::install_github("msberends/AMR")
```
_pkgdown.yml
+3 -5
View File
@@ -245,14 +245,12 @@ reference:
- title: "Other: miscellaneous functions"
desc: >
Miscellaneous functions that support various parts of an AMR analysis,
such as working with ages, joining tables, principal component analysis,
and other utilities. Especially the 'like' function can be useful:
`if (x %like% y) {...}`.
These functions are mostly for internal use, but some of
them may also be suitable for your analysis. Especially the
'like' function can be useful: `if (x %like% y) {...}`.
contents:
- "`age_groups`"
- "`age`"
- "`amr_course`"
- "`export_ncbi_biosample`"
- "`availability`"
- "`get_AMR_locale`"
cran-comments.md
-2
View File
@@ -1,5 +1,3 @@
This version is a bugfix release (v3.0.1) following the release of v3.0.0 in June 2025.
As with all previous >20 releases, some CHECKs on `oldrel` may return a `NOTE` for narrowly exceeding the installation size limit. This has been reduced to a minimum in prior coordination with CRAN maintainers and currently returns only an `INFO` on `release` and `devel`.
We treat this as a high-impact package: it was published in the *Journal of Statistical Software* (2022), is listed in the CRAN Task View "Epidemiology", and (based on cranlogs download statistics) is used globally. If there is anything to address, we would appreciate being informed before archiving the current version. We conduct extensive automated unit testing and have no indication of unresolved issues.
data-raw/_pre_commit_checks.R
+17 -167
View File
@@ -366,12 +366,9 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
pull(ab)
pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
filter(name %like% "novobiocin|clorobiocin") %>%
filter(group %like% "aminoglycoside") %>%
pull(ab)
pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
filter(group %like% "antifungal") %>%
pull(ab)
@@ -400,28 +397,26 @@ pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>%
filter(group %like% "cephalosporin.*5") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
# see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
filter((group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|piromidic|pipemidic|rosoxacin") %>%
pull(ab)
pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
filter(group %like% "glycopeptide") %>%
pull(ab)
pre_commit_lst$AB_FUSIDANES <- antimicrobials %>%
filter(name %like% "fusi") %>%
pull(ab)
pre_commit_lst$AB_IONOPHORES<- antimicrobials %>%
filter(name %like% "alamethicin|beauvericin|calcimycin|chloroquine|clioquinol|diiodohydroxyquinoline|dithiocarbamates|enniatin|epigallocatechin|gramicidin|hinokitiol|ionomycin|laidlomycin|lasalocid|maduramicin|monensin|narasin|nigericin|nonactin|nystatin|pyrazole|pyrithione|quercetin|salinomycin|semduramicin|valinomycin|zincophorin") %>%
pull(ab)
pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antimicrobials %>%
filter(name %like% "oxacillin|cloxacillin|dicloxacillin|flucloxacillin|meth?icillin") %>%
pull(ab)
pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
pre_commit_lst$AB_LINCOSAMIDES <- antimicrobials %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin|clinda)")) %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin)" & name %unlike% "screening|inducible")) %>%
pull(ab)
pre_commit_lst$AB_MACROLIDES <- antimicrobials %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2)) | name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|primycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)") %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)" & name %unlike% "screening|inducible")) %>%
pull(ab)
pre_commit_lst$AB_MONOBACTAMS <- antimicrobials %>%
filter(group %like% "monobactam" | name %like% "aztreonam|carumonam|tigemonam") %>%
filter(group %like% "monobactam") %>%
pull(ab)
pre_commit_lst$AB_NITROFURANS <- antimicrobials %>%
filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
@@ -432,157 +427,39 @@ pre_commit_lst$AB_OXAZOLIDINONES <- antimicrobials %>%
pre_commit_lst$AB_PENICILLINS <- antimicrobials %>%
filter(group %like% "penicillin" & !(name %unlike% "/" & name %like% ".*bactam$")) %>%
pull(ab)
pre_commit_lst$AB_PEPTIDES <- antimicrobials %>%
filter(ab %in% pre_commit_lst$AB_GLYCOPEPTIDES | name %like% "thiostrepton|actinomycin|bacitracin|daptomycin|vancomycin|teixobactin|tyrocidine|gramicidin|zwittermicin|epothilone|fabclavine|bleomycin|ciclosporin|cyclosporine|siderophores|pyoverdine|enterobactin|myxochelin") %>%
pull(ab)
pre_commit_lst$AB_PHENICOLS <- antimicrobials %>%
filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
pull(ab)
pre_commit_lst$AB_PHOSPHONICS <- antimicrobials %>%
filter(group %like% "phosphonic" | name %like% "fosfo") %>%
pull(ab)
pre_commit_lst$AB_PLEUROMUTILINS <- antimicrobials %>%
filter(name %like% "retapamulin|tiamulin|pleuromutilin") %>%
pull(ab)
pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
filter(group %like% "polymyxin") %>%
pull(ab)
pre_commit_lst$AB_QUINOLONES <- antimicrobials %>%
filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone" | name %like% "ozenoxacin") %>%
pull(ab)
pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
# see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
filter(ab %in% pre_commit_lst$AB_QUINOLONES & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|ozenoxacin|piromidic|pipemidic|rosoxacin") %>%
filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone") %>%
pull(ab)
pre_commit_lst$AB_RIFAMYCINS <- antimicrobials %>%
filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
pull(ab)
pre_commit_lst$AB_SPIROPYRIMIDINETRIONES <- antimicrobials %>%
filter(name %like% "zoliflodacin") %>%
pull(ab)
pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
filter(atc_group2 %like% "streptogramin" | name %like% "streptogramin|virginiamycin|ostreogrycin") %>%
filter(atc_group2 %like% "streptogramin") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
filter(group %like% "tetracycline") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>%
filter(group %like% "trimethoprim") %>%
pull(ab)
pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
filter(name %like% "(^|/)sulf[oai]") %>%
filter(group %like% "trimethoprim" & name %unlike% "trimethoprim") %>%
pull(ab)
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
pre_commit_lst$AB_BETALACTAMS <- sort(c(
pre_commit_lst$AB_PENICILLINS,
pre_commit_lst$AB_CEPHALOSPORINS,
pre_commit_lst$AB_CARBAPENEMS,
pre_commit_lst$AB_MONOBACTAMS))
pre_commit_lst$AB_BETALACTAMASE_INHIBITORS <- antimicrobials %>%
filter(atc_group2 %like% "Beta-lactamase inhibitors" | name %like% "bactam") %>%
pull(ab)
# for EUCAST:
pre_commit_lst$AB_BETALACTAMS <- sort(c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS, pre_commit_lst$AB_MONOBACTAMS))
pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
filter(ab %in% pre_commit_lst$AB_BETALACTAMS & name %like% "/" & name %unlike% "EDTA") %>%
filter(name %like% "/" & name %unlike% "EDTA" & ab %in% pre_commit_lst$AB_BETALACTAMS) %>%
pull(ab)
# this will be used for documentation:
pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
# Check that all AB_* groups with >= 4 members have a corresponding function
for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
if (length(pre_commit_lst[[grp]]) >= 4) {
fn_name <- tolower(gsub("^AB_", "", grp))
if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
" members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
call. = FALSE)
}
}
}
# Update the antimicrobials$group column
usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
prettify_group_name <- function(name) {
raw <- gsub("^AB_", "", name)
pretty <- tools::toTitleCase(gsub("_", " ", tolower(raw)))
pretty[pretty %like% " (except|with) "] <- ""
pretty <- gsub(" (1st|2nd|3rd|4th|5th|6th)", " (\\1 gen.)", pretty)
pretty <- gsub("([Bb])eta[-]?", "\\1eta-", pretty)
pretty <- gsub(" Inhibitor", " inhibitor", pretty)
pretty <- pretty[pretty != ""]
return(pretty)
}
group_map <- vector("list", length = nrow(antimicrobials))
names(group_map) <- antimicrobials$ab
for (group_name in pre_commit_lst$DEFINED_AB_GROUPS) {
ab_vector <- pre_commit_lst[[group_name]]
pretty_name <- prettify_group_name(group_name)
for (ab in ab_vector) {
ab_chr <- as.character(ab)
group_map[[ab_chr]] <- sort(unique(c(group_map[[ab_chr]], pretty_name)))
}
}
for (i in seq_along(group_map)) {
if (is.null(group_map[[i]])) {
group_map[[i]] <- "Other"
if (antimicrobials$group[i] %unlike% "other") {
usethis::ui_warn(paste0("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i])))
}
}
group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
}
# create priority list for ab_group()
pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
"Isoxazolylpenicillins",
"Ureidopenicillins",
"Oxazolidinones",
"Carbapenems",
"Cephalosporins (1st gen.)",
"Cephalosporins (2nd gen.)",
"Cephalosporins (3rd gen.)",
"Cephalosporins (4th gen.)",
"Cephalosporins (5th gen.)",
"Cephalosporins",
"Penicillins",
"Monobactams",
"Aminoglycosides",
"Lipoglycopeptides",
"Glycopeptides",
"Peptides",
"Lincosamides",
"Streptogramins",
"Macrolides",
"Nitrofurans",
"Phenicols",
"Phosphonics",
"Polymyxins",
"Fluoroquinolones",
"Quinolones",
"Rifamycins",
"Spiropyrimidinetriones",
"Trimethoprims",
"Sulfonamides",
"Tetracyclines",
"Ionophores",
"Antifungals",
"Antimycobacterials",
"Fusidanes",
"Beta-lactams",
"Beta-lactamase inhibitors",
"Pleuromutilins",
"Aminocoumarins",
"Other")
if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))
}
for (i in seq_along(group_map)) {
group_map[[i]] <- intersect(pre_commit_lst$ABX_PRIORITY_LIST, group_map[[i]])
}
antimicrobials$group <- unname(group_map)
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
@@ -769,33 +646,7 @@ files_changed <- function(paths = "^(R|data)/") {
# Update URLs -------------------------------------------------------------
if (files_changed()) {
usethis::ui_info("Checking URLs for redirects")
# Step 1: Get sources from tools (excluding man/)
sources <- tools:::url_db_from_package_sources(".")
sources <- sources[!grepl("^man/", sources$Parent), ]
# Step 2: Get URLs from .R files in R/
r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE)
# Function to extract URLs from a file
extract_urls_from_file <- function(file_path) {
lines <- readLines(file_path, warn = FALSE)
urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+")
urls <- unlist(urls)
if (length(urls) == 0) {
return(NULL)
}
# Remove trailing punctuation (e.g., .,), etc.)
urls <- stringr::str_replace(urls, "[\\.,;)]+$", "")
data.frame(
URL = urls,
Parent = gsub("^\\./", "", file_path),
stringsAsFactors = FALSE
)
}
r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file))
# Step 3: Combine the two sources
total <- rbind(sources, r_file_urls)
# Step 4: Check URLs and update
results <- urlchecker::url_check(db = total)
invisible(urlchecker::url_update(results = results))
invisible(urlchecker::url_update("."))
}
# Style pkg ---------------------------------------------------------------
@@ -828,6 +679,5 @@ if (files_changed("README.Rmd") ||
}
# Finished ----------------------------------------------------------------
rm(antimicrobials)
usethis::ui_done("All done")
suppressMessages(reset_AMR_locale())
data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R
+1 -76
View File
@@ -912,76 +912,7 @@ antimicrobials <- antimicrobials %>%
oral_ddd = NA_real_
))
# add Taniborbactam and Cefepime/taniborbactam
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(
antimicrobials |>
filter(ab == "FPE") |>
mutate(ab = as.character(ab)) |>
mutate(ab = "FTA",
name = "Cefepime/taniborbactam",
cid = NA_real_),
antimicrobials |>
filter(ab == "TBP") |>
mutate(ab = as.character(ab)) |>
mutate(ab = "TAN",
name = "Taniborbactam",
cid = 76902493,
abbreviations = list("VNRX-5133"))
)
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(
antimicrobials |>
filter(ab == "CTB") |>
mutate(ab = "CTA",
cid = NA_real_,
name = "Ceftibuten/avibactam") |>
select(1:4),
antimicrobials |>
filter(ab == "KAC") |>
mutate(ab = "KAS",
cid = NA_real_,
name = "Kasugamycin") |>
select(1:4),
antimicrobials |>
filter(ab == "PRI") |>
mutate(ab = "OST",
cid = NA_real_,
name = "Ostreogrycin") |>
select(1:4),
antimicrobials |>
filter(ab == "PRI") |>
mutate(ab = "THS",
cid = NA_real_,
name = "Thiostrepton") |>
select(1, 3),
antimicrobials |>
filter(ab == "CLA1") |>
mutate(ab = "XER",
cid = NA_real_,
name = "Xeruborbactam") |>
select(1:4),
antimicrobials |>
filter(ab == "BLM") |>
mutate(ab = "ZOR",
cid = NA_real_,
name = "Zorbamycin") |>
select(1:4),
)
antimicrobials <- antimicrobials |>
mutate(ab = as.character(ab)) |>
bind_rows(
antimicrobials |>
filter(ab == "NOV") |>
mutate(ab = "CLB",
cid = 54706138,
name = "Clorobiocin") |>
select(1:4),
)
# update ATC codes from WHOCC website -------------------------------------
@@ -1158,14 +1089,13 @@ for (i in 1:nrow(antimicrobials)) {
syn <- as.character(sort(unique(tolower(unname(unlist(antimicrobials[i, "synonyms", drop = TRUE]))))))
syn <- gsub("[^a-z]", "", syn)
syn <- gsub(" +", " ", syn)
pharm_terms <- "(antibiotic|pa?ediatric|injection|oral|inhale|otic|sulfate|sulphate|sodium|base|anhydrous|anhydrate|stearate|syrup|natrium|hydrate|x?hcl|gsalt|vet[.]?)"
pharm_terms <- "(pa?ediatric|injection|oral|inhale|otic|sulfate|sulphate|sodium|base|anhydrous|anhydrate|stearate|syrup|natrium|hydrate|x?hcl|gsalt|vet[.]?)"
syn <- gsub(paste0(" ", pharm_terms, "$"), "", syn)
syn <- gsub(paste0("^", pharm_terms, " "), "", syn)
syn <- trimws(syn)
syn <- gsub(" [a-z]{1,3}$", "", syn, perl = TRUE)
syn <- trimws(syn)
syn <- syn[syn != "" & syn %unlike% ":" & !syn %in% tolower(antimicrobials$name)]
syn <- syn[!syn %in% c("antibiotic", "antimicrobial")]
# remove synonyms that are names in the data set
syn <- syn[!sapply(syn, function(s) any(grepl(transform_syn(s), antimicrobials$name)))]
syn <- unique(syn)
@@ -1182,11 +1112,6 @@ for (i in 1:nrow(antimicrobials)) {
antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc))
}
}
antimicrobials$group <- unname(antimicrobials$group)
antimicrobials$atc <- unname(antimicrobials$atc)
antimicrobials$abbreviations <- unname(antimicrobials$abbreviations)
antimicrobials$synonyms <- unname(antimicrobials$synonyms)
antimicrobials$loinc <- unname(antimicrobials$loinc)
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R
+8 -10
View File
@@ -35,26 +35,24 @@ library(readr)
library(tidyr)
devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# (for ASIARS-Net update, also copy C:\WHONET\Codes to the data-raw/WHONET/ folder)
# BE SURE TO RUN data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R FIRST TO GET THE GROUPS!
# READ DATA ----
# files are retrieved from https://github.com/AClark-WHONET/AMRIE
github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
file_organisms <- file.path(github_repo, "Organisms.txt")
file_breakpoints <- file.path(github_repo, "Breakpoints.txt")
file_antibiotics <- file.path(github_repo, "Antibiotics.txt")
whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") |>
mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
whonet_breakpoints <- read_tsv(file_breakpoints, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
whonet_breakpoints <- read_tsv("data-raw/WHONET/Resources/Breakpoints.txt", na = c("", "NA", "-"),
show_col_types = FALSE, guess_max = Inf) |>
filter(GUIDELINES %in% c("CLSI", "EUCAST"))
whonet_antibiotics <- read_tsv(file_antibiotics, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
whonet_antibiotics <- read_tsv("data-raw/WHONET/Resources/Antibiotics.txt", na = c("", "NA", "-"), show_col_types = FALSE) |>
arrange(WHONET_ABX_CODE) |>
distinct(WHONET_ABX_CODE, .keep_all = TRUE)
data-raw/_reproduction_scripts/reproduction_of_microorganisms.R
+541 -1537
View File
File diff suppressed because it is too large Load Diff
data-raw/_reproduction_scripts/reproduction_of_microorganisms.groups.R
+9 -10
View File
@@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
# This data set is being referenced from in the clinical_breakpoints data set, and also by as.sir().
# This data set is being used in the clinical_breakpoints data set, and thus by as.sir().
# It prevents the breakpoints table from being extremely long for species that are part of a species group.
# Also used by eucast_rules() to expand group names.
@@ -36,6 +36,10 @@ library(readr)
library(tidyr)
devtools::load_all()
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Resources to the data-raw/WHONET/ folder
# BACTERIAL COMPLEXES
# find all bacterial complex in the NCBI Taxonomy Browser here:
# https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=6&lin=f&keep=1&srchmode=1&unlock
@@ -44,14 +48,9 @@ devtools::load_all()
# READ DATA ----
# files are retrieved from https://github.com/AClark-WHONET/AMRIE
github_repo <- "https://raw.github.com/AClark-WHONET/AMRIE/main/Interpretation%20Engine/Resources"
file_organisms <- file.path(github_repo, "Organisms.txt")
whonet_organisms <- read_tsv(file_organisms, na = c("", "NA", "-"), show_col_types = FALSE, guess_max = Inf) |>
whonet_organisms <- read_tsv("data-raw/WHONET/Resources/Organisms.txt", na = c("", "NA", "-"), show_col_types = FALSE) %>%
# remove old taxonomic names
filter(TAXONOMIC_STATUS == "C") |>
filter(TAXONOMIC_STATUS == "C") %>%
mutate(ORGANISM_CODE = toupper(WHONET_ORG_CODE))
whonet_organisms <- whonet_organisms %>%
@@ -88,7 +87,7 @@ microorganisms.groups <- whonet_organisms %>%
mo = ifelse(is.na(mo),
as.character(as.mo(ORGANISM, keep_synonyms = TRUE, minimum_matching_score = 0)),
mo)) %>%
# add our own CoNS and CoPS, WHONET does not strictly follow Becker et al. (2014, 2019, 2020)
# add our own CoNS and CoPS, WHONET does not strictly follow Becker et al (2014, 2019, 2020)
filter(mo_group != as.mo("CoNS")) %>%
bind_rows(tibble(mo_group = as.mo("CoNS"), mo = MO_CONS)) %>%
filter(mo_group != as.mo("CoPS")) %>%
@@ -154,7 +153,7 @@ microorganisms.groups <- whonet_organisms %>%
filter(mo_group != "B_YERSN_PSDT-C") %>%
bind_rows(tibble(mo_group = as.mo("B_YERSN_PSDT-C"),
mo = paste("Yersinia", c("pseudotuberculosis", "pestis", "similis", "wautersii")) %>% as.mo(keep_synonyms = TRUE))) %>%
# RGM are Rapidly-growing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
# RGM are Rapidly-grwoing Mycobacteria, see https://pubmed.ncbi.nlm.nih.gov/28084211/
filter(mo_group != "B_MYCBC_RGM") %>%
bind_rows(tibble(mo_group = as.mo("B_MYCBC_RGM"),
mo = paste("Mycobacterium", c( "abscessus abscessus", "abscessus bolletii", "abscessus massiliense", "agri", "aichiense", "algericum", "alvei", "anyangense", "arabiense", "aromaticivorans", "aubagnense", "aubagnense", "aurum", "austroafricanum", "bacteremicum", "boenickei", "bourgelatii", "brisbanense", "brumae", "canariasense", "celeriflavum", "chelonae", "chitae", "chlorophenolicum", "chubuense", "confluentis", "cosmeticum", "crocinum", "diernhoferi", "duvalii", "elephantis", "fallax", "flavescens", "fluoranthenivorans", "fortuitum", "franklinii", "frederiksbergense", "gadium", "gilvum", "goodii", "hassiacum", "hippocampi", "hodleri", "holsaticum", "houstonense", "immunogenum", "insubricum", "iranicum", "komossense", "litorale", "llatzerense", "madagascariense", "mageritense", "monacense", "moriokaense", "mucogenicum", "mucogenicum", "murale", "neoaurum", "neworleansense", "novocastrense", "obuense", "pallens", "parafortuitum", "peregrinum", "phlei", "phocaicum", "phocaicum", "porcinum", "poriferae", "psychrotolerans", "pyrenivorans", "rhodesiae", "rufum", "rutilum", "salmoniphilum", "sediminis", "senegalense", "septicum", "setense", "smegmatis", "sphagni", "thermoresistibile", "tokaiense", "vaccae", "vanbaalenii", "wolinskyi")) %>% as.mo(keep_synonyms = TRUE)))
data-raw/ab.md5
+1 -1
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@@ -1 +1 @@
11aade8a39bfdff02d01fb52b04eacdc
228840b3941753c4adee2b781d901590
data-raw/datasets/antimicrobials.dta
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data-raw/datasets/antimicrobials.feather
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data-raw/datasets/antimicrobials.txt
+408 -416
View File
@@ -1,506 +1,498 @@
"ab" "cid" "name" "group" "atc" "atc_group1" "atc_group2" "abbreviations" "synonyms" "oral_ddd" "oral_units" "iv_ddd" "iv_units" "loinc"
"AMA" 4649 "4-aminosalicylic acid" "Antimycobacterials" "J04AA01" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "aminacyl,aminopar,aminosalyl,aminox,apacil,deapasil,entepas,gabbropas,granupas,helipidyl,hellipidyl,nemasol,nippas,osacyl,pamacyl,pamisyl,paramisan,paramycin,parasal,parasalicil,parasalindon,pasade,pasalon,pasara,pascorbic,pasdium,pasem,paser,pasmed,pasnal,pasnodia,pasolac,passodico,pharmakon,propasa,rezipas,salvis,sanipirol,sanipriol,sodiopas,spectrum" 12 "g" "NA"
"ACM" 6450012 "Acetylmidecamycin" "Macrolides" "NA" "NA" "NA" "NA"
"ASP" 49787020 "Acetylspiramycin" "Macrolides" "NA" "NA" "espiramicin,espiramicina,foromacidin,provamycin,rovamicina,rovamycin,rovamycine,selectomycin,sequamycin,spiramycine,spiramycinum" "NA"
"ALS" 8954 "Aldesulfone sodium" "Other" "J04BA03" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "NA" "adesulfone,aldapsone,aldesulfone,aldesulphone,diamidin,diason,diasone,diasoneenterab,diazon,didimethanesulfinate,novotrone,sulfoxone" 0.33 "g" "NA"
"ACM" 6450012 "Acetylmidecamycin" "Macrolides/lincosamides" "NA" "NA" "NA" "NA"
"ASP" 49787020 "Acetylspiramycin" "Macrolides/lincosamides" "NA" "NA" "antibiotic,espiramicin,espiramicina,foromacidin,provamycin,rovamicina,rovamycin,rovamycine,selectomycin,sequamycin,spiramycine,spiramycinum" "NA"
"ALS" 8954 "Aldesulfone sodium" "Other antibacterials" "J04BA03" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "NA" "adesulfone,aldapsone,aldesulfone,aldesulphone,diamidin,diason,diasone,diasoneenterab,diazon,didimethanesulfinate,novotrone,sulfoxone" 0.33 "g" "NA"
"AMK" 37768 "Amikacin" "Aminoglycosides" "D06AX12,J01GB06,QD06AX12,QJ01GB06,QS01AA21,S01AA21" "Aminoglycoside antibacterials" "Other aminoglycosides" "ak,ami,amik,amikac,amk,an" "amikacillin,amikacina,amikacine,amikacinum,amikavet,amikin,amikozit,amukin,arikace,briclin,butirosins,kaminax,lukadin,mikavir,potentox,prestwick" 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,Phosphonics" "NA" "NA" "NA" "NA"
"AMO" 54260 "Amorolfine" "Antifungals" "D01AE16,QD01AE16" "Antifungals for topical use" "Other antifungals for topical use" "amor" "amorolfina,amorolfinum,bekiron,corbel,curanail,fenpropemorph,fenpropimorph,fenpropimorphe,forbel,funbas,loceryl,locetar,mildofix,mistral,morpholine,odenil,omicur,pekiron" "NA"
"AMX" 33613 "Amoxicillin" "Aminopenicillins,Penicillins,Beta-lactams" "J01CA04,QG51AA03,QJ01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "ac,amox,amoxic,amx" "acuotricina,alfamox,alfida,amitron,amoclen,amodex,amoksicillin,amolin,amopen,amopenixin,amophar,amoran,amoxi,amoxicaps,amoxicilina,amoxicilline,amoxicillinum,amoxidal,amoxiden,amoxil,amoxillat,amoxina,amoxine,amoxipen,amoxivet,amoxycillin,amoxycillinsalt,amoxyke,anemolin,aspenil,atoksilin,bristamox,cemoxin,ciblor,clamoxyl,damoxy,danoxillin,delacillin,demoksil,dispermox,efpenix,eupen,flemoxin,flemoxine,galenamox,gramidil,hiconcil,himinomax,histocillin,ibiamox,imacillin,izoltil,kentrocyllin,lamoxy,largopen,larotid,matasedrin,metifarma,moksilin,moxacin,moxal,moxaline,moxatag,neotetranase,novabritine,ospamox,pacetocin,pamocil,paradroxil,pasetocin,penamox,piramox,promoxil,quimiopen,remoxil,riotapen,robamox,sawacillin,siganopen,simplamox,sintopen,sumox,topramoxin,trifamox,trimox,unicillin,utimox,velamox,vetramox,wymox,zamocillin,zamocilline,zimox" 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" "Aminopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR02,QJ01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/c,amcl,aml,amocla,aug,xl" "amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,ancla,augmentan,augmentin,augmentine,auspilic,clamentin,clamobit,clavam,clavamox,clavinex,clavumox,coamoxiclav,curam,eumetinex,kesium,kmoxilin,spectramox,synulox,viaclav,xiclav" 1.5 "g" 3 "g" "NA"
"AXS" 465441 "Amoxicillin/sulbactam" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR02,QJ01CR02" "NA" "NA" 1.5 "g" 3 "g" "55614-2,55615-9,55616-7"
"AMB" 5280965 "Amphotericin B" "Antifungals" "A01AB04,A07AA07,G01AA03,J02AA01,QA01AB04,QA07AA07,QG01AA03,QJ02AA01" "Antimycotics for systemic use" "Antibiotics" "amf,amfb,amph,amphot" "abelcet,abelecet,ambil,ambisome,amphocin,amphomoronal,amphotec,amphotericin,amphotocerin,amphozone,funganiline,fungilin,fungisome,fungisone,fungizone,halizon,nystatine,nystatinum,terrastatin" 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" "NA" "amfo b high,amhl,ampho b high,amphotericin high" "NA" "NA"
"AMP" 6249 "Ampicillin" "Aminopenicillins,Penicillins,Beta-lactams" "J01CA01,QJ01CA01,QJ51CA01,QS01AA19,S01AA19" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "am,amp,amp100,amp200,ampi,ampici" "adobacillin,alpen,amblosin,amcap,amcill,amfipen,ampen,amperil,ampichel,ampicilina,ampicillina,ampicilline,ampicillinesalt,ampicillinsalt,ampicillinum,ampifarm,ampikel,ampimed,ampinova,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,austrapen,bayer,binotal,bonapicillin,britacil,cimex,citteral,copharcilin,cymbi,delcillin,deripen,divercillin,doktacillin,domicillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,omnipen,orbicilina,penbristol,penbritin,penbrock,penialmen,penicline,penimic,penizillin,pensyn,pentrex,pentrexl,pentrexyl,pentritin,ponecil,princillin,principen,racenacillin,redicilin,rosampline,roscillin,semicillin,servicillin,sumipanto,supen,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trafarbiot,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,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" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR01,QJ01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/s,ab,ampsul,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" "QP51BX02" "NA" "amprol,amprolio,amprovine,anticoccid,cocciprol,corid,mepyrium,picolinium,pyridinium,thiacoccid" "NA"
"ANI" 166548 "Anidulafungin" "Antifungals" "J02AX06,QJ02AX06" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid,anidul" "anidulafungina,anidulafungine,anidulafunginum,biafungin,ecalta,eraxis" 0.1 "g" "55343-8,57095-2,58420-1,77162-6"
"APL" 6602341 "Apalcillin" "Penicillins,Beta-lactams" "NA" "apalci" "apalcilina,apalcilline,apalcillinsalt,apalcillinum,lumota" "NA"
"AKF" "Amikacin/fosfomycin" "Aminoglycosides" "NA" "NA" "NA" "NA"
"AMO" 54260 "Amorolfine" "Antifungals/antimycotics" "D01AE16,QD01AE16" "Antifungals for topical use" "Other antifungals for topical use" "amor" "amorolfina,amorolfinum,bekiron,corbel,curanail,fenpropemorph,fenpropimorph,fenpropimorphe,forbel,funbas,loceryl,locetar,mildofix,mistral,morpholine,odenil,omicur,pekiron" "NA"
"AMX" 33613 "Amoxicillin" "Beta-lactams/penicillins" "J01CA04,QG51AA03,QJ01CA04" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "ac,amox,amoxic,amx" "acuotricina,alfamox,alfida,amitron,amoclen,amodex,amoksicillin,amolin,amopen,amopenixin,amophar,amoran,amoxi,amoxicaps,amoxicilina,amoxicilline,amoxicillinum,amoxidal,amoxiden,amoxil,amoxillat,amoxina,amoxine,amoxipen,amoxivet,amoxycillin,amoxycillinsalt,amoxyke,anemolin,aspenil,atoksilin,bristamox,cemoxin,ciblor,clamoxyl,damoxy,danoxillin,delacillin,demoksil,dispermox,efpenix,eupen,flemoxin,flemoxine,galenamox,gramidil,hiconcil,himinomax,histocillin,ibiamox,imacillin,izoltil,kentrocyllin,lamoxy,largopen,larotid,matasedrin,metifarma,moksilin,moxacin,moxal,moxaline,moxatag,neotetranase,novabritine,ospamox,pacetocin,pamocil,paradroxil,pasetocin,penamox,piramox,promoxil,quimiopen,remoxil,riotapen,robamox,sawacillin,siganopen,simplamox,sintopen,sumox,topramoxin,trifamox,trimox,unicillin,utimox,velamox,vetramox,wymox,zamocillin,zamocilline,zimox" 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,QJ01CR02" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/c,amcl,aml,amocla,aug,xl" "amocla,amoclan,amoclav,amoksiclav,amoxsiklav,amoxyclav,ancla,augmentan,augmentin,augmentine,auspilic,clamentin,clamobit,clavam,clavamox,clavinex,clavumox,coamoxiclav,curam,eumetinex,kesium,kmoxilin,spectramox,synulox,viaclav,xiclav" 1.5 "g" 3 "g" "NA"
"AXS" 465441 "Amoxicillin/sulbactam" "Beta-lactams/penicillins" "J01CR02,QJ01CR02" "NA" "NA" 1.5 "g" 3 "g" "55614-2,55615-9,55616-7"
"AMB" 5280965 "Amphotericin B" "Antifungals/antimycotics" "A01AB04,A07AA07,G01AA03,J02AA01,QA01AB04,QA07AA07,QG01AA03,QJ02AA01" "Antimycotics for systemic use" "Antibiotics" "amf,amfb,amph,amphot" "abelcet,abelecet,ambil,ambisome,amphocin,amphomoronal,amphotec,amphotericin,amphotocerin,amphozone,funganiline,fungilin,fungisome,fungisone,fungizone,halizon,nystatine,nystatinum,terrastatin" 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" "NA" "NA"
"AMP" 6249 "Ampicillin" "Beta-lactams/penicillins" "J01CA01,QJ01CA01,QJ51CA01,QS01AA19,S01AA19" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "am,amp,amp100,amp200,ampi,ampici" "adobacillin,alpen,amblosin,amcap,amcill,amfipen,ampen,amperil,ampichel,ampicilina,ampicillina,ampicilline,ampicillinesalt,ampicillinsalt,ampicillinum,ampifarm,ampikel,ampimed,ampinova,ampipenin,ampiscel,ampisyn,ampivax,ampivet,amplacilina,amplin,amplipenyl,amplisom,amplital,austrapen,bayer,binotal,bonapicillin,britacil,cimex,citteral,copharcilin,cymbi,delcillin,deripen,divercillin,doktacillin,domicillin,duphacillin,grampenil,guicitrina,guicitrine,lifeampil,marcillin,morepen,norobrittin,nuvapen,omnipen,orbicilina,penbristol,penbritin,penbrock,penialmen,penicline,penimic,penizillin,pensyn,pentrex,pentrexl,pentrexyl,pentritin,ponecil,princillin,principen,racenacillin,redicilin,rosampline,roscillin,semicillin,servicillin,sumipanto,supen,synpenin,texcillin,tokiocillin,tolomol,totacillin,totalciclina,totapen,trafarbiot,trifacilina,ukapen,ultrabion,ultrabron,vampen,viccillin,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,QJ01CR01" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "a/s,ab,ampsul,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" "NA" "amprol,amprolio,amprovine,anticoccid,cocciprol,corid,mepyrium,picolinium,pyridinium,thiacoccid" "NA"
"ANI" 166548 "Anidulafungin" "Antifungals/antimycotics" "J02AX06,QJ02AX06" "Antimycotics for systemic use" "Other antimycotics for systemic use" "anid,anidul" "anidulafungina,anidulafungine,anidulafunginum,biafungin,ecalta,eraxis" 0.1 "g" "55343-8,57095-2,58420-1,77162-6"
"APL" 6602341 "Apalcillin" "Beta-lactams/penicillins" "NA" "apalci" "apalcilina,apalcilline,apalcillinsalt,apalcillinum,lumota" "NA"
"APR" 3081545 "Apramycin" "Aminoglycosides" "QA07AA92,QJ01GB90,QJ51GB90" "apramy" "ambylan,apralan,apramicina,apramycine,apramycinum" "23659-6,73652-0,73653-8"
"ARB" 68682 "Arbekacin" "Aminoglycosides" "J01GB12,QJ01GB12" "arbeka" "arbekacina,arbekacine,arbekacinum,haberacin" 0.2 "g" "32373-3,53818-1,54173-0"
"APX" 71961 "Aspoxicillin" "Penicillins,Beta-lactams" "J01CA19,QJ01CA19" "apoxic,aspoxi" "aspoxicilina,aspoxicillan,aspoxicilline,aspoxicillinum,doyle" 4 "g" "NA"
"APX" 71961 "Aspoxicillin" "Beta-lactams/penicillins" "J01CA19,QJ01CA19" "apoxic,aspoxi" "aspoxicilina,aspoxicillan,aspoxicilline,aspoxicillinum,doyle" 4 "g" "NA"
"AST" 5284517 "Astromicin" "Aminoglycosides" "NA" "astrom" "abbott,astromicina,astromicine,astromicinum,fortimicin,istamycin,istamycins" "NA"
"AVB" 9835049 "Avibactam" "Beta-lactamase inhibitors" "NA" "NA" "avibactamfreeacid" "NA"
"AVI" 71674 "Avilamycin" "Other" "QA07AA95" "avilam" "avilamycina,avilamycine,avilamycinum,inteprity,kavault,surmax" "35754-1,35755-8,35756-6,55619-1"
"AVO" 16131159 "Avoparcin" "Glycopeptides,Peptides" "NA" "NA" "firvanq,tagocid,targocid,targosid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanina,teicoplanine,teicoplaninum,teikoplanin,ticocin" "NA"
"AZD" 15574941 "Azidocillin" "Penicillins,Beta-lactams" "J01CE04,QJ01CE04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "azidocilina,azidocillina,azidocilline,azidocillinum" 1.5 "g" "NA"
"AZM" 447043 "Azithromycin" "Macrolides" "J01FA10,QJ01FA10,QS01AA26,S01AA26" "Macrolides, lincosamides and streptogramins" "Macrolides" "az,azi,azit,azithr,azm" "aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,tobil,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zifin,zithrax,zithromac,zithromax,zitrim,zitromax,zitrotek,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" "J01RA07,QJ01RA07" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"AZL" 6479523 "Azlocillin" "Ureidopenicillins,Penicillins,Beta-lactams" "J01CA09,QJ01CA09" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "az,azl,azlo,azloci" "azlin,azlocilina,azlocilline,azlocillinsalt,azlocillinum,securopen" 12 "g" "16422-8,18867-2,3368-8,39-8,40-6,41-4,41661-0,42-2"
"ATM" 5742832 "Aztreonam" "Monobactams,Beta-lactams" "J01DF01,QJ01DF01" "Other beta-lactam antibacterials" "Monobactams" "at,atm,azm,azt,azt1,aztr,aztreo" "azactam,azetreonam,azonam,azthreonam,aztreon,aztreonamum,cayston,dynabiotic,nebactam,primbactam,squibb" 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" "Monobactams,Beta-lactams,Beta-lactamase inhibitors" "J01DF51,QJ01DF51" "NA" "NA" "NA"
"ANC" "Aztreonam/nacubactam" "Monobactams,Beta-lactams,Beta-lactamase inhibitors" "J01DF51,QJ01DF51" "NA" "NA" "NA"
"BAM" 441397 "Bacampicillin" "Penicillins,Beta-lactams" "J01CA06,QJ01CA06" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "bacamp" "alphacilina,alphacillin,ambacamp,ambaxin,bacacil,bacampicilina,bacampicilline,bacampicillinum,bacampicine,berocillin,centurina,devonium,diancina,inacilin,maxifen,penglobe,pivatil,pondocil,pondocillin,pondocillina,sanguicillin,spectrobid,velbacil" 1.2 "g" "18869-8,47-1,48-9,49-7,50-5,55620-9"
"BAC" 78358334 "Bacitracin" "Peptides" "D06AX05,J01XX10,QA07AA93,QD06AX05,QJ01XX10,QR02AB04,QS01AA32,R02AB04,S01AA32" "baci,bacitr" "albac,altracin,ayfivin,baciferm,baciguent,baciim,baciliquin,bacilliquin,baciquent,bacitracina,bacitracine,bacitracinum,fortracin,mycitracin,parentracin,penitracin,septa,topitracin,topitrasin,tropitracin,zutracin" "10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
"BDQ" 5388906 "Bedaquiline" "Other" "J04AK05,QJ04AK05" "NA" "NA" 86 "mg" "80637-2,88703-4,88704-2,94274-8,96107-8"
"AVB" 9835049 "Avibactam" "Beta-lactams/penicillins" "NA" "NA" "avibactamfreeacid" "NA"
"AVI" 71674 "Avilamycin" "Other antibacterials" "QA07AA95" "avilam" "avilamycina,avilamycine,avilamycinum,inteprity,kavault,surmax" "35754-1,35755-8,35756-6,55619-1"
"AVO" 16131159 "Avoparcin" "Glycopeptides" "NA" "NA" "firvanq,tagocid,targocid,targosid,tecoplanina,tecoplanine,tecoplaninum,teichomycin,teicoplanina,teicoplanine,teicoplaninum,teikoplanin,ticocin" "NA"
"AZD" 15574941 "Azidocillin" "Beta-lactams/penicillins" "J01CE04,QJ01CE04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "azidocilina,azidocillina,azidocilline,azidocillinum" 1.5 "g" "NA"
"AZM" 447043 "Azithromycin" "Macrolides/lincosamides" "J01FA10,QJ01FA10,QS01AA26,S01AA26" "Macrolides, lincosamides and streptogramins" "Macrolides" "az,azi,azit,azithr,azm" "aritromicina,aruzilina,azasite,azenil,azifast,azigram,azimakrol,azithramycine,azithrocin,azithromycine,azithromycinum,azitrocin,azitromax,azitromicina,azitromicine,azitromin,aziwin,aziwok,aztrin,azyter,hemomycin,macrozit,misultina,mixoterin,setron,sumamed,tobil,toraseptol,tromix,trozocina,trulimax,xithrone,zentavion,zifin,zithrax,zithromac,zithromax,zitrim,zitromax,zitrotek,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,QJ01RA07" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"AZL" 6479523 "Azlocillin" "Beta-lactams/penicillins" "J01CA09,QJ01CA09" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "az,azl,azlo,azloci" "azlin,azlocilina,azlocilline,azlocillinsalt,azlocillinum,securopen" 12 "g" "16422-8,18867-2,3368-8,39-8,40-6,41-4,41661-0,42-2"
"ATM" 5742832 "Aztreonam" "Monobactams" "J01DF01,QJ01DF01" "Other beta-lactam antibacterials" "Monobactams" "at,atm,azm,azt,azt1,aztr,aztreo" "azactam,azetreonam,azonam,azthreonam,aztreon,aztreonamum,cayston,dynabiotic,nebactam,primbactam,squibb" 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" "Monobactams" "J01DF51,QJ01DF51" "NA" "NA" "NA"
"ANC" "Aztreonam/nacubactam" "Monobactams" "J01DF51,QJ01DF51" "NA" "NA" "NA"
"BAM" 441397 "Bacampicillin" "Beta-lactams/penicillins" "J01CA06,QJ01CA06" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "bacamp" "alphacilina,alphacillin,ambacamp,ambaxin,bacacil,bacampicilina,bacampicilline,bacampicillinum,bacampicine,berocillin,centurina,devonium,diancina,inacilin,maxifen,penglobe,pivatil,pondocil,pondocillin,pondocillina,sanguicillin,spectrobid,velbacil" 1.2 "g" "18869-8,47-1,48-9,49-7,50-5,55620-9"
"BAC" 78358334 "Bacitracin" "Other antibacterials" "D06AX05,J01XX10,QA07AA93,QD06AX05,QJ01XX10,QR02AB04,QS01AA32,R02AB04,S01AA32" "baci,bacitr" "albac,altracin,ayfivin,baciferm,baciguent,baciim,baciliquin,bacilliquin,baciquent,bacitracina,bacitracine,bacitracinum,fortracin,mycitracin,parentracin,penitracin,septa,topitracin,topitrasin,tropitracin,zutracin" "10868-8,16428-5,18870-6,6827-0,6983-1,87603-7"
"BDQ" 5388906 "Bedaquiline" "Other antibacterials" "J04AK05,QJ04AK05" "NA" "NA" 86 "mg" "80637-2,88703-4,88704-2,94274-8,96107-8"
"BEK" 439318 "Bekanamycin" "Aminoglycosides" "J01GB13,QJ01GB13" "NA" "aminodeoxykanamycin,becanamicina,bekanamicina,bekanamycine,bekanamycinum" 0.6 "g" "NA"
"BNB" "Benzathine benzylpenicillin" "Penicillins,Beta-lactams" "J01CE08,QJ01CE08" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "NA" 3.6 "g" "NA"
"BNP" 64725 "Benzathine phenoxymethylpenicillin" "Penicillins,Beta-lactams" "J01CE10,QJ01CE10" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "bicillin,biphecillin" 2 "g" "NA"
"PEN" 5904 "Benzylpenicillin" "Penicillins,Beta-lactams" "J01CE01,QJ01CE01,QJ51CE01,QS01AA14,S01AA14" "Combinations of antibacterials" "Combinations of antibacterials" "bepe,pen,peni,peni g,penic8,penica,penici,penicillin,penicillin g,penora,pg" "bencilpenicilina,benzopenicillin,benzylpenicilline,benzylpenicillinum,capicillin,cillora,cilloral,cilopen,cintrisul,cosmopen,cristapen,crystapen,dropcillin,eskacillin,falapen,forpen,galofak,gelacillin,hipercilina,hyasorb,hylenta,lemopen,liquacillin,liquapen,monocillin,monopen,mycofarm,novocillin,penalev,penicillinum,penilaryn,penisem,pentid,pentids,pfizerpen,pharmacillin,pradupen,scotcil,sugracillin,sugracillinsalt,tabilin,ursopen,veticillin" 3.6 "g" "NA"
"PEN-S" "Benzylpenicillin screening test" "Penicillins,Beta-lactams" "NA" "pen screen" "NA" "NA"
"BES" 10178705 "Besifloxacin" "Fluoroquinolones,Quinolones" "QS01AE08,S01AE08" "besifl" "besivance" "73606-6,73628-0,73651-2"
"BNB" "Benzathine benzylpenicillin" "Beta-lactams/penicillins" "J01CE08,QJ01CE08" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "NA" 3.6 "g" "NA"
"BNP" 64725 "Benzathine phenoxymethylpenicillin" "Beta-lactams/penicillins" "J01CE10,QJ01CE10" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "bicillin,biphecillin" 2 "g" "NA"
"PEN" 5904 "Benzylpenicillin" "Beta-lactams/penicillins" "J01CE01,QJ01CE01,QJ51CE01,QS01AA14,S01AA14" "Combinations of antibacterials" "Combinations of antibacterials" "bepe,pen,peni,peni g,penic8,penica,penici,penicillin,penicillin g,penora,pg" "bencilpenicilina,benzopenicillin,benzylpenicilline,benzylpenicillinum,capicillin,cillora,cilloral,cilopen,cintrisul,cosmopen,cristapen,crystapen,dropcillin,eskacillin,falapen,forpen,galofak,gelacillin,hipercilina,hyasorb,hylenta,lemopen,liquacillin,liquapen,monocillin,monopen,mycofarm,novocillin,penalev,penicillinum,penilaryn,penisem,pentid,pentids,pfizerpen,pharmacillin,pradupen,scotcil,sugracillin,sugracillinsalt,tabilin,ursopen,veticillin" 3.6 "g" "NA"
"PEN-S" "Benzylpenicillin screening test" "Beta-lactams/penicillins" "NA" "pen screen" "NA" "NA"
"BES" 10178705 "Besifloxacin" "Fluoroquinolones" "QS01AE08,S01AE08" "besifl" "besivance" "73606-6,73628-0,73651-2"
"BLA-S" "Beta-lactamase screening test" "Other" "NA" "beta-lactamase,betalactamase,bl screen,blt screen" "NA" "NA"
"BIA" 71339 "Biapenem" "Carbapenems,Beta-lactams" "J01DH05,QJ01DH05" "biapen" "biapenern,omegacin" 1.2 "g" "41665-1,41666-9,41667-7,41728-7"
"BCZ" 65807 "Bicyclomycin" "Other" "NA" "bicozamycin" "aizumycin,bacfeed,bacteron,bicozamicina,bicozamycin,bicozamycine,bicozamycinum" "NA"
"BLM" 5360373 "Bleomycin" "Glycopeptides,Peptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA"
"BIA" 71339 "Biapenem" "Carbapenems" "J01DH05,QJ01DH05" "biapen" "biapenern,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" "NA"
"BLM" 5360373 "Bleomycin" "Glycopeptides" "L01DC01,QL01DC01" "NA" "blenamax,blenoxane,bleocin,bleomicin,bleomicina,bleomycine,bleomycins,bleomycinum,blexane,nbleomycinamide" "NA"
"BDP" 68760 "Brodimoprim" "Trimethoprims" "J01EA02,QJ01EA02" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "NA" "brodimoprima,brodimoprime,brodimoprimum,bromdimoprim,hyprim,unitrim" 0.2 "g" "NA"
"BUT" 47472 "Butoconazole" "Antifungals" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA"
"BUT" 47472 "Butoconazole" "Antifungals/antimycotics" "G01AF15,QG01AF15" "NA" "butaconazole,butoconazol,butoconazolum,gynofort" "NA"
"CDZ" 44242317 "Cadazolid" "Oxazolidinones" "NA" "NA" "NA" "NA"
"CLA" "Calcium aminosalicylate" "Antimycobacterials" "J04AA03,QJ04AA03" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "NA" 15 "g" "NA"
"CAP" 135565060 "Capreomycin" "Antimycobacterials" "J04AB30,QJ04AB30" "Drugs for treatment of tuberculosis" "Antibiotics" "capr,capreo" "NA" 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" "Penicillins,Beta-lactams" "J01CA03,QJ01CA03" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "bar,carb,carben,cb" "anabactyl,carbecin,carbenicilina,carbenicillina,carbenicilline,carbenicillinum,dicarbenicillin,dipenicillin,fugacillin,geopen,gripenin,hyoper,microcillin,piopen,pyocianil,pyoclox,pyopan,pyopen,pyopene" 12 "g" "18873-0,3434-8,41668-5,59-6,60-4,61-2,62-0"
"CRN" 93184 "Carindacillin" "Penicillins,Beta-lactams" "J01CA05,QJ01CA05" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "carindacilina,carindacilline,carindacillinsalt,carindacillinum,geocillin,indanylcarbinicillin,urobac" 4 "g" "NA"
"CAR" 6540466 "Carumonam" "Monobactams,Beta-lactams" "J01DF02,QJ01DF02" "NA" "carumonamum" 2 "g" "51694-8"
"CAS" 2826718 "Caspofungin" "Antifungals" "J02AX04,QJ02AX04" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp,caspof" "cancidas,caspofungina" 50 "mg" "32378-2,54175-5,54176-3,54185-4,58419-3"
"CAC" 91562 "Cefacetrile" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB10,QJ01DB10,QJ51DB10" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephac" "cefacetril,cefacetrilo,cefacetrilum,celospor,cephacetrile,vetrimast" "55624-1,55625-8,55626-6,55627-4"
"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC04,QJ01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac" "alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,lopac,panacef,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.),Cephalosporins,Beta-lactams" "J01DB05,QJ01DB05" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefadr,cfdx,cfr,fad" "bidocel,cefadrops,cefadroxilo,cefadroxilum,cefradroxil,cefzil,cephadroxil,duracef,duricef,kefroxil,sumacef,ultracef" 2 "g" "16565-4,18875-5,55628-2,63-8,64-6,65-3,66-1"
"LEX" 27447 "Cefalexin" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB01,QJ01DB01,QJ51DB01" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cepale,cflx" "adcadina,alcephin,alsporin,ambal,amplex,aristosporin,azabort,bactopenor,beliam,biocef,carnosporin,cefablan,cefacet,cefadal,cefadin,cefadina,cefalekey,cefaleksin,cefalessina,cefalexgobens,cefalexina,cefalexine,cefalexinum,cefalin,cefalival,cefaloto,cefanex,cefaseptin,cefax,ceffanex,cefibacter,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexine,cephalexinum,cephalobene,cephanasten,cephaxin,cephin,cepol,ceporex,ceporexin,ceporexine,cerexin,cerexins,check,cophalexin,domucef,doriman,durantel,efemida,erocetin,factagard,felexin,fexin,ibilex,ibrexin,inphalex,karilexina,kefalospes,keflet,keflex,kefolan,keforal,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,loisine,lonflex,lopilexin,losporal,madlexin,maksipor,mamalexin,mamlexin,medolexin,medoxine,neokef,neolexina,noveol,novolexin,nufex,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine,pectril,prindex,pyassan,rilexine,roceph,rogevil,sanaxin,sartosona,sencephalin,sepexin,servicef,servispor,sialexin,sinthecillin,sintolexyn,sporicef,sporidex,syncl,syncle,synecl,taicelexin,tepaxin,theratrex,tokiolexin,uphalexin,viosporine,voxxim,winlex,zabytrex,zozarine" 2 "g" "NA"
"RID" 5773 "Cefaloridine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB02,QJ01DB02" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa,ceplor" "aliporina,ampligram,cefaloridin,cefaloridina,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,sasperin,sefacin,verolgin,vioviantine" 3 "g" "NA"
"CEP" 6024 "Cefalotin" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB03,QJ01DB03" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephal,cfal,cflt" "averon,cefalothin,cefalothine,cefalothinsalt,cefalotina,cefalotine,cefalotinsalt,cefalotinum,cemastin,cephalothin,cephalothinsalt,cephalothinum,cephalotin,cephalotinsalt,ceporacin,cepovenin,coaxin,keflin,lospoven,microtin,seffin,synclotin,toricelocin" 4 "g" "NA"
"MAN" 456255 "Cefamandole" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC03,QJ01DC03" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefama,cfam,cfmn" "cefadole,cefamandol,cefamandolum,cephadole,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.),Cephalosporins,Beta-lactams" "J01DB08,QG51AA05,QJ01DB08,QJ51DB08" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephap" "ambrocef,brisfirina,brisporin,bristocef,cefadyl,cefalak,cefaloject,cefapirina,cefapirine,cefapirinsalt,cefapirinum,cefaprin,cefatrex,cefatrexyl,cephapirin,cephapirine,cephapirinsalt,cephatrexil,cephatrexyl,metricure" 4 "g" "NA"
"CTZ" 6410758 "Cefatrizine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB07,QJ01DB07" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefatr" "bricef,cefathiamidine,cefatrix,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,orotric,seapuron,trizina" 1 "g" "18877-1,55639-9,71-1,72-9,73-7,74-5"
"CZD" 71736 "Cefazedone" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB06,QJ01DB06" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefaze" "cefazedon,cefazedona,cefazedonesalt,cefazedonum,refosporen,refosporene,refosporin,refosporinsalt" 3 "g" "NA"
"CZO" 33255 "Cefazolin" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB04,QJ01DB04,QJ51DB04" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefazo,cfz,cfzl,cz,czol,faz,kz" "ancef,atirin,biazolina,cefabiozim,cefacidal,cefalomicina,cefamedin,cefamezin,cefazil,cefazina,cefazolina,cefazoline,cefazolinsalt,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,gramaxin,kefzol,lampocef,liviclina,neofazol,oprea,recef,totacef,zolicef,zolisint" 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" "J01DC13,QJ01DC13" "cefbup" "cefbuperazona,cefbuperazonesalt,cefbuperazonum,cefbuperzaone,cerbuperazone,keiperazon,tomiporan" 2 "g" "NA"
"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD17,QJ01DD17" "cefcap" "flomox" 0.45 "g" "100044-7,76143-7"
"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "NA" "cefcamate,flumax" "NA"
"CDR" 6915944 "Cefdinir" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD15,QJ01DD15" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cd,cdn,cdr,cefdin,cfd,din" "cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef" 0.6 "g" "23636-4,23637-2,35757-4,35758-2"
"DIT" 9870843 "Cefditoren" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD16,QJ01DD16" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn,cefdit" "cefditoreno,spectracef" 0.4 "g" "35759-0,35760-8,35761-6,35762-4"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "NA" "cefditorin,meiact,pivaloyloxymethyl" "NA"
"FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE01,QJ01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cefep4,cefepi,cfep,cfpi,cpe,cpm,fep,pm,xpm" "anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime" 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" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE51,QJ01DE51" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE51,QJ01DE51" "cefcla,cicl,xpml" "NA" "NA"
"FPE" 23653540 "Cefepime/enmetazobactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FNC" "Cefepime/nacubactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FTA" "Cefepime/taniborbactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FPZ" "Cefepime/zidebactam" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"CAT" 5487888 "Cefetamet" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD10,QJ01DD10" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefeta,cefmtm" "cefetametum,deacetoxycefotaxime,epocelin" 1 "g" "32377-4,35764-0,35765-7,55640-7"
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "NA" "cefetametpivoxil,cefyl,globocef" "NA"
"CCL" 71719688 "Cefetecol" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "NA" "cefcatacol" "NA" "NA"
"CZL" 193956 "Cefetrizole" "Cephalosporins,Beta-lactams" "NA" "NA" "cefetrizolum" "NA"
"FDC" 77843966 "Cefiderocol" "Cephalosporins,Beta-lactams" "J01DI04,QJ01DI04" "NA" "fetcroja" 6 "g" "95767-0,99280-0,99503-5"
"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD08,QJ01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefixi,cfe,cfix,cfxm,dcfm,fix,ix" "cefixim,cefixima,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oraken,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" "J01DD58,QJ01DD58" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD05,QJ01DD05,QS01AA31,QS02AA18,S01AA31,S02AA18" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefmen" "bestron,cefmenoxima,cefmenoximum,tacef" 2 "g" "32375-8,54174-8,54203-5,55641-5"
"CMZ" 42008 "Cefmetazole" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC09,QJ01DC09" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefmet" "cefmetazol,cefmetazolo,cefmetazolum,cefmetazon,metafar,zefazone" 4 "g" "11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
"CNX" 71141 "Cefminox" "Other" "J01DC12,QJ01DC12" "cefmin" "alteporina,cefminoxhydrate,cefminoxum,meicelin,tencef" 4 "g" "54908-9"
"DIZ" 5361871 "Cefodizime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD09,QJ01DD09" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "NA" "cefodizima,cefodizimum,cefodizme,diezime,kenicef,modivid,neucef,timecef" 2 "g" "18882-1,6988-0,91-9,92-7,93-5,94-3"
"CID" 43594 "Cefonicid" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC06,QJ01DC06" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoni" "cefonicide,cefonicido,cefonicidsalt,cefonicidum,monocef,monocid" 1 "g" "18883-9,25237-9,3444-7,55642-3,95-0,96-8,97-6,98-4"
"CFP" 44187 "Cefoperazone" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD12,QJ01DD12,QJ51DD12" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefope,cfp,cfpz,cp,cpz,fop,per" "bioperazone,cefob,cefobid,cefobis,cefoneg,cefoper,cefoperazin,cefoperazine,cefoperazon,cefoperazona,cefoperazonesalt,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef,tomabef" 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.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DD62,QJ01DD62" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "fopsul" "NA" 4 "g" "35768-1,54166-4,54167-2,54168-0"
"CND" 43507 "Ceforanide" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC11,QJ01DC11" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefora" "ceforanido,ceforanidum,precef" 4 "g" "103-2,104-0,105-7,106-5,18885-4,55643-1"
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "NA" "cefose" "winsef" "NA"
"CTX" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD01,QJ01DD01" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefo32,cefota,cfot,cft,cftx,ct,ctx,fot,fot1,tax,taxmen,taxnme,xct" "anticefotaxime,cefotax,cefotaxim,cefotaxima,cefotaximesalt,cefotaximsalt,cefotaximum,cephotaxim,cephotaxime,claforan,kefotex,omnatax,pretor,ralopar,tolycar,tolycor,zariviz" 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"
"CTX-S" "Cefotaxime screening test" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "ctx screen" "NA" "NA"
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD51,QJ01DD51" "cxcl,taxcla,xctl" "NA" "NA"
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DD51,QJ01DD51" "NA" "NA" "54191-2,54192-0,54193-8,55644-9"
"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC05,QJ01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefote,cftt,cn,cte,ctn,ctt,tans" "apacef,apatef,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.),Cephalosporins,Beta-lactams" "J01DC07,QJ01DC07" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoti" "aspil,cefotiamum,ceradon,halospor,pansporin,pansporine,spizef" 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.),Cephalosporins,Beta-lactams" "NA" "NA" "taketiam,texodil" "55737-1,55738-9,55739-7,55740-5"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "QJ01DD91" "cefove" "cefovecinsalt,convenia" "76147-8,87792-8"
"FOX" 441199 "Cefoxitin" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC01,QJ01DC01" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoxi,cfox,cfx,cfxt,cx,fox,fx" "betacef,cefoxil,cefoxitina,cefoxitine,cefoxitinsalt,cefoxitinum,cefoxotin,cenomycin,farmoxin,mefoxin,mefoxithin,mefoxitin,merxin,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"
"FOX-S" "Cefoxitin screening test" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "NA" "cfsc,fox1" "NA" "NA"
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE03,QJ01DE03" "cefozo" "firstcin,imidazo" 4 "g" "100045-4,53820-7"
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "cefpim" "ajicef,cefpimizol,cefpimizolesalt,cefpimizolum,renilan" "NA"
"CPM" 636405 "Cefpiramide" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD11,QJ01DD11" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefpam" "cefpiramida,cefpiramidesalt,cefpiramido,cefpiramidum,sepatren,suncefal" 2 "g" "NA"
"CPO" 5479539 "Cefpirome" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "J01DE02,QJ01DE02" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cefpom,cfpr" "broact,cefir,cefpiroma,cefpiromum,cefrom,keiten,romecef" 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.),Cephalosporins,Beta-lactams" "J01DD13,QJ01DD13" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefpod,cfpd,cfpo,cpd,pod,pod4,px" "cefpodoxima,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.),Cephalosporins,Beta-lactams" "NA" "NA" "banan,cefodox,cefoprox,cefpoderm,cefpodoximproxetil,cepodem,doxef,orelox,otreon,podomexef,simplicef,vantin" "NA"
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD64,QJ01DD64" "cecl,podcla" "NA" 0.4 "g" "NA"
"CPR" 5281006 "Cefprozil" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC10,QJ01DC10" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefpro,cpr,cpz,fp" "arzimol,brisoral,cefprozilo,cefprozilum,cronocef,procef,serozil" 1 "g" "123-0,124-8,125-5,126-3,18891-2,6994-8"
"CEQ" 5464355 "Cefquinome" "Cephalosporins (4th gen.),Cephalosporins,Beta-lactams" "QG51AA07,QJ01DE90,QJ51DE90" "cefqui" "cefquinoma,cefquinomum,cobactan,quinolinium" "100046-2,76150-2"
"CRD" 5284529 "Cefroxadine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB11,QJ01DB11" "Other beta-lactam antibacterials" "First-generation cephalosporins" "ceftix" "cefroxadin,cefroxadino,cefroxadinum,oraspor" 2.1 "g" "NA"
"CFS" 656575 "Cefsulodin" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD03,QJ01DD03" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefsul,cfsl,cfsu" "cefomonil,cefonomil,cefsulodine,cefsulodinhydrate,cefsulodino,cefsulodinum,pseudocef,pseudomonil,pyocefal,sulcephalosporin,takesulin,tilmapor,ulfaret" 4 "g" "127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
"CSU" 68718 "Cefsumide" "Cephalosporins,Beta-lactams" "NA" "NA" "cefsulmid,cefsumido,cefsumidum" "NA"
"CPT" 56841980 "Ceftaroline" "Cephalosporins (5th gen.),Cephalosporins,Beta-lactams" "J01DI02,QJ01DI02" "ceftar,cfro" "ceftaroine,teflaro,zinforo" "73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" "73604-1,73626-4,73649-6"
"CAZ" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD02,QJ01DD02" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "caz,cef,cefta,ceftaz,cfta,cftz,taz,tz,xtz" "ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime" 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.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DD52,QJ01DD52" "cfav" "avycaz,zavicefta" 6 "g" "101483-6,73603-3,73625-6,73648-8,87734-0"
"CCV" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD52,QJ01DD52" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "czcl,tazcla,xtzl" "NA" 6 "g" "NA"
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD18,QJ01DD18" "cefter" "cefterame,cefteramum,ceftetrame" 0.4 "g" "100047-0,76144-5"
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "NA" "NA" "cefterampivoxil,tomiron" "NA"
"CTL" 65755 "Ceftezole" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "J01DB12,QJ01DB12" "Other beta-lactam antibacterials" "First-generation cephalosporins" "ceftez" "alomen,ceftezol,ceftezolesalt,ceftezolo,ceftezolum,celoslin,demethylcefazolin,falomesin" 3 "g" "NA"
"CTB" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD14,QJ01DD14" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cb,ceftib,cfbu,ctb,tib" "cedax,ceftem,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,ceprifran,isocef,keimax,seftem" 0.4 "g" "35777-2,35778-0,35779-8,6996-3"
"CTA" "Ceftibuten/avibactam" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" "NA"
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "QJ01DD90,QJ51DD90" "ceftif" "ceftiofurum,excenel,naxcel" "23709-9,35780-6,35781-4,55652-2"
"CZX" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD07,QJ01DD07" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "ceftiz,cfzx,ctz,cz,czx,tiz,zox" "cefizox,ceftix,ceftizoxima,ceftizoximesalt,ceftizoximum,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.),Cephalosporins,Beta-lactams" "NA" "NA" "NA" "NA"
"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.),Cephalosporins,Beta-lactams" "NA" "ceftob" "NA" "43269-0,43270-8,43271-6,43272-4,85052-9"
"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.),Cephalosporins,Beta-lactams" "J01DI01,QJ01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "NA" "zevtera" 1.5 "g" "NA"
"CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.),Cephalosporins,Beta-lactams,Beta-lactamase inhibitors" "J01DI54,QJ01DI54" "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.),Cephalosporins,Beta-lactams" "J01DD04,QJ01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "axo,cax,ceftri,cftr,cro,ctr,frx,trimen,trinme,tx" "biotrakson,ceftriaxon,ceftriaxona,ceftriaxonum,ceftriazone,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.),Cephalosporins,Beta-lactams" "J01DD63,QJ01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "NA" "NA" 2 "g" "NA"
"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC02,QJ01DC02,QJ51DC02,QS01AA27,S01AA27" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefaxe,cefrox,cefuro,cfrx,cfur,cfx,crm,cxm,fur,rox,xm" "anaptivan,biociclin,biofuroksym,bioxima,cefofix,cefumax,cefurex,cefuril,cefurox,cefuroxim,cefuroxima,cefuroximesalt,cefuroximine,cefuroximo,cefuroximum,cephuroxime,cetroxil,colifossim,curoxim,curoxima,curoxime,froxal,furoxil,kefurox,kesint,ketocef,lifurox,medoxim,sharox,spectrazolr,ultroxim,zinacef,zinnat" 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.),Cephalosporins,Beta-lactams" "NA" "cfax" "bioracef,ceftin,cefurax,cefuroximaxetil,celocid,cepazine,cethixim,cetoxil,coliofossim,curocef,elobact,kalcef,maxitil,medoxm,nivador,novador,novocef,oraxim,zinat,zoref" "NA"
"CFM2" "Cefuroxime/metronidazole" "Other" "J01DC52,QJ01DC52" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" 0.5 "g" "NA"
"ZON" 6336505 "Cefuzonam" "Other" "NA" "cefuzo" "cefuzoname,cefuzonamum,cefzoname,cosmosin" "NA"
"CED" 38103 "Cephradine" "Cephalosporins (1st gen.),Cephalosporins,Beta-lactams" "NA" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephra,cfra,cfrd" "anspor,cefradin,cefradina,cefradine,cefradinum,cekodin,cephradin,ecosporina,eskacef,infexin,megacef,sefril,velocef,velosef" "168-5,169-3,170-1,171-9,18902-7,55646-4"
"CRB" 20824 "Carbenicillin" "Beta-lactams/penicillins" "J01CA03,QJ01CA03" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "bar,carb,carben,cb" "anabactyl,carbecin,carbenicilina,carbenicillina,carbenicilline,carbenicillinum,dicarbenicillin,dipenicillin,fugacillin,geopen,gripenin,hyoper,microcillin,piopen,pyocianil,pyoclox,pyopan,pyopen,pyopene" 12 "g" "18873-0,3434-8,41668-5,59-6,60-4,61-2,62-0"
"CRN" 93184 "Carindacillin" "Beta-lactams/penicillins" "J01CA05,QJ01CA05" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "carindacilina,carindacilline,carindacillinsalt,carindacillinum,geocillin,indanylcarbinicillin,urobac" 4 "g" "NA"
"CAR" 6540466 "Carumonam" "Monobactams" "J01DF02,QJ01DF02" "NA" "carumonamum" 2 "g" "51694-8"
"CAS" 2826718 "Caspofungin" "Antifungals/antimycotics" "J02AX04,QJ02AX04" "Antimycotics for systemic use" "Other antimycotics for systemic use" "casp,caspof" "cancidas,caspofungina" 50 "mg" "32378-2,54175-5,54176-3,54185-4,58419-3"
"CAC" 91562 "Cefacetrile" "Cephalosporins (1st gen.)" "J01DB10,QJ01DB10,QJ51DB10" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephac" "cefacetril,cefacetrilo,cefacetrilum,celospor,cephacetrile,vetrimast" "55624-1,55625-8,55626-6,55627-4"
"CEC" 51039 "Cefaclor" "Cephalosporins (2nd gen.)" "J01DC04,QJ01DC04" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "ccl,cec,cefacl,cf,cfac,cfc,cfcl,cfr,fac" "alenfral,alfacet,alfatil,ceclor,cefachlor,cefaclorum,cefeaclor,cephaclor,compound,distaclor,keflor,kefolor,kefral,keftab,keftid,lilly,lopac,panacef,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,QJ01DB05" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefadr,cfdx,cfr,fad" "bidocel,cefadrops,cefadroxilo,cefadroxilum,cefradroxil,cefzil,cephadroxil,duracef,duricef,kefroxil,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,QJ01DB01,QJ51DB01" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cepale,cflx" "adcadina,alcephin,alsporin,ambal,amplex,aristosporin,azabort,bactopenor,beliam,biocef,carnosporin,cefablan,cefacet,cefadal,cefadin,cefadina,cefalekey,cefaleksin,cefalessina,cefalexgobens,cefalexina,cefalexine,cefalexinum,cefalin,cefalival,cefaloto,cefanex,cefaseptin,cefax,ceffanex,cefibacter,ceflax,ceforal,cefovit,celexin,cepastar,cepexin,cephacillin,cephalexine,cephalexinum,cephalobene,cephanasten,cephaxin,cephin,cepol,ceporex,ceporexin,ceporexine,cerexin,cerexins,check,cophalexin,domucef,doriman,durantel,efemida,erocetin,factagard,felexin,fexin,ibilex,ibrexin,inphalex,karilexina,kefalospes,keflet,keflex,kefolan,keforal,kekrinal,kidolex,lafarine,larixin,lenocef,lexibiotico,loisine,lonflex,lopilexin,losporal,madlexin,maksipor,mamalexin,mamlexin,medolexin,medoxine,neokef,neolexina,noveol,novolexin,nufex,optocef,oracef,oriphex,oroxin,ortisporina,ospexin,palitrex,panixine,pectril,prindex,pyassan,rilexine,roceph,rogevil,sanaxin,sartosona,sencephalin,sepexin,servicef,servispor,sialexin,sinthecillin,sintolexyn,sporicef,sporidex,syncl,syncle,synecl,taicelexin,tepaxin,theratrex,tokiolexin,uphalexin,viosporine,voxxim,winlex,zabytrex,zozarine" 2 "g" "NA"
"RID" 5773 "Cefaloridine" "Cephalosporins (1st gen.)" "J01DB02,QJ01DB02" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefa,ceplor" "aliporina,ampligram,cefaloridin,cefaloridina,cefaloridinum,cefalorizin,ceflorin,cepaloridin,cepalorin,cephalomycine,cephaloridin,cephaloridine,cephaloridinum,ceporan,ceporin,ceporine,cilifor,deflorin,faredina,floridin,glaxoridin,intrasporin,keflodin,keflordin,kefloridin,kefspor,lloncefal,sasperin,sefacin,verolgin,vioviantine" 3 "g" "NA"
"CEP" 6024 "Cefalotin" "Cephalosporins (1st gen.)" "J01DB03,QJ01DB03" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephal,cfal,cflt" "averon,cefalothin,cefalothine,cefalothinsalt,cefalotina,cefalotine,cefalotinsalt,cefalotinum,cemastin,cephalothin,cephalothinsalt,cephalothinum,cephalotin,cephalotinsalt,ceporacin,cepovenin,coaxin,keflin,lospoven,microtin,seffin,synclotin,toricelocin" 4 "g" "NA"
"MAN" 456255 "Cefamandole" "Cephalosporins (2nd gen.)" "J01DC03,QJ01DC03" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefama,cfam,cfmn" "cefadole,cefamandol,cefamandolum,cephadole,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,QG51AA05,QJ01DB08,QJ51DB08" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephap" "ambrocef,brisfirina,brisporin,bristocef,cefadyl,cefalak,cefaloject,cefapirina,cefapirine,cefapirinsalt,cefapirinum,cefaprin,cefatrex,cefatrexyl,cephapirin,cephapirine,cephapirinsalt,cephatrexil,cephatrexyl,metricure" 4 "g" "NA"
"CTZ" 6410758 "Cefatrizine" "Cephalosporins (1st gen.)" "J01DB07,QJ01DB07" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefatr" "bricef,cefathiamidine,cefatrix,cefatrizino,cefatrizinum,cephatriazine,cepticol,cetrazil,latocef,orosporina,orotric,seapuron,trizina" 1 "g" "18877-1,55639-9,71-1,72-9,73-7,74-5"
"CZD" 71736 "Cefazedone" "Cephalosporins (1st gen.)" "J01DB06,QJ01DB06" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefaze" "cefazedon,cefazedona,cefazedonesalt,cefazedonum,refosporen,refosporene,refosporin,refosporinsalt" 3 "g" "NA"
"CZO" 33255 "Cefazolin" "Cephalosporins (1st gen.)" "J01DB04,QJ01DB04,QJ51DB04" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cefazo,cfz,cfzl,cz,czol,faz,kz" "ancef,atirin,biazolina,cefabiozim,cefacidal,cefalomicina,cefamedin,cefamezin,cefazil,cefazina,cefazolina,cefazoline,cefazolinsalt,cefazolinum,cephamezine,cephazolidin,cephazolin,cephazoline,elzogram,firmacef,gramaxin,kefzol,lampocef,liviclina,neofazol,oprea,recef,totacef,zolicef,zolisint" 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,QJ01DC13" "cefbup" "cefbuperazona,cefbuperazonesalt,cefbuperazonum,cefbuperzaone,cerbuperazone,keiperazon,tomiporan" 2 "g" "NA"
"CCP" 6436055 "Cefcapene" "Cephalosporins (3rd gen.)" "J01DD17,QJ01DD17" "cefcap" "flomox" 0.45 "g" "100044-7,76143-7"
"CCX" 5282438 "Cefcapene pivoxil" "Cephalosporins (3rd gen.)" "NA" "NA" "cefcamate,flumax" "NA"
"CDR" 6915944 "Cefdinir" "Cephalosporins (3rd gen.)" "J01DD15,QJ01DD15" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cd,cdn,cdr,cefdin,cfd,din" "cefdinirum,cefdinyl,cefdirnir,ceftinex,cefzon,omnicef" 0.6 "g" "23636-4,23637-2,35757-4,35758-2"
"DIT" 9870843 "Cefditoren" "Cephalosporins (3rd gen.)" "J01DD16,QJ01DD16" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cdn,cefdit" "cefditoreno,spectracef" 0.4 "g" "35759-0,35760-8,35761-6,35762-4"
"DIX" 6437877 "Cefditoren pivoxil" "Cephalosporins (3rd gen.)" "NA" "NA" "cefditorin,meiact,pivaloyloxymethyl" "NA"
"FEP" 5479537 "Cefepime" "Cephalosporins (4th gen.)" "J01DE01,QJ01DE01" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cefep4,cefepi,cfep,cfpi,cpe,cpm,fep,pm,xpm" "anticefepime,axepim,cefepima,cefepimum,maxipime,pyrrolidinium,renapime" 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" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CPC" 9567559 "Cefepime/clavulanic acid" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "cefcla,cicl,xpml" "NA" "NA"
"FPE" 23653540 "Cefepime/enmetazobactam" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FNC" "Cefepime/nacubactam" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FPT" 9567558 "Cefepime/tazobactam" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"FPZ" "Cefepime/zidebactam" "Cephalosporins (4th gen.)" "J01DE51,QJ01DE51" "NA" "NA" "NA"
"CAT" 5487888 "Cefetamet" "Cephalosporins (3rd gen.)" "J01DD10,QJ01DD10" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefeta,cefmtm" "cefetametum,deacetoxycefotaxime,epocelin" 1 "g" "32377-4,35764-0,35765-7,55640-7"
"CPI" 5486182 "Cefetamet pivoxil" "Cephalosporins (3rd gen.)" "NA" "NA" "cefetametpivoxil,cefyl,globocef" "NA"
"CCL" 71719688 "Cefetecol" "Cephalosporins (4th gen.)" "NA" "cefcatacol" "NA" "NA"
"CZL" 193956 "Cefetrizole" "Cephalosporins (unclassified gen.)" "NA" "NA" "cefetrizolum" "NA"
"FDC" 77843966 "Cefiderocol" "Cephalosporins (unclassified gen.)" "J01DI04,QJ01DI04" "NA" "fetcroja" 6 "g" "95767-0,99280-0,99503-5"
"CFM" 5362065 "Cefixime" "Cephalosporins (3rd gen.)" "J01DD08,QJ01DD08" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefixi,cfe,cfix,cfxm,dcfm,fix,ix" "cefixim,cefixima,cefiximum,cefixoral,cefspan,cephoral,citropen,denvar,necopen,oraken,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" "J01DD58,QJ01DD58" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CMX" 9570757 "Cefmenoxime" "Cephalosporins (3rd gen.)" "J01DD05,QJ01DD05,QS01AA31,QS02AA18,S01AA31,S02AA18" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefmen" "bestron,cefmenoxima,cefmenoximum,tacef" 2 "g" "32375-8,54174-8,54203-5,55641-5"
"CMZ" 42008 "Cefmetazole" "Cephalosporins (2nd gen.)" "J01DC09,QJ01DC09" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefmet" "cefmetazol,cefmetazolo,cefmetazolum,cefmetazon,metafar,zefazone" 4 "g" "11575-8,18881-3,25222-1,87-7,88-5,89-3,90-1"
"CNX" 71141 "Cefminox" "Other antibacterials" "J01DC12,QJ01DC12" "cefmin" "alteporina,cefminoxhydrate,cefminoxum,meicelin,tencef" 4 "g" "54908-9"
"DIZ" 5361871 "Cefodizime" "Cephalosporins (3rd gen.)" "J01DD09,QJ01DD09" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "NA" "cefodizima,cefodizimum,cefodizme,diezime,kenicef,modivid,neucef,timecef" 2 "g" "18882-1,6988-0,91-9,92-7,93-5,94-3"
"CID" 43594 "Cefonicid" "Cephalosporins (2nd gen.)" "J01DC06,QJ01DC06" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoni" "cefonicide,cefonicido,cefonicidsalt,cefonicidum,monocef,monocid" 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,QJ01DD12,QJ51DD12" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefope,cfp,cfpz,cp,cpz,fop,per" "bioperazone,cefob,cefobid,cefobis,cefoneg,cefoper,cefoperazin,cefoperazine,cefoperazon,cefoperazona,cefoperazonesalt,cefoperazono,cefoperazonum,cefozon,medocef,myticef,pathozone,peracef,tomabef" 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,QJ01DD62" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "fopsul" "NA" 4 "g" "35768-1,54166-4,54167-2,54168-0"
"CND" 43507 "Ceforanide" "Cephalosporins (2nd gen.)" "J01DC11,QJ01DC11" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefora" "ceforanido,ceforanidum,precef" 4 "g" "103-2,104-0,105-7,106-5,18885-4,55643-1"
"CSE" 9830519 "Cefoselis" "Cephalosporins (4th gen.)" "NA" "cefose" "winsef" "NA"
"CTX" 5742673 "Cefotaxime" "Cephalosporins (3rd gen.)" "J01DD01,QJ01DD01" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefo32,cefota,cfot,cft,cftx,ct,ctx,fot,fot1,tax,taxmen,taxnme,xct" "anticefotaxime,cefotax,cefotaxim,cefotaxima,cefotaximesalt,cefotaximsalt,cefotaximum,cephotaxim,cephotaxime,claforan,kefotex,omnatax,pretor,ralopar,tolycar,tolycor,zariviz" 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"
"CTX-S" "Cefotaxime screening test" "Cephalosporins (3rd gen.)" "NA" "ctx screen" "NA" "NA"
"CTC" 9575353 "Cefotaxime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD51,QJ01DD51" "cxcl,taxcla,xctl" "NA" "NA"
"CTS" 9574753 "Cefotaxime/sulbactam" "Cephalosporins (3rd gen.)" "J01DD51,QJ01DD51" "NA" "NA" "54191-2,54192-0,54193-8,55644-9"
"CTT" 53025 "Cefotetan" "Cephalosporins (2nd gen.)" "J01DC05,QJ01DC05" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefote,cftt,cn,cte,ctn,ctt,tans" "apacef,apatef,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,QJ01DC07" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoti" "aspil,cefotiamum,ceradon,halospor,pansporin,pansporine,spizef" 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" "NA" "taketiam,texodil" "55737-1,55738-9,55739-7,55740-5"
"FOV" 9578573 "Cefovecin" "Cephalosporins (3rd gen.)" "QJ01DD91" "cefove" "cefovecinsalt,convenia" "76147-8,87792-8"
"FOX" 441199 "Cefoxitin" "Cephalosporins (2nd gen.)" "J01DC01,QJ01DC01" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefoxi,cfox,cfx,cfxt,cx,fox,fx" "betacef,cefoxil,cefoxitina,cefoxitine,cefoxitinsalt,cefoxitinum,cefoxotin,cenomycin,farmoxin,mefoxin,mefoxithin,mefoxitin,merxin,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"
"FOX-S" "Cefoxitin screening test" "Cephalosporins (2nd gen.)" "NA" "cfsc,fox1" "NA" "NA"
"ZOP" 9571080 "Cefozopran" "Cephalosporins (4th gen.)" "J01DE03,QJ01DE03" "cefozo" "firstcin,imidazo" 4 "g" "100045-4,53820-7"
"CFZ" 68597 "Cefpimizole" "Cephalosporins (3rd gen.)" "NA" "cefpim" "ajicef,cefpimizol,cefpimizolesalt,cefpimizolum,renilan" "NA"
"CPM" 636405 "Cefpiramide" "Cephalosporins (3rd gen.)" "J01DD11,QJ01DD11" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefpam" "cefpiramida,cefpiramidesalt,cefpiramido,cefpiramidum,sepatren,suncefal" 2 "g" "NA"
"CPO" 5479539 "Cefpirome" "Cephalosporins (4th gen.)" "J01DE02,QJ01DE02" "Other beta-lactam antibacterials" "Fourth-generation cephalosporins" "cefpom,cfpr" "broact,cefir,cefpiroma,cefpiromum,cefrom,keiten,romecef" 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,QJ01DD13" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefpod,cfpd,cfpo,cpd,pod,pod4,px" "cefpodoxima,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" "NA" "banan,cefodox,cefoprox,cefpoderm,cefpodoximproxetil,cepodem,doxef,orelox,otreon,podomexef,simplicef,vantin" "NA"
"CDC" "Cefpodoxime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD64,QJ01DD64" "cecl,podcla" "NA" 0.4 "g" "NA"
"CPR" 5281006 "Cefprozil" "Cephalosporins (2nd gen.)" "J01DC10,QJ01DC10" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefpro,cpr,cpz,fp" "arzimol,brisoral,cefprozilo,cefprozilum,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" "cefqui" "cefquinoma,cefquinomum,cobactan,quinolinium" "100046-2,76150-2"
"CRD" 5284529 "Cefroxadine" "Cephalosporins (1st gen.)" "J01DB11,QJ01DB11" "Other beta-lactam antibacterials" "First-generation cephalosporins" "ceftix" "cefroxadin,cefroxadino,cefroxadinum,oraspor" 2.1 "g" "NA"
"CFS" 656575 "Cefsulodin" "Cephalosporins (3rd gen.)" "J01DD03,QJ01DD03" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cefsul,cfsl,cfsu" "cefomonil,cefonomil,cefsulodine,cefsulodinhydrate,cefsulodino,cefsulodinum,pseudocef,pseudomonil,pyocefal,sulcephalosporin,takesulin,tilmapor,ulfaret" 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" "NA" "cefsulmid,cefsumido,cefsumidum" "NA"
"CPT" 56841980 "Ceftaroline" "Cephalosporins (5th gen.)" "J01DI02,QJ01DI02" "ceftar,cfro" "ceftaroine,teflaro,zinforo" "73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
"CPA" "Ceftaroline/avibactam" "Cephalosporins (5th gen.)" "NA" "NA" "NA" "73604-1,73626-4,73649-6"
"CAZ" 5481173 "Ceftazidime" "Cephalosporins (3rd gen.)" "J01DD02,QJ01DD02" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "caz,cefta,ceftaz,cfta,cftz,taz,tz,xtz" "ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime" 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.)" "J01DD52,QJ01DD52" "cfav" "avycaz,zavicefta" 6 "g" "101483-6,73603-3,73625-6,73648-8,87734-0"
"CCV" 9575352 "Ceftazidime/clavulanic acid" "Cephalosporins (3rd gen.)" "J01DD52,QJ01DD52" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "czcl,tazcla,xtzl" "NA" 6 "g" "NA"
"CEM" 6537431 "Cefteram" "Cephalosporins (3rd gen.)" "J01DD18,QJ01DD18" "cefter" "cefterame,cefteramum,ceftetrame" 0.4 "g" "100047-0,76144-5"
"CPL" 5362114 "Cefteram pivoxil" "Cephalosporins (3rd gen.)" "NA" "NA" "cefterampivoxil,tomiron" "NA"
"CTL" 65755 "Ceftezole" "Cephalosporins (1st gen.)" "J01DB12,QJ01DB12" "Other beta-lactam antibacterials" "First-generation cephalosporins" "ceftez" "alomen,ceftezol,ceftezolesalt,ceftezolo,ceftezolum,celoslin,demethylcefazolin,falomesin" 3 "g" "NA"
"CTB" 5282242 "Ceftibuten" "Cephalosporins (3rd gen.)" "J01DD14,QJ01DD14" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "cb,ceftib,cfbu,ctb,tib" "cedax,ceftem,ceftibutene,ceftibuteno,ceftibutenum,ceftibutin,ceprifran,isocef,keimax,seftem" 0.4 "g" "35777-2,35778-0,35779-8,6996-3"
"TIO" 6328657 "Ceftiofur" "Cephalosporins (3rd gen.)" "QJ01DD90,QJ51DD90" "ceftif" "ceftiofurum,excenel,naxcel" "23709-9,35780-6,35781-4,55652-2"
"CZX" 6533629 "Ceftizoxime" "Cephalosporins (3rd gen.)" "J01DD07,QJ01DD07" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "ceftiz,cfzx,ctz,cz,czx,tiz,zox" "cefizox,ceftix,ceftizoxima,ceftizoximesalt,ceftizoximum,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" "NA" "NA" "NA"
"BPR" 135413542 "Ceftobiprole" "Cephalosporins (5th gen.)" "NA" "ceftob" "NA" "43269-0,43270-8,43271-6,43272-4,85052-9"
"CFM1" 135413544 "Ceftobiprole medocaril" "Cephalosporins (5th gen.)" "J01DI01,QJ01DI01" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "NA" "zevtera" 1.5 "g" "NA"
"CZT" 86291594 "Ceftolozane/tazobactam" "Cephalosporins (5th gen.)" "J01DI54,QJ01DI54" "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,QJ01DD04" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "axo,cax,ceftri,cftr,cro,ctr,frx,trimen,trinme,tx" "biotrakson,ceftriaxon,ceftriaxona,ceftriaxonum,ceftriazone,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,QJ01DD63" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "NA" "NA" 2 "g" "NA"
"CXM" 5479529 "Cefuroxime" "Cephalosporins (2nd gen.)" "J01DC02,QJ01DC02,QJ51DC02,QS01AA27,S01AA27" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "cefaxe,cefrox,cefuro,cfrx,cfur,cfx,crm,cxm,fur,rox,xm" "anaptivan,biociclin,biofuroksym,bioxima,cefofix,cefumax,cefurex,cefuril,cefurox,cefuroxim,cefuroxima,cefuroximesalt,cefuroximine,cefuroximo,cefuroximum,cephuroxime,cetroxil,colifossim,curoxim,curoxima,curoxime,froxal,furoxil,kefurox,kesint,ketocef,lifurox,medoxim,sharox,spectrazolr,ultroxim,zinacef,zinnat" 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" "bioracef,ceftin,cefurax,cefuroximaxetil,celocid,cepazine,cethixim,cetoxil,coliofossim,curocef,elobact,kalcef,maxitil,medoxm,nivador,novador,novocef,oraxim,zinat,zoref" "NA"
"CFM2" "Cefuroxime/metronidazole" "Other antibacterials" "J01DC52,QJ01DC52" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" 0.5 "g" "NA"
"ZON" 6336505 "Cefuzonam" "Other antibacterials" "NA" "cefuzo" "cefuzoname,cefuzonamum,cefzoname,cosmosin" "NA"
"CED" 38103 "Cephradine" "Cephalosporins (1st gen.)" "NA" "Other beta-lactam antibacterials" "First-generation cephalosporins" "cephra,cfra,cfrd" "anspor,cefradin,cefradina,cefradine,cefradinum,cekodin,cephradin,ecosporina,eskacef,infexin,megacef,sefril,velocef,velosef" "168-5,169-3,170-1,171-9,18902-7,55646-4"
"CTO" 71402 "Cetocycline" "Tetracyclines" "NA" "NA" "cetocyline,cetotetrine,chelocardin" "NA"
"CHL" 5959 "Chloramphenicol" "Phenicols" "D06AX02,D10AF03,G01AA05,J01BA01,QD06AX02,QD10AF03,QG01AA05,QJ01BA01,QJ51BA01,QS01AA01,QS02AA01,QS03AA08,S01AA01,S02AA01,S03AA08" "Amphenicols" "Amphenicols" "c,chl,chlo,chlora,cl" "alficetyn,ambofen,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocide,chlorocin,chlorocol,chlorofair,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chlorovules,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextramycin,dextromycetin,doctamicina,econochlor,embacetin,emetren,enteromycetin,erbaplast,ertilen,farmicetina,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,intramycetin,isicetin,ismicetina,isophenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromisan,loromisin,mastiphen,maybridge,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,petnamycetin,quemicetina,rivomycin,romphenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,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,QA01AB21,QD06AA02,QG51AA08,QJ01AA03,QJ51AA03,QS01AA02,S01AA02" "Tetracyclines" "Tetracyclines" "chltet" "acronize,alexomycin,aueromycin,aureocarmyl,aureociclina,aureocina,aureocycline,aureomycin,aureomykoin,aurofac,auxeomycin,biomitsin,biomycin,chlormax,chlorotetracycline,chlortetracyclinum,chrysomykine,clorocipan,clortetraciclina,clortetrin,declomycin,declostatin,deganol,demeclor,demeplus,demetraciclina,demetraclin,detracin,detravis,diuciclin,duomycin,elkamicina,flamycin,isphamycin,ledermicina,ledermycin,ledermycine,mexocine,novotriclina,pennchlor,perciclina,periciclina,sumaclina,uromycin,veraciclina" 1 "g" "176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
"CIC" 19003 "Ciclacillin" "Penicillins,Beta-lactams" "NA" "cyclac" "bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital" "NA"
"CIX" "Ciclopirox" "Antifungals" "D01AE14,G01AX12,QD01AE14,QG01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "NA" "NA"
"CIC" 19003 "Ciclacillin" "Beta-lactams/penicillins" "NA" "cyclac" "bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital" "NA"
"CIX" 47472 "Ciclopirox" "Antifungals/antimycotics" "D01AE14,G01AX12,QD01AE14,QG01AX12" "Antifungals for topical use" "Other antifungals for topical use" "cipx" "NA" "NA"
"CIN" 2762 "Cinoxacin" "Quinolones" "J01MB06,QJ01MB06" "Quinolone antibacterials" "Other quinolones" "cino,cinoxa,cnox" "cinobac,cinobactin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm" 1 "g" "180-0,181-8,182-6,183-4,18905-0,55656-3"
"CIP" 2764 "Ciprofloxacin" "Fluoroquinolones,Quinolones" "J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07" "Quinolone antibacterials" "Fluoroquinolones" "ci,cip,cipr,ciprof,cp" "alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,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" "Fluoroquinolones,Quinolones" "J01RA10,QJ01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CIO" "Ciprofloxacin/ornidazole" "Fluoroquinolones,Quinolones" "J01RA12,QJ01RA12" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CIT" "Ciprofloxacin/tinidazole" "Fluoroquinolones,Quinolones" "J01RA11,QJ01RA11" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CLR" 84029 "Clarithromycin" "Macrolides" "J01FA09,QJ01FA09" "Macrolides, lincosamides and streptogramins" "Macrolides" "ch,cla,clar,claryt,clm,clr" "abbotic,abboticine,astromen,biaxin,bicrolid,bristamycin,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycine,clarithromycinum,claritromicina,clarosip,clathromycin,crixan,cyllid,cyllind,eratrex,esinol,fromilid,gallimycin,helas,heliclar,klabax,klacid,klaciped,klaricid,klarid,klarin,kofron,mabicrol,macladin,maclar,mavid,meberyt,pediamycin,qidmycin,veclam,wyamycin,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" "NA" "NA" "amonate,clavulanate,clavulanateacid,clavulansaeure,clavulansaure,clavulox,serdaxin" "NA"
"CLX" 60063 "Clinafloxacin" "Fluoroquinolones,Quinolones" "NA" "clinaf" "NA" "32376-6,33284-1,35785-5,35786-3,7004-5"
"CLI" 446598 "Clindamycin" "Lincosamides" "D10AF01,G01AA10,J01FF01,QD10AF01,QG01AA10,QJ01FF01" "Macrolides, lincosamides and streptogramins" "Lincosamides" "cc,cd,cli,clin,clin32,clinda,cm,da" "antirobe,chlolincocin,chlorlincocin,cleocin,clindamicina,clindamycine,clindamycinum,clinimycin,clinsol,clintabs,dalacine,klimicin,klindan,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"
"CLI-S" "Clindamycin inducible screening test" "Lincosamides,Macrolides" "NA" "clin inducible,clinda inducible,clindamycin inducible" "NA" "NA"
"CIP" 2764 "Ciprofloxacin" "Fluoroquinolones" "J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07" "Quinolone antibacterials" "Fluoroquinolones" "ci,cip,cipr,ciprof,cp" "alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,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" "Fluoroquinolones" "J01RA10,QJ01RA10" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CIO" "Ciprofloxacin/ornidazole" "Fluoroquinolones" "J01RA12,QJ01RA12" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CIT" "Ciprofloxacin/tinidazole" "Fluoroquinolones" "J01RA11,QJ01RA11" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"CLR" 84029 "Clarithromycin" "Macrolides/lincosamides" "J01FA09,QJ01FA09" "Macrolides, lincosamides and streptogramins" "Macrolides" "ch,cla,clar,claryt,clm,clr" "abbotic,abboticine,astromen,biaxin,bicrolid,bristamycin,clacee,clacid,clacine,clambiotic,clarem,claribid,claricide,claridar,claripen,clarith,clarithromycine,clarithromycinum,claritromicina,clarosip,clathromycin,crixan,cyllid,cyllind,eratrex,esinol,fromilid,gallimycin,helas,heliclar,klabax,klacid,klaciped,klaricid,klarid,klarin,kofron,mabicrol,macladin,maclar,mavid,meberyt,pediamycin,qidmycin,veclam,wyamycin,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" "NA" "amonate,clavulanate,clavulanateacid,clavulansaeure,clavulansaure,clavulox,serdaxin" "NA"
"CLX" 60063 "Clinafloxacin" "Fluoroquinolones" "NA" "clinaf" "NA" "32376-6,33284-1,35785-5,35786-3,7004-5"
"CLI" 446598 "Clindamycin" "Macrolides/lincosamides" "D10AF01,G01AA10,J01FF01,QD10AF01,QG01AA10,QJ01FF01" "Macrolides, lincosamides and streptogramins" "Lincosamides" "cc,cd,cli,clin,clin32,clinda,cm,da" "antirobe,chlolincocin,chlorlincocin,cleocin,clindamicina,clindamycine,clindamycinum,clinimycin,clinsol,clintabs,dalacine,klimicin,klindan,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"
"CLI-S" "Clindamycin inducible screening test" "Macrolides/lincosamides" "NA" "clin inducible,clinda inducible,clindamycin inducible" "NA" "NA"
"CLF" 2794 "Clofazimine" "Antimycobacterials" "J04BA01,QJ04BA01" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "clof,clofam" "chlofazimine,clofazimina,clofaziminum,colfazimine,lampren,lamprene,phenazine,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" "J01XX03,QJ01XX03" "Other antibacterials" "Other antibacterials" "NA" "clofoctolo,clofoctolum,gramplus,octofene,phenol" "NA"
"CLM" 71807 "Clometocillin" "Penicillins,Beta-lactams" "J01CE07,QJ01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen" 1 "g" "NA"
"CLF1" 2799 "Clofoctol" "Other antibacterials" "J01XX03,QJ01XX03" "Other antibacterials" "Other antibacterials" "NA" "clofoctolo,clofoctolum,gramplus,octofene,phenol" "NA"
"CLM" 71807 "Clometocillin" "Beta-lactams/penicillins" "J01CE07,QJ01CE07" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen" 1 "g" "NA"
"CLM1" 54680675 "Clomocycline" "Tetracyclines" "J01AA11,QJ01AA11" "Tetracyclines" "Tetracyclines" "NA" "clomociclina,clomocyclinum,megaclor" 1 "g" "NA"
"CLB" 54706138 "Clorobiocin" "Aminocoumarins" "NA" "NA" "chlorobiocin" "NA"
"CTR" 2812 "Clotrimazole" "Antifungals" "A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90" "clot" "alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole" "10653-4,10654-2,18909-2,54177-1,55663-9"
"CLO" 6098 "Cloxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF02,QJ01CF02,QJ51CF02,QS01AA90" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,cloxac" "ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen" 2 "g" 2 "g" "16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
"CTR" 2812 "Clotrimazole" "Antifungals/antimycotics" "A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90" "clot" "alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole" "10653-4,10654-2,18909-2,54177-1,55663-9"
"CLO" 6098 "Cloxacillin" "Beta-lactams/penicillins" "J01CF02,QJ01CF02,QJ51CF02,QS01AA90" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,cloxac" "ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,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,QA07AA10,QJ01XB01,QJ51XB01" "Other antibacterials" "Polymyxins" "cl,coli,colist,cs,cst,ct" "colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,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" "NA" "NA" "NA" "NA"
"COP" "Colistin/polysorbate" "Other antibacterials" "NA" "NA" "NA" "NA"
"CYC" 6234 "Cycloserine" "Oxazolidinones" "J04AB01,QJ04AB01" "Drugs for treatment of tuberculosis" "Antibiotics" "cycl,cyclos" "cicloserina,closina,cyclorin,cycloserin,cycloserinum,farmiserina,levcicloserina,levcycloserine,levcycloserinum,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,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" "Lipoglycopeptides,Glycopeptides,Peptides" "J01XA04,QJ01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb,dalbav" "dalbavancina,dalvance,xydalba,zeven" 1.5 "g" "41688-3,41689-1,41690-9,41734-5"
"DAN" 71335 "Danofloxacin" "Fluoroquinolones,Quinolones" "QJ01MA92" "danofl" "advocin,danofloxacine,danofloxacino,danofloxacinum" "73601-7,73623-1,73646-2"
"DPS" 2955 "Dapsone" "Other" "D10AX05,J04BA02,QD10AX05,QJ04BA02" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "dao" "aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac" 50 "mg" "51698-9,9747-7"
"DAP" 16134395 "Daptomycin" "Peptides" "J01XX09,QJ01XX09" "Other antibacterials" "Other antibacterials" "dap,dapt,dapt25,dapt50,daptom" "cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin" 0.28 "g" "35787-1,35788-9,35789-7,41691-7"
"DFX" 487101 "Delafloxacin" "Fluoroquinolones,Quinolones" "J01MA23,QJ01MA23" "NA" "baxdela,delafloxacinum,quofenix" 0.9 "g" 0.6 "g" "88885-9,90447-4,93790-4"
"DAL" 23724878 "Dalbavancin" "Glycopeptides" "J01XA04,QJ01XA04" "Other antibacterials" "Glycopeptide antibacterials" "dalb,dalbav" "dalbavancina,dalvance,xydalba,zeven" 1.5 "g" "41688-3,41689-1,41690-9,41734-5"
"DAN" 71335 "Danofloxacin" "Fluoroquinolones" "QJ01MA92" "danofl" "advocin,danofloxacine,danofloxacino,danofloxacinum" "73601-7,73623-1,73646-2"
"DPS" 2955 "Dapsone" "Other antibacterials" "D10AX05,J04BA02,QD10AX05,QJ04BA02" "Drugs for treatment of lepra" "Drugs for treatment of lepra" "NA" "aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac" 50 "mg" "51698-9,9747-7"
"DAP" 16134395 "Daptomycin" "Other antibacterials" "J01XX09,QJ01XX09" "Other antibacterials" "Other antibacterials" "dap,dapt,dapt25,dapt50,daptom" "cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin" 0.28 "g" "35787-1,35788-9,35789-7,41691-7"
"DFX" 487101 "Delafloxacin" "Fluoroquinolones" "J01MA23,QJ01MA23" "NA" "baxdela,delafloxacinum,quofenix" 0.9 "g" 0.6 "g" "88885-9,90447-4,93790-4"
"DLM" 6480466 "Delamanid" "Antimycobacterials" "J04AK06,QJ04AK06" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "dela" "deltyba" 0.2 "g" "93851-4,96109-4"
"DEM" 54680690 "Demeclocycline" "Tetracyclines" "D06AA01,J01AA01,QD06AA01,QJ01AA01" "Tetracyclines" "Tetracyclines" "demecy" "demeclociclina,demeclocyclinum" 0.6 "g" "10982-7,18915-9,216-2,217-0,218-8,219-6,29494-2,7006-0"
"DKB" 470999 "Dibekacin" "Aminoglycosides" "J01GB09,QJ01GB09,QS01AA29,S01AA29" "Aminoglycoside antibacterials" "Other aminoglycosides" "dibeka" "debecacin,dibekacina,dibekacine,dibekacinum,kappati,panamicin" 0.14 "g" "55669-6,55670-4,55671-2,55672-0"
"DIC" 18381 "Dicloxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF01,QJ01CF01,QJ51CF01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "dicl,diclox" "dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,maclicine" 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" "Fluoroquinolones,Quinolones" "QJ01MA94" "diflox" "dicural,difloxacine,pulsaflox" "35790-5,35791-3,35792-1"
"DIR" 6473883 "Dirithromycin" "Macrolides" "J01FA13,QJ01FA13" "Macrolides, lincosamides and streptogramins" "Macrolides" "dirith" "dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin" 0.5 "g" "35793-9,35794-7,35795-4,7007-8"
"DOR" 73303 "Doripenem" "Carbapenems,Beta-lactams" "J01DH04,QJ01DH04" "Other beta-lactam antibacterials" "Carbapenems" "dori,doripe" "doribax,dripenem,finibax" 1.5 "g" "56031-8,58711-3,60535-2,72893-1"
"DIC" 18381 "Dicloxacillin" "Beta-lactams/penicillins" "J01CF01,QJ01CF01,QJ51CF01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "dicl,diclox" "dichloroxacillin,diclossacillina,dicloxaciclin,dicloxacilin,dicloxacilina,dicloxacillina,dicloxacilline,dicloxacillinum,dicloxacycline,maclicine" 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" "Fluoroquinolones" "QJ01MA94" "diflox" "dicural,difloxacine,pulsaflox" "35790-5,35791-3,35792-1"
"DIR" 6473883 "Dirithromycin" "Macrolides/lincosamides" "J01FA13,QJ01FA13" "Macrolides, lincosamides and streptogramins" "Macrolides" "dirith" "dirithromycine,dirithromycinum,diritromicina,divitross,dynabac,noriclan,valodin" 0.5 "g" "35793-9,35794-7,35795-4,7007-8"
"DOR" 73303 "Doripenem" "Carbapenems" "J01DH04,QJ01DH04" "Other beta-lactam antibacterials" "Carbapenems" "dori,doripe" "doribax,dripenem,finibax" 1.5 "g" "56031-8,58711-3,60535-2,72893-1"
"DOX" 54671203 "Doxycycline" "Tetracyclines" "A01AB22,J01AA02,QA01AB22,QJ01AA02" "Tetracyclines" "Tetracyclines" "dox,doxy,doxycy" "abbocin,alamycin,aquacycline,biosolvomycin,biotet,bisolvomycin,chrysocin,dalimycin,dalinmycin,deoxymykoin,dossiciclina,doxiciclina,doxirobe,doxitard,doxivetin,doxycen,doxychel,doxycin,doxycyclin,doxycyclinum,doxylin,doxysol,doxytetracycline,elinton,engemycin,hydrocyclin,imperacin,intaloxin,investin,jenacyclin,liquachel,liviatin,macodyn,mepatar,microdox,mondoxyne,monodox,morgidox,ocudox,okebo,oracea,otetryn,oxacycline,oxamycen,oxatet,oxlopar,oxybiocycline,oxydon,oxyject,oxymykoin,oxysteclin,oxytet,oxytetral,oxytetrin,oxytracyl,oxyvet,stecsolin,supracyclin,terraject,terramycin,toxinal,unimycin,vendarcin,vibramycin,vibramycine,vivox,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" "D01AC03,G01AF05,QD01AC03,QG01AF05" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "bromazil,chloramizol,clinafarm,deccosil,deccozil,econazolum,ecostatin,ekonazole,enilconazol,enilconazole,eniloconazol,fecundal,florasan,freshgard,freshguard,fungaflor,fungazil,imaverol,imaversol,imazalil,magnate,spectazole" "25595-0,25637-0,54178-9,55673-8"
"ECO" 3198 "Econazole" "Antifungals/antimycotics" "D01AC03,G01AF05,QD01AC03,QG01AF05" "Antifungals for topical use" "Imidazole and triazole derivatives" "econ" "bromazil,chloramizol,clinafarm,deccosil,deccozil,econazolum,ecostatin,ekonazole,enilconazol,enilconazole,eniloconazol,fecundal,florasan,freshgard,freshguard,fungaflor,fungazil,imaverol,imaversol,imazalil,magnate,spectazole" "25595-0,25637-0,54178-9,55673-8"
"EFF" "Efflux" "Other" "NA" "effflux pump" "NA" "NA"
"ENX" 3229 "Enoxacin" "Fluoroquinolones,Quinolones" "J01MA04,QJ01MA04" "Quinolone antibacterials" "Fluoroquinolones" "enox,enoxa" "abenox,almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,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" "Fluoroquinolones,Quinolones" "QJ01MA90" "enrofl" "baytril,enroflox,enrofloxacine,enrofloxacino,enrofloxacinum,enroquin,enrosite,enroxil,quellaxcin,tenotryl,zobuxa" "23712-3,35796-2,35797-0,35798-8"
"ENX" 3229 "Enoxacin" "Fluoroquinolones" "J01MA04,QJ01MA04" "Quinolone antibacterials" "Fluoroquinolones" "enox,enoxa" "abenox,almitil,bactidan,bactidron,comprecin,enofloxacine,enoksetin,enoram,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" "Fluoroquinolones" "QJ01MA90" "enrofl" "baytril,enroflox,enrofloxacine,enrofloxacino,enrofloxacinum,enroquin,enrosite,enroxil,quellaxcin,tenotryl,zobuxa" "23712-3,35796-2,35797-0,35798-8"
"ENV" 135565326 "Enviomycin" "Antimycobacterials" "J04AB06,QJ04AB06" "tuberactinomycin" "enviomicina,enviomycina,enviomycine,enviomycinum,tuberactin" 1 "g" "NA"
"EPE" "Eperozolid" "Other" "NA" "NA" "NA" "NA"
"EPC" 71392 "Epicillin" "Penicillins,Beta-lactams" "J01CA07,QJ01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "dexacillin,dihydroampicillin,epicilina,epicilline,epicillinum,spectacillin" 2 "g" 2 "g" "NA"
"EPP" 68916 "Epiroprim" "Other" "NA" "NA" "epiroprima,epiroprime,epiroprimum" "NA"
"EPE" "Eperozolid" "Other antibacterials" "NA" "NA" "NA" "NA"
"EPC" 71392 "Epicillin" "Beta-lactams/penicillins" "J01CA07,QJ01CA07" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "dexacillin,dihydroampicillin,epicilina,epicilline,epicillinum,spectacillin" 2 "g" 2 "g" "NA"
"EPP" 68916 "Epiroprim" "Other antibacterials" "NA" "NA" "epiroprima,epiroprime,epiroprimum" "NA"
"ERV" 54726192 "Eravacycline" "Tetracyclines" "J01AA13,QJ01AA13" "Tetracyclines" "Tetracyclines" "erav" "xerava" 0.14 "g" "100049-6,85423-2,93767-2"
"ETP" 150610 "Ertapenem" "Carbapenems,Beta-lactams" "J01DH03,QJ01DH03" "Other beta-lactam antibacterials" "Carbapenems" "erta,ertape,etp" "ertapenemsalt,invanz" 1 "g" "101486-9,35799-6,35800-2,35801-0,35802-8"
"ERY" 12560 "Erythromycin" "Macrolides" "D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17" "Macrolides, lincosamides and streptogramins" "Macrolides" "e,em,ery,ery32,eryt,eryth" "abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid" 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,QJ04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "emb,etha,ethamb" "aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,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"
"ETP" 150610 "Ertapenem" "Carbapenems" "J01DH03,QJ01DH03" "Other beta-lactam antibacterials" "Carbapenems" "erta,ertape,etp" "ertapenemsalt,invanz" 1 "g" "101486-9,35799-6,35800-2,35801-0,35802-8"
"ERY" 12560 "Erythromycin" "Macrolides/lincosamides" "D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17" "Macrolides, lincosamides and streptogramins" "Macrolides" "e,em,ery,ery32,eryt,eryth" "abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid" 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,QJ04AK02" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "etha,ethamb" "aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,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,QJ04AM03" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"ETI1" 2761171 "Ethionamide" "Antimycobacterials" "J04AD03,QJ04AD03" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "ethi,ethion" "aethionamidum,aetina,aetiva,amidazin,amidazine,atina,ethimide,ethina,ethinamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,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" "QP51AX17" "NA" "ethopabat" "NA"
"EXE" "Exebacase" "Other" "NA" "NA" "NA" "NA"
"FAR" 65894 "Faropenem" "Other" "J01DI03,QJ01DI03" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "farope" "farom,faropenemhydrate,faropenemsalt,fropenem,fropenum,furopenem" 0.75 "g" "73600-9,73622-3,73645-4"
"FDX" 10034073 "Fidaxomicin" "Other" "A07AA12,QA07AA12" "NA" "dificid,dificlir,difimicin,fidaxomicina,lipiarmicin,lipiarmycin,lipiarrmycin" 0.4 "g" "73599-3,73621-5,73644-7"
"FIN" 11567473 "Finafloxacin" "Fluoroquinolones,Quinolones" "NA" "NA" "xtoro" "73598-5,73620-7,73643-9"
"FLA" 46783781 "Flavomycin" "Other" "NA" "flavom" "bambermicina,bambermycine,bambermycinum,flavofosfolipol,flavophospholipol,gainpro,menomycin" "NA"
"FLE" 3357 "Fleroxacin" "Fluoroquinolones,Quinolones" "J01MA08,QJ01MA08" "Quinolone antibacterials" "Fluoroquinolones" "fler,flerox" "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" "J01DC14,QJ01DC14" "flomox" "flomoxefo,flomoxefsalt,flomoxefum,flumarin" 2 "g" "100052-0,53822-3"
"ETO" 6034 "Ethopabate" "Other antibacterials" "QP51AX17" "NA" "ethopabat" "NA"
"EXE" "Exebacase" "NA" "NA" "NA" "NA"
"FAR" 65894 "Faropenem" "Other antibacterials" "J01DI03,QJ01DI03" "Other beta-lactam antibacterials" "Other cephalosporins and penems" "farope" "farom,faropenemhydrate,faropenemsalt,fropenem,fropenum,furopenem" 0.75 "g" "73600-9,73622-3,73645-4"
"FDX" 10034073 "Fidaxomicin" "Other antibacterials" "A07AA12,QA07AA12" "NA" "dificid,dificlir,difimicin,fidaxomicina,lipiarmicin,lipiarmycin,lipiarrmycin" 0.4 "g" "73599-3,73621-5,73644-7"
"FIN" 11567473 "Finafloxacin" "Fluoroquinolones" "NA" "NA" "xtoro" "73598-5,73620-7,73643-9"
"FLA" 46783781 "Flavomycin" "Other antibacterials" "NA" "flavom" "bambermicina,bambermycine,bambermycinum,flavofosfolipol,flavophospholipol,gainpro,menomycin" "NA"
"FLE" 3357 "Fleroxacin" "Fluoroquinolones" "J01MA08,QJ01MA08" "Quinolone antibacterials" "Fluoroquinolones" "fler,flerox" "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,QJ01DC14" "flomox" "flomoxefo,flomoxefsalt,flomoxefum,flumarin" 2 "g" "100052-0,53822-3"
"FLR" 114811 "Florfenicol" "Phenicols" "QJ01BA90,QJ51BA90" "florfe" "aquafen,descocin,dexawin,efnicol,fricol,hyrazin,loncor,macphenicol,masatirin,neomyson,norfenicol,nuflor,racephenicol,rincrol,thiamcol,urfamicina,urophenyl" "23740-4,35807-7,35808-5,87599-7"
"FLC" 21319 "Flucloxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF05,QJ01CF05,QJ51CF05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,fluclo,flux" "bactopen,cloxacap,cloxacillinhydrate,cloxypen,floxacillin,floxacillinanhydrous,floxapen,floxapensalt,fluclomix,flucloxacilina,flucloxacilline,flucloxacillinum,flucloxin,fluorochloroxacillin,galfloxin,latocillin,orbeninhydrate,rimaflox,staphobristol,zoxin" 2 "g" 2 "g" "NA"
"FLU" 3365 "Fluconazole" "Antifungals" "D01AC15,J02AC01,QD01AC15,QJ02AC01" "Antimycotics for systemic use" "Triazole derivatives" "fluc,flucon,fluz,flz" "alflucoz,alkanazole,baten,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,fluzon,forcan,fuconal,fungata,loitin,mutum,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zemyc,zoltec,zonal" 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" "D01AE21,J02AX01,QD01AE21,QJ02AX01" "Antifungals for topical use" "Other antifungals for topical use" "5flc,fcu,flucyt,fluo,fluy" "alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucytosin,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine" 10 "g" 10 "g" "NA"
"FLC" 21319 "Flucloxacillin" "Beta-lactams/penicillins" "J01CF05,QJ01CF05,QJ51CF05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "clox,fluclo,flux" "bactopen,cloxacap,cloxacillinhydrate,cloxypen,floxacillin,floxacillinanhydrous,floxapen,floxapensalt,fluclomix,flucloxacilina,flucloxacilline,flucloxacillinum,flucloxin,fluorochloroxacillin,galfloxin,latocillin,orbeninhydrate,rimaflox,staphobristol,zoxin" 2 "g" 2 "g" "NA"
"FLU" 3365 "Fluconazole" "Antifungals/antimycotics" "D01AC15,J02AC01,QD01AC15,QJ02AC01" "Antimycotics for systemic use" "Triazole derivatives" "fluc,flucon,fluz,flz" "alflucoz,alkanazole,baten,biocanol,biozole,biozolene,canzol,cryptal,diflazon,diflucan,dimycon,elazor,flucazol,fluconazoli,fluconazolum,flucoral,flucostat,flukezol,flunazol,flunizol,fluzon,forcan,fuconal,fungata,loitin,mutum,oxifugol,pritenzol,syscan,trican,triconal,triflucan,zemyc,zoltec,zonal" 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,QD01AE21,QJ02AX01" "Antifungals for topical use" "Other antifungals for topical use" "5flc,fcu,flucyt,fluo,fluy" "alcobon,ancoban,ancobon,ancotil,ancotyl,flourocytosine,flucitosina,flucytosin,flucytosinum,flucytosone,fluocytosine,fluorcytosine,fluorocytosine" 10 "g" 10 "g" "NA"
"FLM" 3374 "Flumequine" "Quinolones" "J01MB07,QJ01MB07" "Quinolone antibacterials" "Other quinolones" "flumeq" "apurone,fantacin,flumequina,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl" 1.2 "g" "55675-3,55676-1,55677-9,55678-7"
"FLR1" 71260 "Flurithromycin" "Macrolides" "J01FA14,QJ01FA14" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar" 0.75 "g" "NA"
"FFL" 214356 "Fosfluconazole" "Antifungals" "NA" "NA" "fosfluconazol,procif,prodif" "NA"
"FOS" 446987 "Fosfomycin" "Phosphonics" "J01XX01,QJ01XX01,QS02AA17,S02AA17" "Other antibacterials" "Other antibacterials" "ff,fm,fo,fof,fos,fosf,fosfom,fosmyc" "fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina" 3 "g" 8 "g" "25596-8,25653-7,35809-3,35810-1"
"FMD" 572 "Fosmidomycin" "Other" "NA" "NA" "fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum" "NA"
"FLR1" 71260 "Flurithromycin" "Macrolides/lincosamides" "J01FA14,QJ01FA14" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar" 0.75 "g" "NA"
"FFL" 214356 "Fosfluconazole" "Antifungals/antimycotics" "NA" "NA" "fosfluconazol,procif,prodif" "NA"
"FOS" 446987 "Fosfomycin" "Other antibacterials" "J01XX01,QJ01XX01,QS02AA17,S02AA17" "Other antibacterials" "Other antibacterials" "ff,fm,fo,fof,fos,fosf,fosfom,fosmyc" "fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina" 3 "g" 8 "g" "25596-8,25653-7,35809-3,35810-1"
"FMD" 572 "Fosmidomycin" "Other antibacterials" "NA" "NA" "fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum" "NA"
"FRM" 8378 "Framycetin" "Aminoglycosides" "D09AA01,QD09AA01,QJ01GB91,QR01AX08,QS01AA07,R01AX08,S01AA07" "fram,framyc" "actilin,actiline,antibiotique,bycomycin,enterfram,fradiomycin,fradiomycinum,framicetina,framidal,framycetine,framycetinum,framycin,framygen,francetin,jernadex,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycine,neomycinum,nivemycin,soframycin,soframycine" "18926-6,257-6,258-4,259-2,260-0,55679-5"
"FUR" 6870646 "Furazidin" "Nitrofurans" "J01XE03,QJ01XE03" "Other antibacterials" "Nitrofuran derivatives" "NA" "akritoin,furagin,furaginum,furamag,furazidine,hydantoin" 0.3 "g" "NA"
"FRZ" 5323714 "Furazolidone" "Nitrofurans" "G01AX06,QG01AX06,QJ01XE90" "furazo" "bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furanzolidone,furaxon,furaxone,furazolidine,furazolidon,furazolidona,furazolidonum,furazolum,furidon,furmethoxadone,furovag,furoxal,furoxane,furoxon,furoxone,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofuradoxon,nitrofurazolidone,nitrofurazolidonum,nitrofuroxon,optazol,ortazol,puradin,roptazol,sclaventerol,tikofuran,topazone,trichofuron,tricofuron,tricoron,trifurox,viofuragyn" "69574-2,87794-4"
"FUS" 3000226 "Fusidic acid" "Fusidanes" "D06AX01,D09AA02,J01XC01,QD06AX01,QD09AA02,QJ01XC01,QS01AA13,S01AA13" "Other antibacterials" "Steroid antibacterials" "fa,fusaci,fusi" "flucidin,fucidate,fucidina,fucidine,fucithalmic,fusidate,fusidicacid,fusidin,fusidine,taksta" 1.5 "g" 1.5 "g" "NA"
"GAM" 59364992 "Gamithromycin" "Macrolides" "QJ01FA95" "NA" "zactran" "100054-6,88376-9,88378-5"
"GRN" 124093 "Garenoxacin" "Fluoroquinolones,Quinolones" "J01MA19,QJ01MA19" "gareno" "ganefloxacin,garenfloxacin" 0.4 "g" "35811-9,35812-7,35813-5"
"GAT" 5379 "Gatifloxacin" "Fluoroquinolones,Quinolones" "J01MA16,QJ01MA16,QS01AE06,S01AE06" "Quinolone antibacterials" "Fluoroquinolones" "gati,gatifl" "acorafloxacin,avarofloxacin,balofloxacin,balofox,bazucin,bilimin,bonoq,gaity,gatiflo,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,kinome,tequin,tymer,zymar,zymaxid,zymer" 0.4 "g" 0.4 "g" "31036-7,31038-3,31040-9,31042-5,41494-6"
"GEM" 9571107 "Gemifloxacin" "Fluoroquinolones,Quinolones" "J01MA15,QJ01MA15" "Quinolone antibacterials" "Fluoroquinolones" "gemifl" "factiv,gemifioxacin,gemifloxacine,gemifloxacino,gemifloxacinum" 0.32 "g" 0.2 "g" "35814-3,35815-0,35816-8,41697-4"
"FUR" 6870646 "Furazidin" "Other antibacterials" "J01XE03,QJ01XE03" "Other antibacterials" "Nitrofuran derivatives" "NA" "akritoin,furagin,furaginum,furamag,furazidine,hydantoin" 0.3 "g" "NA"
"FRZ" 5323714 "Furazolidone" "Other antibacterials" "G01AX06,QG01AX06,QJ01XE90" "furazo" "bifuron,corizium,coryzium,diafuron,enterotoxon,furall,furanzolidone,furaxon,furaxone,furazolidine,furazolidon,furazolidona,furazolidonum,furazolum,furidon,furmethoxadone,furovag,furoxal,furoxane,furoxon,furoxone,furozolidine,giardil,giarlam,medaron,neftin,nicolen,nifulidone,nifuran,nifurazolidone,nifurazolidonum,nitrofuradoxon,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,QD06AX01,QD09AA02,QJ01XC01,QS01AA13,S01AA13" "Other antibacterials" "Steroid antibacterials" "fa,fusaci,fusi" "flucidin,fucidate,fucidina,fucidine,fucithalmic,fusidate,fusidicacid,fusidin,fusidine,taksta" 1.5 "g" 1.5 "g" "NA"
"GAM" 59364992 "Gamithromycin" "Macrolides/lincosamides" "QJ01FA95" "NA" "zactran" "100054-6,88376-9,88378-5"
"GRN" 124093 "Garenoxacin" "Fluoroquinolones" "J01MA19,QJ01MA19" "gareno" "ganefloxacin,garenfloxacin" 0.4 "g" "35811-9,35812-7,35813-5"
"GAT" 5379 "Gatifloxacin" "Fluoroquinolones" "J01MA16,QJ01MA16,QS01AE06,S01AE06" "Quinolone antibacterials" "Fluoroquinolones" "gati,gatifl" "acorafloxacin,avarofloxacin,balofloxacin,balofox,bazucin,bilimin,bonoq,gaity,gatiflo,gatifloxacine,gatifloxcin,gatilox,gatiquin,gatispan,kinome,tequin,tymer,zymar,zymaxid,zymer" 0.4 "g" 0.4 "g" "31036-7,31038-3,31040-9,31042-5,41494-6"
"GEM" 9571107 "Gemifloxacin" "Fluoroquinolones" "J01MA15,QJ01MA15" "Quinolone antibacterials" "Fluoroquinolones" "gemifl" "factiv,gemifioxacin,gemifloxacine,gemifloxacino,gemifloxacinum" 0.32 "g" 0.2 "g" "35814-3,35815-0,35816-8,41697-4"
"GEN" 3467 "Gentamicin" "Aminoglycosides" "D06AX07,J01GB03,QA07AA91,QD06AX07,QG01AA91,QG51AA04,QJ01GB03,QJ51GB03,QS01AA11,QS02AA14,QS03AA06,S01AA11,S02AA14,S03AA06" "Aminoglycoside antibacterials" "Other aminoglycosides" "cn,ge1000,ge2000,gen,gen128,gen500,gent,genta1,gentam,gm" "centicin,cidomycin,garamicin,garamycin,gentacycol,gentamicina,gentamicine,gentamicins,gentamicinum,gentamycins,gentamycinum,gentocin,lyramycin,oksitselanim,septigen,septocin" 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" "NA" "18929-0,35817-6,7017-7,7018-5"
"GEP" 25101874 "Gepotidacin" "Other" "J01XX13,QJ01XX13" "NA" "gepotidacina,gepotidacine" "NA"
"GRX" 72474 "Grepafloxacin" "Fluoroquinolones,Quinolones" "J01MA11,QJ01MA11" "Quinolone antibacterials" "Fluoroquinolones" "grep,grepaf" "grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar" 0.4 "g" "21316-5,23638-0,23639-8,35818-4"
"GRI" 441140 "Griseofulvin" "Antifungals" "D01AA08,D01BA01,QD01AA08,QD01BA01" "NA" "amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spiro,spirofulvin,xuanjing" 0.5 "g" "12402-4,54200-1,54201-9,54202-7"
"GEP" 25101874 "Gepotidacin" "Other antibacterials" "J01XX13,QJ01XX13" "NA" "gepotidacina,gepotidacine" "NA"
"GRX" 72474 "Grepafloxacin" "Fluoroquinolones" "J01MA11,QJ01MA11" "Quinolone antibacterials" "Fluoroquinolones" "grep,grepaf" "grepafloxacine,grepafloxacino,lungaskin,raxar,vaxar" 0.4 "g" "21316-5,23638-0,23639-8,35818-4"
"GRI" 441140 "Griseofulvin" "Antifungals/antimycotics" "D01AA08,D01BA01,QD01AA08,QD01BA01" "NA" "amudane,delmofulvina,epigriseofulvin,fulcin,fulcine,fulvicin,fulvidex,fulvina,fulvinil,fulvistatin,fungivin,greosin,gresfeed,gricin,grifulin,grifulvin,grisactin,griscofulvin,grisefuline,griseo,griseofulviin,griseofulvina,griseofulvine,griseofulvinum,griseomix,griseostatin,grisetin,grisofulvin,grisovin,grisowen,grizeofulvin,grysio,guservin,lamoryl,likuden,likunden,murfulvin,poncyl,spiro,spirofulvin,xuanjing" 0.5 "g" "12402-4,54200-1,54201-9,54202-7"
"HAB" 175989 "Habekacin" "Aminoglycosides" "NA" "NA" "amikafur,amikan,amitrex,arikayce,biklin,biodacyn,chemacin,fabianol,habekacinxsulfate,likacin,pierami" "NA"
"HCH" 11979956 "Hachimycin" "Antifungals" "D01AA03,G01AA06,J02AA02,QD01AA03,QG01AA06,QJ02AA02" "Antimycotics for systemic use" "Antibiotics" "NA" "cabimicina,hachimicina,hachimycine,hachimycinum,trichomycinum,trichonat" "NA"
"HET" 443387 "Hetacillin" "Penicillins,Beta-lactams" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4"
"HCH" 11979956 "Hachimycin" "Antifungals/antimycotics" "D01AA03,G01AA06,J02AA02,QD01AA03,QG01AA06,QJ02AA02" "Antimycotics for systemic use" "Antibiotics" "NA" "cabimicina,hachimicina,hachimycine,hachimycinum,trichomycinum,trichonat" "NA"
"HET" 443387 "Hetacillin" "Beta-lactams/penicillins" "J01CA18,QJ01CA18" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "hetaci" "etacillina,hetacilina,hetacilline,hetacillinum,natacillin,phenazacillin,versapen,versatrex" 2 "g" "18931-6,274-1,275-8,276-6,277-4"
"HYG" 56928061 "Hygromycin" "Aminoglycosides" "NA" "NA" "antihelmycin,destomysin,hyanthelmix,hygromix,hygrovectine,hygrovetine" "NA"
"IBX" "Ibrexafungerp" "Antifungals" "J02AX07,QJ02AX07" "NA" "NA" "NA"
"ICL" 213043 "Iclaprim" "Trimethoprims" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1"
"IPM" 104838 "Imipenem" "Carbapenems,Beta-lactams" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,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,Beta-lactams" "NA" "NA" "NA" "35819-2,54170-6,54171-4,54172-2"
"IMR" "Imipenem/relebactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8"
"ISV" 6918485 "Isavuconazole" "Antifungals" "J02AC05,QJ02AC05" "isav" "benzonitrile,ravuconazole" 0.2 "g" 0.2 "g" "85381-2,88887-5"
"ICL" 213043 "Iclaprim" "Other antibacterials" "J01EA03,QJ01EA03" "iclapr" "iclaprime,mersarex" "73597-7,73619-9,73642-1"
"IPM" 104838 "Imipenem" "Carbapenems" "J01DH51,QJ01DH51" "Other beta-lactam antibacterials" "Carbapenems" "imci,imi,imip,imip32,imipen,imp" "imipemide,imipenemum,imipenen,primaxin,recarbrio,tienam,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" "NA" "NA" "35819-2,54170-6,54171-4,54172-2"
"IMR" "Imipenem/relebactam" "Carbapenems" "J01DH56,QJ01DH56" "NA" "NA" 2 "g" "85424-0,93232-7,96372-8"
"ISV" 6918485 "Isavuconazole" "Antifungals/antimycotics" "J02AC05,QJ02AC05" "isav" "benzonitrile,ravuconazole" 0.2 "g" 0.2 "g" "85381-2,88887-5"
"ISE" 3037209 "Isepamicin" "Aminoglycosides" "J01GB11,QJ01GB11" "Aminoglycoside antibacterials" "Other aminoglycosides" "isepam" "isepacin,isepalline,isepamicina,isepamicine,isepamicinsulphate,isepamicinum" 0.4 "g" "32381-6,35820-0,35821-8,55680-3"
"ISO" 3760 "Isoconazole" "Antifungals" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5"
"ISO" 3760 "Isoconazole" "Antifungals/antimycotics" "D01AC05,G01AF07,QD01AC05,QG01AF07" "Antimycotics for topic use" "Triazole derivatives" "NA" "isoconazol,isoconazolum,travogen" "55681-1,55682-9,55683-7,55684-5"
"INH" 3767 "Isoniazid" "Antimycobacterials" "J04AC01,QJ04AC01" "Drugs for treatment of tuberculosis" "Hydrazides" "inh,isonia" "abdizide,acetylisoniazide,andrazide,anidrasona,antimicina,antituberkulosum,armacide,armazid,armazide,atcotibine,azuren,cedin,cemidon,chemiazid,chemidon,continazine,cortinazine,cotinazin,cotinizin,defonin,dianicotyl,dibutin,diforin,dinacrin,dinocrin,ditubin,ebidene,eralon,ertuban,eutizon,evalon,fetefu,fimalene,hidranizil,hidrasonil,hidrulta,hidrun,hycozid,hydra,hydrazid,hyozid,hyzyd,idrazil,inizid,ipcazide,iscotin,isidrina,ismazide,isobicina,isocid,isocidene,isocotin,isohydrazide,isokin,isolyn,isonerit,isonex,isoniacid,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,mayambutol,mybasan,neoteben,neoxin,neumandin,nevin,niadrin,nicazide,nicetal,nicizina,niconyl,nicotibina,nicotibine,nicotisan,nicozide,nidaton,nidrazid,nikozid,niplen,nitadon,niteban,nitebannsc,nydrazid,nyscozid,pelazid,percin,phthisen,preparation,pycazide,pyreazid,pyricidin,pyridicin,pyrizidin,raumanon,razide,retozide,rifater,rimicid,rimifon,rimiphone,rimitsid,robiselin,robisellin,roxifen,sanohidrazina,sauterazid,sauterzid,stanozide,tebecid,tebenic,tebexin,tebilon,tebos,teebaconin,tekazin,tibazide,tibemid,tibiazide,tibinide,tibison,tibivis,tibizide,tibusan,tisin,tisiodrazida,tizide,tubazid,tubazide,tubeco,tubecotubercid,tuberian,tubicon,tubilysin,tubizid,tubomel,tyvid,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" "Trimethoprims,Sulfonamides,Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"ITR" 3793 "Itraconazole" "Antifungals" "J02AC02,QJ02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra,itraco" "candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin" 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" "J01FA07,QJ01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "josamy" "jomybel,josamicina,josamycine,josamycinum" 2 "g" "25597-6,25702-2,41698-2,41699-0"
"IST" "Isoniazid/sulfamethoxazole/trimethoprim/pyridoxine" "Antimycobacterials" "NA" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"ITR" 3793 "Itraconazole" "Antifungals/antimycotics" "J02AC02,QJ02AC02" "Antimycotics for systemic use" "Triazole derivatives" "itra,itraco" "candistat,canditral,cladosal,fungitraxx,intraconazole,itraconazol,itraconazolo,itraconazolum,itraconzaole,itrafungol,itralek,itrizole,lozanoc,onmel,sempera,sporamelt,sporanox,sporonox,traconal,triasporin" 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,QJ01FA07" "Macrolides, lincosamides and streptogramins" "Macrolides" "josamy" "jomybel,josamicina,josamycine,josamycinum" 2 "g" "25597-6,25702-2,41698-2,41699-0"
"KAN" 6032 "Kanamycin" "Aminoglycosides" "A07AA08,J01GB04,QA07AA08,QJ01GB04,QS01AA24,S01AA24" "Aminoglycoside antibacterials" "Other aminoglycosides" "hlk,k,kan,kana,kanamy,km" "kanamicina,kanamycine,kanamycins,kanamycinum,kantrex,klebcil" 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" "NA" "18936-5,7023-5,7024-3"
"KAC" "Kanamycin/cephalexin" "Aminoglycosides" "NA" "NA" "NA" "NA"
"KAS" 65174 "Kasugamycin" "Aminoglycosides" "NA" "NA" "kasumin,kasuminl" "NA"
"KET" 456201 "Ketoconazole" "Antifungals" "D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ketoco,ktc" "brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,tocris,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" "QJ01FA93" "leucomycin" "NA" "NA"
"LAS" 5360807 "Lasalocid" "Ionophores" "QP51BB02" "NA" "avatec,bovate,bovatec,lasalocide,lasalocido,lasalocidsalt,lasalocidum" "87598-9"
"LSC" 71528768 "Lascufloxacin" "Fluoroquinolones,Quinolones" "J01MA25,QJ01MA25" "Quinolone antibacterials" "Fluoroquinolones" "NA" "lasvic" 75 "mg" "NA"
"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.),Cephalosporins,Beta-lactams" "J01DD06,QJ01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "mox,moxa,moxalactam" "dilatamoxef,festamoxin,lamoxactam,latamoxefum,morrhuate,moxalactamsalt,moxam,shiomarin" 4 "g" "NA"
"LMU" 25185057 "Lefamulin" "Other" "J01XX12,QJ01XX12" "NA" "lefamulinacetate,xenleta" "85425-7,99281-8"
"LEN" 65646 "Lenampicillin" "Penicillins,Beta-lactams" "NA" "NA" "lenampicilina,lenampicilline,lenampicillinum,takacillin,valacillin,varacillin" "NA"
"LVX" 149096 "Levofloxacin" "Fluoroquinolones,Quinolones" "J01MA12,QJ01MA12,QS01AE05,S01AE05" "Quinolone antibacterials" "Fluoroquinolones" "le,lev,levo,levofl,lvx" "aeroquin,cravit,dextrofloxacin,dynaquin,elequine,iquix,levaquin,levofiexacin,levofloxacine,levofloxacino,levofloxacinum,loxof,ofloxcacin,oftaquix,quinsair,quixin,tavanic,unibiotic,venaxan" 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" "Fluoroquinolones,Quinolones" "J01RA05,QJ01RA05" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"LND" 9850038 "Levonadifloxacin" "Fluoroquinolones,Quinolones" "J01MA24,QJ01MA24" "NA" "NA" "NA"
"LSP" "Linco-spectin" "Other" "NA" "lincomycin/spectinomycin" "NA" "NA"
"LIN" 3000540 "Lincomycin" "Lincosamides" "J01FF02,QJ01FF02,QJ51FF02" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc,lincom" "albiotic,bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincogap,lincolcina,lincolnensin,lincomicina,lincomix,lincomycine,lincomycinum,lincomyocin,lincorex,linocin,mycivin" 1.8 "g" 1.8 "g" "18938-1,298-0,299-8,300-4,301-2,41700-6,87597-1"
"KET" 456201 "Ketoconazole" "Antifungals/antimycotics" "D01AC08,G01AF11,H02CA03,J02AB02,QD01AC08,QG01AF11,QH02CA03,QJ02AB02" "Antimycotics for systemic use" "Imidazole derivatives" "keto,ketoco,ktc" "brizoral,ethanone,extina,fungarest,fungoral,ketaconazole,ketocanazole,ketoconazol,ketoconazolum,ketodan,ketoderm,ketoisdin,ketozole,kuric,levoketoconazole,nizoral,normocort,panfungol,piperazine,recorlev,sebazole,teryzolin,terzolin,tocris,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" "NA" "NA"
"LAS" 5360807 "Lasalocid" "Other antibacterials" "QP51BB02" "NA" "avatec,bovate,bovatec,lasalocide,lasalocido,lasalocidsalt,lasalocidum" "87598-9"
"LSC" 71528768 "Lascufloxacin" "Fluoroquinolones" "J01MA25,QJ01MA25" "Quinolone antibacterials" "Fluoroquinolones" "NA" "lasvic" 75 "mg" "NA"
"LTM" 47499 "Latamoxef" "Cephalosporins (3rd gen.)" "J01DD06,QJ01DD06" "Other beta-lactam antibacterials" "Third-generation cephalosporins" "mox,moxa,moxalactam" "dilatamoxef,festamoxin,lamoxactam,latamoxefum,morrhuate,moxalactamsalt,moxam,shiomarin" 4 "g" "NA"
"LMU" 25185057 "Lefamulin" "Other antibacterials" "J01XX12,QJ01XX12" "NA" "lefamulinacetate,xenleta" "85425-7,99281-8"
"LEN" 65646 "Lenampicillin" "Beta-lactams/penicillins" "NA" "NA" "lenampicilina,lenampicilline,lenampicillinum,takacillin,valacillin,varacillin" "NA"
"LVX" 149096 "Levofloxacin" "Fluoroquinolones" "J01MA12,QJ01MA12,QS01AE05,S01AE05" "Quinolone antibacterials" "Fluoroquinolones" "le,lev,levo,levofl,lvx" "aeroquin,cravit,dextrofloxacin,dynaquin,elequine,iquix,levaquin,levofiexacin,levofloxacine,levofloxacino,levofloxacinum,loxof,ofloxcacin,oftaquix,quinsair,quixin,tavanic,unibiotic,venaxan" 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" "Fluoroquinolones" "J01RA05,QJ01RA05" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"LND" 9850038 "Levonadifloxacin" "Fluoroquinolones" "J01MA24,QJ01MA24" "NA" "NA" "NA"
"LSP" "Linco-spectin" "Other antibacterials" "NA" "lincomycin/spectinomycin" "NA" "NA"
"LIN" 3000540 "Lincomycin" "Macrolides/lincosamides" "J01FF02,QJ01FF02,QJ51FF02" "Macrolides, lincosamides and streptogramins" "Lincosamides" "linc,lincom" "albiotic,bactramycin,cillimycin,frademicina,jiemycin,lincocin,lincogap,lincolcina,lincolnensin,lincomicina,lincomix,lincomycine,lincomycinum,lincomyocin,lincorex,linocin,mycivin" 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,QJ01XX08" "Other antibacterials" "Other antibacterials" "line,linezo,lnz,lz,lzd" "desfluorolinezolid,linezoid,linezolidum,zivoxid,zyvox,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" "NA" "linflo" "NA" "NA"
"LOM" 3948 "Lomefloxacin" "Fluoroquinolones,Quinolones" "J01MA07,QJ01MA07,QS01AE04,S01AE04" "Quinolone antibacterials" "Fluoroquinolones" "lmf,lom,lome,lomefl" "bareon,logiflox,lomebact,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin,maxaquine,mazaquin,okacin,okacyn,uniquin" 0.4 "g" "18939-9,302-0,303-8,304-6,305-3,41701-4"
"LOR" 5284585 "Loracarbef" "Cephalosporins (2nd gen.),Cephalosporins,Beta-lactams" "J01DC08,QJ01DC08" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "lora,loraca" "carbac,lorabid,loracarbefum,lorafem,lorbef,loribid" 0.6 "g" "18940-7,306-1,307-9,308-7,309-5,7027-6"
"LFE" "Linoprist-flopristin" "Other antibacterials" "NA" "linflo" "NA" "NA"
"LOM" 3948 "Lomefloxacin" "Fluoroquinolones" "J01MA07,QJ01MA07,QS01AE04,S01AE04" "Quinolone antibacterials" "Fluoroquinolones" "lmf,lom,lome,lomefl" "bareon,logiflox,lomebact,lomefloxacine,lomefloxacino,lomefloxacinum,maxaquin,maxaquine,mazaquin,okacin,okacyn,uniquin" 0.4 "g" "18939-9,302-0,303-8,304-6,305-3,41701-4"
"LOR" 5284585 "Loracarbef" "Cephalosporins (2nd gen.)" "J01DC08,QJ01DC08" "Other beta-lactam antibacterials" "Second-generation cephalosporins" "lora,loraca" "carbac,lorabid,loracarbefum,lorafem,lorbef,loribid" 0.6 "g" "18940-7,306-1,307-9,308-7,309-5,7027-6"
"LYM" 54707177 "Lymecycline" "Tetracyclines" "J01AA04,QJ01AA04" "Tetracyclines" "Tetracyclines" "NA" "armyl,chlortetracyclin,ciclisin,ciclolysal,ciclolysine,eficiclina,infaciclina,limeciclina,lisinbiotic,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" "B05CA06,J01XX06,QB05CA06,QJ01XX06" "Other antibacterials" "Other antibacterials" "NA" "amygdalate,mandelsaeure,paramandelate,phenylglycolate,phenylhydroxyacetate,uromaline" 12 "g" "NA"
"MNA" 1292 "Mandelic acid" "Other antibacterials" "B05CA06,J01XX06,QB05CA06,QJ01XX06" "Other antibacterials" "Other antibacterials" "NA" "amygdalate,mandelsaeure,paramandelate,phenylglycolate,phenylhydroxyacetate,uromaline" 12 "g" "NA"
"MGX" "Manogepix" "Antifungals" "NA" "NA" "NA" "NA"
"MAR" 60651 "Marbofloxacin" "Fluoroquinolones,Quinolones" "QJ01MA93" "marbof" "marbocyl,marbofloxacine,marbofloxacino,marbofloxacinum,marboquin,zeniquin" "73596-9,73618-1,73641-3"
"MEC" 36273 "Mecillinam" "Penicillins,Beta-lactams" "J01CA11,QJ01CA11" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "amdinocillin,mecill" "amdinocillin,coactin,hexacillin,mecilinamo,mecillinamum,selexidin" 1.2 "g" "NA"
"MEL" 71306732 "Meleumycin" "Macrolides" "NA" "NA" "NA" "NA"
"MEM" 441130 "Meropenem" "Carbapenems,Beta-lactams" "J01DH02,QJ01DH02" "Other beta-lactam antibacterials" "Carbapenems" "mem,mer,mero,merope,mp,mrp" "meronem,meropen,meropenemum,merrem" 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,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" "NA"
"MEV" "Meropenem/vaborbactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "J01DH52,QJ01DH52" "Other beta-lactam antibacterials" "Carbapenems" "NA" "NA" 3 "g" "101222-8,101489-3,85427-3,88892-5,90980-4"
"MES" 176886 "Mesulfamide" "Other" "NA" "NA" "mesulfamida,mesulfamido,mesulfamidum" "NA"
"MAR" 60651 "Marbofloxacin" "Fluoroquinolones" "QJ01MA93" "marbof" "marbocyl,marbofloxacine,marbofloxacino,marbofloxacinum,marboquin,zeniquin" "73596-9,73618-1,73641-3"
"MEC" 36273 "Mecillinam" "Beta-lactams/penicillins" "J01CA11,QJ01CA11" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "amdinocillin,mecill" "amdinocillin,coactin,hexacillin,mecilinamo,mecillinamum,selexidin" 1.2 "g" "NA"
"MEL" 71306732 "Meleumycin" "Macrolides/lincosamides" "NA" "NA" "NA" "NA"
"MEM" 441130 "Meropenem" "Carbapenems" "J01DH02,QJ01DH02" "Other beta-lactam antibacterials" "Carbapenems" "mem,mer,mero,merope,mp,mrp" "meronem,meropen,meropenemum,merrem" 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" "NA" "NA" "NA"
"MEV" "Meropenem/vaborbactam" "Carbapenems" "J01DH52,QJ01DH52" "Other beta-lactam antibacterials" "Carbapenems" "NA" "NA" 3 "g" "101222-8,101489-3,85427-3,88892-5,90980-4"
"MES" 176886 "Mesulfamide" "Other antibacterials" "NA" "NA" "mesulfamida,mesulfamido,mesulfamidum" "NA"
"MTC" 54675785 "Metacycline" "Tetracyclines" "J01AA05,QJ01AA05" "Tetracyclines" "Tetracyclines" "methcy" "bialatan,metaciclina,metacyclinum,methacyclin,methacycline,methacyclinum,methylenecycline,physiomycine,rondomycin" 0.6 "g" "NA"
"MTM" 6713928 "Metampicillin" "Penicillins,Beta-lactams" "J01CA14,QJ01CA14" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "blomopen,bonopen,celinmicina,elatocilline,filorex,magnipen,metambac,metampen,metampicilina,metampicillina,metampicilline,metampicillinsalt,metampicillinum,micinovo,ocelina,pangocilin,probiotic,relyothenate,ruticina,rutizina,sedomycin,serfabiotic,suvipen,viderpen,viderpin,vioplex" 1.5 "g" 1.5 "g" "NA"
"MTH" 4101 "Methenamine" "Other" "J01XX05,QJ01XX05" "Other antibacterials" "Other antibacterials" "NA" "aminoform,aminoformaldehyde,ammoform,ammonioformaldehyde,antihydral,carin,cystamin,cystex,cystogen,duirexol,esametilentetramina,formamine,formin,grasselerator,heterin,hexaform,hexaloids,hexamethylamine,hexamethylenamine,hexamethyleneamine,hexamethylentetramin,hexamine,hexaminum,hexasan,hexilmethylenamine,metenamina,metenamine,methamin,methamine,methenamin,methenaminum,metramine,naphthamine,pellurin,resotropin,uramin,urasal,uratrine,urisol,uritone,urodeine,urotropin,urotropine,vesaloin,xametrin" 3 "g" "NA"
"MET" 6087 "Meticillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF03,QJ01CF03,QJ51CF03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "methic,meti" "belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin" 4 "g" "NA"
"MTP" 68590 "Metioprim" "Other" "NA" "NA" "methioprim,metioprima,metioprime,metioprimum" "NA"
"MXT" 3047729 "Metioxate" "Fluoroquinolones,Quinolones" "NA" "NA" "metioxato,metioxatum" "NA"
"MTR" 4173 "Metronidazole" "Other" "A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01" "Other antibacterials" "Imidazole derivatives" "metr,metron,mnz,mtz" "acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,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" "Ureidopenicillins,Penicillins,Beta-lactams" "J01CA10,QJ01CA10" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "mez,mezl,mezlo,mz" "baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,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" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "NA" "mezsul" "NA" "54194-6,54195-3,54196-1"
"MIF" 477468 "Micafungin" "Antifungals" "J02AX05,QJ02AX05" "Antimycotics for systemic use" "Other antimycotics for systemic use" "mica,micafu" "fungard,funguard,micafungina,micafunginsalt,mycamine" 0.1 "g" "53812-4,58418-5,65340-2,85048-7"
"MCZ" 4189 "Miconazole" "Antifungals" "A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,QA01AB09,QA07AC01,QD01AC02,QG01AF04,QJ02AB01,QS02AA13,S02AA13" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "aflorix,albistat,andergin,brentan,conofite,dactarin,florid,micantin,miconazol,miconazolo,miconazolum,micozole,minostate,monazole,monista,monistat,oravig,vusion,zimybase,zimycan" 0.2 "g" 1 "g" "17278-3,25607-3,25722-0,54180-5,55686-0"
"MTM" 6713928 "Metampicillin" "Beta-lactams/penicillins" "J01CA14,QJ01CA14" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "blomopen,bonopen,celinmicina,elatocilline,filorex,magnipen,metambac,metampen,metampicilina,metampicillina,metampicilline,metampicillinsalt,metampicillinum,micinovo,ocelina,pangocilin,probiotic,relyothenate,ruticina,rutizina,sedomycin,serfabiotic,suvipen,viderpen,viderpin,vioplex" 1.5 "g" 1.5 "g" "NA"
"MTH" 4101 "Methenamine" "Other antibacterials" "J01XX05,QJ01XX05" "Other antibacterials" "Other antibacterials" "NA" "aminoform,aminoformaldehyde,ammoform,ammonioformaldehyde,antihydral,carin,cystamin,cystex,cystogen,duirexol,esametilentetramina,formamine,formin,grasselerator,heterin,hexaform,hexaloids,hexamethylamine,hexamethylenamine,hexamethyleneamine,hexamethylentetramin,hexamine,hexaminum,hexasan,hexilmethylenamine,metenamina,metenamine,methamin,methamine,methenamin,methenaminum,metramine,naphthamine,pellurin,resotropin,uramin,urasal,uratrine,urisol,uritone,urodeine,urotropin,urotropine,vesaloin,xametrin" 3 "g" "NA"
"MET" 6087 "Meticillin" "Beta-lactams/penicillins" "J01CF03,QJ01CF03,QJ51CF03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "methic,meti" "belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin" 4 "g" "NA"
"MTP" 68590 "Metioprim" "Other antibacterials" "NA" "NA" "methioprim,metioprima,metioprime,metioprimum" "NA"
"MXT" 3047729 "Metioxate" "Fluoroquinolones" "NA" "NA" "metioxato,metioxatum" "NA"
"MTR" 4173 "Metronidazole" "Other antibacterials" "A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01" "Other antibacterials" "Imidazole derivatives" "metr,metron,mnz" "acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,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,QJ01CA10" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "mez,mezl,mezlo,mz" "baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,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" "mezsul" "NA" "54194-6,54195-3,54196-1"
"MIF" 477468 "Micafungin" "Antifungals/antimycotics" "J02AX05,QJ02AX05" "Antimycotics for systemic use" "Other antimycotics for systemic use" "mica,micafu" "fungard,funguard,micafungina,micafunginsalt,mycamine" 0.1 "g" "53812-4,58418-5,65340-2,85048-7"
"MCZ" 4189 "Miconazole" "Antifungals/antimycotics" "A01AB09,A07AC01,D01AC02,G01AF04,J02AB01,QA01AB09,QA07AC01,QD01AC02,QG01AF04,QJ02AB01,QS02AA13,S02AA13" "Antimycotics for systemic use" "Imidazole derivatives" "mico" "aflorix,albistat,andergin,brentan,conofite,dactarin,florid,micantin,miconazol,miconazolo,miconazolum,micozole,minostate,monazole,monista,monistat,oravig,vusion,zimybase,zimycan" 0.2 "g" 1 "g" "17278-3,25607-3,25722-0,54180-5,55686-0"
"MCR" 3037206 "Micronomicin" "Aminoglycosides" "QS01AA22,S01AA22" "micron" "micromicin,micromycin,micronomicina,micronomicine,micronomicinum,sagamicin,santemycin" "NA"
"MID" 5282169 "Midecamycin" "Macrolides" "J01FA03,QJ01FA03" "Macrolides, lincosamides and streptogramins" "Macrolides" "mideka" "macropen,madecacine,medemycin,midecamicina,midecamycine,midecamycinum,midecin,momicine,myoxam,normicina,rubimycin" 1.2 "g" 1 "g" "NA"
"MIL" 37614 "Miloxacin" "Fluoroquinolones,Quinolones" "NA" "amiflo" "miloxacine,miloxacino,miloxacinum" "NA"
"MID" 5282169 "Midecamycin" "Macrolides/lincosamides" "J01FA03,QJ01FA03" "Macrolides, lincosamides and streptogramins" "Macrolides" "mideka" "macropen,madecacine,medemycin,midecamicina,midecamycine,midecamycinum,midecin,momicine,myoxam,normicina,rubimycin" 1.2 "g" 1 "g" "NA"
"MIL" 37614 "Miloxacin" "Fluoroquinolones" "NA" "amiflo" "miloxacine,miloxacino,miloxacinum" "NA"
"MNO" 54675783 "Minocycline" "Tetracyclines" "A01AB23,D10AF07,J01AA08,QA01AB23,QD10AF07,QJ01AA08" "Tetracyclines" "Tetracyclines" "mc,mh,mi,min,mino,minocy,mn,mno" "acnez,arestin,borymycin,dynacin,lederderm,minociclina,minocin,minocline,minocyclin,minocyclinum,minocyn,minomax,minomycin,mynocine,periocline,solodyn,vectrin,ximino" 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" "J01FA11,QJ01FA11" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "acecamycin,macroral,miocamen,miocamycine,miokamycin,mosil,myocamicin,ponsinomycin" 1.2 "g" "18949-8,338-4,339-2,340-0,341-8,55687-8"
"MON" 23667299 "Monensin sodium" "Ionophores" "NA" "NA" "coban,elancoban,monelan,monensin,monensina,monensine,monensinum,monovet,romensin,rumensin" "NA"
"MCM" 5282188 "Miocamycin" "Macrolides/lincosamides" "J01FA11,QJ01FA11" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "acecamycin,macroral,miocamen,miocamycine,miokamycin,mosil,myocamicin,ponsinomycin" 1.2 "g" "18949-8,338-4,339-2,340-0,341-8,55687-8"
"MON" 23667299 "Monensin sodium" "Other antibacterials" "NA" "NA" "coban,elancoban,monelan,monensin,monensina,monensine,monensinum,monovet,romensin,rumensin" "NA"
"MRN" 70374 "Morinamide" "Antimycobacterials" "J04AK04,QJ04AK04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "morfazinamide,morfazinammide,morfgazinamide,morinamida,morinamidum,morphazinamid,morphazinamide,piazofolina,piazolin,piazolina" "NA"
"MFX" 152946 "Moxifloxacin" "Fluoroquinolones,Quinolones" "J01MA14,QJ01MA14,QS01AE07,S01AE07" "Quinolone antibacterials" "Fluoroquinolones" "mox,moxi,moxifl,mxf" "actira,actura,avalox,avelox,avolex,izilox,moxeza,moxifloxacine,moxifloxacino,octegra,vegamox,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" "D06AX09,QD06AX09,QR01AX06,R01AX06" "mup,mupi,mupiro" "bactoderm,bactroban,centany,mupirocina,mupirocine,mupirocinum,plasimine,turixin" "20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
"NAC" 73386748 "Nacubactam" "Beta-lactamase inhibitors" "NA" "NA" "NA" "NA"
"NAD" 4410 "Nadifloxacin" "Fluoroquinolones,Quinolones" "D10AF05,QD10AF05" "NA" "acuatim,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin" "NA"
"NAF" 8982 "Nafcillin" "Penicillins,Beta-lactams" "J01CF06,QJ01CF06" "nafcil" "nafcil,nafcilin,nafcilina,nafcillinanhydrous,nafcilline,nafcillinhydrate,nafcillinmonohydrate,nafcillinsalt,nafcillinum,naftopen,nallpen,naphcillin,naphthicillin,unipen" 3 "g" "10993-4,18951-4,25232-0,346-7,347-5,348-3,349-1,41704-8"
"ZWK" 117587595 "Nafithromycin" "Macrolides" "NA" "NA" "NA" "NA"
"MFX" 152946 "Moxifloxacin" "Fluoroquinolones" "J01MA14,QJ01MA14,QS01AE07,S01AE07" "Quinolone antibacterials" "Fluoroquinolones" "mox,moxi,moxifl,mxf" "actira,actura,avalox,avelox,avolex,izilox,moxeza,moxifloxacine,moxifloxacino,octegra,vegamox,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,QD06AX09,QR01AX06,R01AX06" "mup,mupi,mupiro" "bactoderm,bactroban,centany,mupirocina,mupirocine,mupirocinum,plasimine,turixin" "20389-3,35822-6,35823-4,60542-8,60543-6,7033-4"
"NAC" 73386748 "Nacubactam" "Beta-lactams/penicillins" "NA" "NA" "NA" "NA"
"NAD" 4410 "Nadifloxacin" "Fluoroquinolones" "D10AF05,QD10AF05" "NA" "acuatim,nadifloxacine,nadifloxacino,nadifloxacinum,nadixa,nadoxin" "NA"
"NAF" 8982 "Nafcillin" "Beta-lactams/penicillins" "J01CF06,QJ01CF06" "nafcil" "nafcil,nafcilin,nafcilina,nafcillinanhydrous,nafcilline,nafcillinhydrate,nafcillinmonohydrate,nafcillinsalt,nafcillinum,naftopen,nallpen,naphcillin,naphthicillin,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" "NA" "NA" "NA"
"NAL" 4421 "Nalidixic acid" "Quinolones" "J01MB02,QJ01MB02" "Quinolone antibacterials" "Other quinolones" "na,nal,nalac,nali" "amfonelinsaeure,baktogram,betaxina,chemiurin,cybis,dixiben,dixilina,dixinal,eucisten,eucistin,innoxalomn,innoxalon,jicsron,kusnarin,nalidicron,nalidixan,nalidixane,nalidixate,nalidixateanhydrous,nalidixic,nalidixin,nalidixinsaure,nalitucsan,nalix,nalurin,narigix,naxuril,negram,nevigramon,nicelate,nogram,poleon,sicmylon,specifen,specifin,unaserus,uralgin,uriben,uriclar,urisal,urodixin,uroman,uroneg,uronidix,uropan,wintomylon,wintron" 4 "g" "NA"
"NAL-S" "Nalidixic acid screening test" "Quinolones" "NA" "nal screen" "NA" "NA"
"NAR" 65452 "Narasin" "Ionophores" "QP51BB04" "narasi" "monteban,narasine,narasino,narasinum,skycis" "87570-8"
"NEM" 11993740 "Nemonoxacin" "Fluoroquinolones,Quinolones" "J01MB08,QJ01MB08" "Quinolone antibacterials" "Other quinolones" "NA" "NA" "NA"
"NEO" "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom,neomyc" "NA" 5 "g" 1 "g" "10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
"NAR" 65452 "Narasin" "Other antibacterials" "QP51BB04" "narasi" "monteban,narasine,narasino,narasinum,skycis" "87570-8"
"NEM" 11993740 "Nemonoxacin" "Fluoroquinolones" "J01MB08,QJ01MB08" "Quinolone antibacterials" "Other quinolones" "NA" "NA" "NA"
"NEO" 8378 "Neomycin" "Aminoglycosides" "A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01" "Aminoglycoside antibacterials" "Other aminoglycosides" "neom,neomyc" "NA" 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,QJ01GB07,QS01AA23,S01AA23" "Aminoglycoside antibacterials" "Other aminoglycosides" "neti,netilm" "netillin,netilmicina,netilmicine,netilmicinum,netilyn,netira,netromicine,netromycin,nettacin,ntromicine,ntromycin,vectacin,zetamicin" 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" "NA" "NA" "nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin" "NA"
"NIF" 71946 "Nifuroquine" "Fluoroquinolones,Quinolones" "NA" "NA" "abimasten,nifuroquina,nifuroquinum,quinaldofur" "NA"
"NFR" 9571062 "Nifurtoinol" "Nitrofurans" "J01XE02,QJ01XE02" "Other antibacterials" "Nitrofuran derivatives" "NA" "levantin,nifurmazol,nifurmazole,nifurmazolo,nifurmazolum,nifurtoinolo,nifurtoinolum,urfadin,urfadine,urfadyn" 0.16 "g" "NA"
"NTZ" 41684 "Nitazoxanide" "Other" "P01AX11" "NA" "alinia,benzamide,colufase,cryptaz,daxon,dexidex,heliton,kidonax,nitax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanidum,nitrazoxanide,pacovanton,paramix,phavic" 1 "g" "73595-1,73617-3,73640-5"
"NIT" 6604200 "Nitrofurantoin" "Nitrofurans" "J01XE01,QJ01XE01" "Other antibacterials" "Nitrofuran derivatives" "f,f/m,fd,ft,ni,nit,nit16,nitr,nitro" "alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fuamed,furabid,furachel,furadantin,furadantine,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furalan,furaloid,furantoina,furatoin,furedan,furina,furobactina,furodantin,gerofuran,ituran,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifuraden,nifuradene,nifuradeno,nifuradenum,nifuradine,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,oxafuradene,oxafurandene,oxifuradene,oxyfuradene,parfuran,phenurin,renafur,siraliden,trantoin,uerineks,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" "Nitrofurans" "NA" "nitfur" "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,furazyme,furesol,furosem,fuvacillin,hemofuran,hydrazinecarboxamide,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nefco,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,rivopon,sanfuran,semioxamazide,vabrocid,vadrocid,yatrocin" "20388-5,87793-6"
"NTR" 19910 "Nitroxoline" "Fluoroquinolones,Quinolones" "J01XX07,QJ01XX07" "Other antibacterials" "Other antibacterials" "NA" "galinok,isinok,nibiol,nicene,nitroxlina,nitroxolin,nitroxolina,nitroxolinum,noxibiol,noxin" 1 "g" "25608-1,25723-8,32382-4,54181-3,55688-6"
"NOR" 4539 "Norfloxacin" "Fluoroquinolones,Quinolones" "J01MA06,QJ01MA06,QS01AE02,S01AE02" "Quinolone antibacterials" "Fluoroquinolones" "nor,norf,norflo,nx,nxn" "baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,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"
"NOR-S" "Norfloxacin screening test" "Fluoroquinolones,Quinolones" "NA" "nor screen" "NA" "NA"
"NME" "Norfloxacin/metronidazole" "Fluoroquinolones,Quinolones" "J01RA14,QJ01RA14" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"NTI" "Norfloxacin/tinidazole" "Fluoroquinolones,Quinolones" "J01RA13,QJ01RA13" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"NVA" 10419027 "Norvancomycin" "Glycopeptides,Peptides" "NA" "NA" "NA" "NA"
"NOV" 54675769 "Novobiocin" "Aminocoumarins" "QJ01XX95" "novo,novobi" "albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
"NYS" 6433272 "Nystatin" "Ionophores,Antifungals" "A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01" "nyst,nystan" "biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex" 1.5 "MU" "10697-1,10698-9,18958-9,35824-2,55689-4"
"OFX" 4583 "Ofloxacin" "Fluoroquinolones,Quinolones" "J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16" "Quinolone antibacterials" "Fluoroquinolones" "of,ofl,oflo,ofloxa,ofx" "exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,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" "Fluoroquinolones,Quinolones" "J01RA09,QJ01RA09" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"OLE" 72493 "Oleandomycin" "Macrolides" "J01FA05,QJ01FA05" "Macrolides, lincosamides and streptogramins" "Macrolides" "oleand" "amimycin,landomycin,matromycin,oleandomicina,oleandomycine,oleandomycinum,romicil" 1 "g" "18960-5,378-0,379-8,380-6,381-4,55690-2"
"NIC" 9507 "Nicarbazin" "Other antibacterials" "NA" "NA" "nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin" "NA"
"NIF" 71946 "Nifuroquine" "Fluoroquinolones" "NA" "NA" "abimasten,nifuroquina,nifuroquinum,quinaldofur" "NA"
"NFR" 9571062 "Nifurtoinol" "Other antibacterials" "J01XE02,QJ01XE02" "Other antibacterials" "Nitrofuran derivatives" "NA" "levantin,nifurmazol,nifurmazole,nifurmazolo,nifurmazolum,nifurtoinolo,nifurtoinolum,urfadin,urfadine,urfadyn" 0.16 "g" "NA"
"NTZ" 41684 "Nitazoxanide" "Other antibacterials" "P01AX11" "NA" "alinia,benzamide,colufase,cryptaz,daxon,dexidex,heliton,kidonax,nitax,nitaxozanid,nitaxozanide,nitazox,nitazoxamide,nitazoxanid,nitazoxanida,nitazoxanidum,nitrazoxanide,pacovanton,paramix,phavic" 1 "g" "73595-1,73617-3,73640-5"
"NIT" 6604200 "Nitrofurantoin" "Other antibacterials" "J01XE01,QJ01XE01" "Other antibacterials" "Nitrofuran derivatives" "f,f/m,fd,ft,ni,nit,nit16,nitr,nitro" "alfuran,benkfuran,berkfuran,berkfurin,ceduran,chemiofuran,cistofuran,cyantin,cystit,dantafur,fuamed,furabid,furachel,furadantin,furadantine,furadantoin,furadoin,furadoine,furadonin,furadonine,furadoninum,furadontin,furalan,furaloid,furantoina,furatoin,furedan,furina,furobactina,furodantin,gerofuran,ituran,macpac,macrobid,macrodantin,macrodantina,macrofuran,macrofurin,nierofu,nifuraden,nifuradene,nifuradeno,nifuradenum,nifuradine,nifurantin,nifuretten,nitoin,nitrex,nitrofuradantin,nitrofurantoina,nitrofurantoine,nitrofurantoinum,novofuran,orafuran,oxafuradene,oxafurandene,oxifuradene,oxyfuradene,parfuran,phenurin,renafur,siraliden,trantoin,uerineks,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" "nitfur" "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,furazyme,furesol,furosem,fuvacillin,hemofuran,hydrazinecarboxamide,ibiofural,mammex,mastofuran,monafuracin,monafuracis,monofuracin,nefco,nifucin,nifurid,nifuzon,nitrofural,nitrofuralum,nitrofuran,nitrofurane,nitrofurazan,nitrofurazonum,nitrofurol,nitrozone,otofural,otofuran,rivafurazon,rivopon,sanfuran,semioxamazide,vabrocid,vadrocid,yatrocin" "20388-5,87793-6"
"NTR" 19910 "Nitroxoline" "Fluoroquinolones" "J01XX07,QJ01XX07" "Other antibacterials" "Other antibacterials" "NA" "galinok,isinok,nibiol,nicene,nitroxlina,nitroxolin,nitroxolina,nitroxolinum,noxibiol,noxin" 1 "g" "25608-1,25723-8,32382-4,54181-3,55688-6"
"NOR" 4539 "Norfloxacin" "Fluoroquinolones" "J01MA06,QJ01MA06,QS01AE02,S01AE02" "Quinolone antibacterials" "Fluoroquinolones" "nor,norf,norflo,nx,nxn" "baccidal,barazan,chibroxin,chibroxine,chibroxol,fulgram,gonorcin,lexinor,nolicin,noracin,noraxin,norflo,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"
"NOR-S" "Norfloxacin screening test" "Fluoroquinolones" "NA" "nor screen" "NA" "NA"
"NME" "Norfloxacin/metronidazole" "Fluoroquinolones" "J01RA14,QJ01RA14" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"NTI" "Norfloxacin/tinidazole" "Fluoroquinolones" "J01RA13,QJ01RA13" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"NVA" 10419027 "Norvancomycin" "Glycopeptides" "NA" "NA" "NA" "NA"
"NOV" 54675769 "Novobiocin" "Other antibacterials" "QJ01XX95" "novo,novobi" "albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin" "17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
"NYS" 6433272 "Nystatin" "Antifungals/antimycotics" "A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01" "nyst,nystan" "biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex" 1.5 "MU" "10697-1,10698-9,18958-9,35824-2,55689-4"
"OFX" 4583 "Ofloxacin" "Fluoroquinolones" "J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16" "Quinolone antibacterials" "Fluoroquinolones" "of,ofl,oflo,ofloxa,ofx" "exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,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" "Fluoroquinolones" "J01RA09,QJ01RA09" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"OLE" 72493 "Oleandomycin" "Macrolides/lincosamides" "J01FA05,QJ01FA05" "Macrolides, lincosamides and streptogramins" "Macrolides" "oleand" "amimycin,landomycin,matromycin,oleandomicina,oleandomycine,oleandomycinum,romicil" 1 "g" "18960-5,378-0,379-8,380-6,381-4,55690-2"
"OMC" 54697325 "Omadacycline" "Tetracyclines" "J01AA15,QJ01AA15" "NA" "amadacycline" 0.3 "g" 0.1 "g" "73594-4,73616-5,73639-7"
"OPT" 87880 "Optochin" "Other" "NA" "NA" "aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin" "100055-3,73665-2"
"ORB" 60605 "Orbifloxacin" "Fluoroquinolones,Quinolones" "QJ01MA95" "orbifl" "orbax" "35825-9,35826-7,35827-5"
"ORI" 16136912 "Oritavancin" "Lipoglycopeptides,Glycopeptides,Peptides" "J01XA05,QJ01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit,oritav" "NA" "41707-1,41708-9,41709-7,41736-0"
"ORS" "Ormetroprim/sulfamethoxazole" "Trimethoprims,Sulfonamides" "NA" "NA" "NA" "73593-6,73615-7,73638-9"
"ORN" 28061 "Ornidazole" "Other" "G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03" "Other antibacterials" "Imidazole derivatives" "NA" "levornidazole,madelen,ornidal,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4"
"OST" 11136668 "Ostreogrycin" "Streptogramins" "NA" "NA" "eskamicin,linopristin,stephylomycin" "NA"
"OTE" 77050711 "Oteseconazole" "Antifungals" "J02AC06,QJ02AC06" "Antimycotics for systemic use" "Triazole derivatives" "NA" "quilseconazole,vivijoa" 21 "mg" "NA"
"OXA" 6196 "Oxacillin" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "J01CF04,QJ01CF04,QJ51CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxacil,oxal,oxs" "bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
"OXA-S" "Oxacillin screening test" "Isoxazolylpenicillins,Penicillins,Beta-lactams" "NA" "oxa screen" "NA" "NA"
"OPT" 87880 "Optochin" "Other antibacterials" "NA" "NA" "aflukin,auriquin,biquinate,chinidin,chinidine,chinimetten,chinin,chinine,conchinin,conchinine,conquinine,dentojel,dihydrochinidin,dihydroquinidine,dihydroquinine,hydroconchinine,hydroconquinine,hydroquinidine,kinidin,numoquin,optochine,optoquine,pitayine,qualaquin,quinaglute,quinicardine,quinidex,quinidine,quiniduran,quinindine,quinine,quinineanhydrous,quinora,quinsan,rezquin" "100055-3,73665-2"
"ORB" 60605 "Orbifloxacin" "Fluoroquinolones" "QJ01MA95" "orbifl" "orbax" "35825-9,35826-7,35827-5"
"ORI" 16136912 "Oritavancin" "Glycopeptides" "J01XA05,QJ01XA05" "Other antibacterials" "Glycopeptide antibacterials" "orit,oritav" "NA" "41707-1,41708-9,41709-7,41736-0"
"ORS" "Ormetroprim/sulfamethoxazole" "Other antibacterials" "NA" "NA" "NA" "73593-6,73615-7,73638-9"
"ORN" 28061 "Ornidazole" "Other antibacterials" "G01AF06,J01XD03,P01AB03,QG01AF06,QJ01XD03,QP51AA03" "Other antibacterials" "Imidazole derivatives" "NA" "levornidazole,madelen,ornidal,ornidazolum,tiberal" 1.5 "g" 1 "g" "55691-0,55692-8,55693-6,55694-4"
"OTE" 77050711 "Oteseconazole" "Antifungals/antimycotics" "J02AC06,QJ02AC06" "Antimycotics for systemic use" "Triazole derivatives" "NA" "quilseconazole,vivijoa" 21 "mg" "NA"
"OXA" 6196 "Oxacillin" "Beta-lactams/penicillins" "J01CF04,QJ01CF04,QJ51CF04" "Beta-lactam antibacterials, penicillins" "Beta-lactamase resistant penicillins" "ox,oxa,oxac,oxacil,oxal,oxs" "bactocill,bristopen,cryptocillin,micropenin,ossacillina,oxabel,oxabelsalt,oxacilina,oxacillinanhydrous,oxacilline,oxacillinhydrate,oxacillinsalt,oxacillinum,oxazocillin,oxazocilline,penstapho,prostaphlin,prostaphlyn,resistopen,stapenor" 2 "g" 2 "g" "18961-3,25265-0,382-2,383-0,384-8,385-5,3882-8,7039-1"
"OXA-S" "Oxacillin screening test" "Beta-lactams/penicillins" "NA" "oxa screen" "NA" "NA"
"OXO" 4628 "Oxolinic acid" "Quinolones" "J01MB05,QJ01MB05" "Quinolone antibacterials" "Other quinolones" "oxoaci" "aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid" 1 "g" "NA"
"OXY" 54675779 "Oxytetracycline" "Tetracyclines" "A01AB25,D06AA03,G01AA07,J01AA06,QA01AB25,QD06AA03,QG01AA07,QG51AA01,QJ01AA06,QJ51AA06,QS01AA04,S01AA04" "Tetracyclines" "Tetracyclines" "oxytet" "achromycin,actisite,adamycin,artomycin,berkmycen,biostat,bristacycline,cancycline,cyclopar,dabicycline,diacycine,dumocyclin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hostacycline,hydroxytetracyclinum,lenocycline,macocyn,medamycin,mephacyclin,nitox,oksisyklin,ossitetraciclina,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxymycin,oxypam,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracyclinum,paltet,partrex,pennox,piracaps,proteroxyna,qidtet,quadracycline,quatrex,remicyclin,retet,ricycline,riomitsin,ryomycin,solkaciclina,stevacin,stilciclina,subamycin,sumycin,supramycin,sustamycin,tarocyn,tarosin,tefilin,teline,telotrex,teravit,terrafungine,terramitsin,terramycine,tetrabakat,tetrabid,tetrablet,tetracaps,tetracompren,tetrakap,tetralution,tetramavan,tetramed,tetran,tetrosol,topicycline,triphacyclin,unicin,ursocyclin,ursocycline,vetquamycin" 1 "g" 1 "g" "17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
"OZN" "Ozenoxacin" "Quinolones" "D06AX14,QD06AX14" "NA" "NA" "NA"
"PAS" "P-aminosalicylic acid" "Antimycobacterials" "NA" "pasraa" "NA" "NA"
"PAN" 72015 "Panipenem" "Carbapenems,Beta-lactams" "NA" "NA" "carbenin,panipenemum,penipanem" "100056-1,53823-1"
"PAR" 165580 "Paromomycin" "Other" "A07AA06,QA07AA06,QJ01GB92" "NA" "aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum" 3 "g" "51719-3,53824-9,55700-9,55701-7,55702-5"
"PAZ" 65957 "Pazufloxacin" "Fluoroquinolones,Quinolones" "J01MA18,QJ01MA18" "Quinolone antibacterials" "Fluoroquinolones" "NA" "pazufloxacine,pazufloxacino,pazufloxacinum" 1 "g" "NA"
"PEF" 51081 "Pefloxacin" "Fluoroquinolones,Quinolones" "J01MA03,QJ01MA03" "Quinolone antibacterials" "Fluoroquinolones" "pefl,perflo" "labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox" 0.8 "g" 0.8 "g" "18963-9,35828-3,390-5,3906-5,7040-9"
"PEF-S" "Pefloxacin screening test" "Fluoroquinolones,Quinolones" "NA" "pef screen" "NA" "NA"
"PNM" 10250769 "Penamecillin" "Penicillins,Beta-lactams" "J01CE06,QJ01CE06" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum" 1.05 "g" "NA"
"PNO" "Penicillin/novobiocin" "Penicillins,Beta-lactams,Aminocoumarins" "NA" "pennov" "NA" "35872-1,35873-9,35874-7"
"PSU" "Penicillin/sulbactam" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" "NA"
"OZN" "Ozenoxacin" "D06AX14,QD06AX14" "NA" "NA" "NA"
"PAS" 4649 "P-aminosalicylic acid" "Antimycobacterials" "NA" "pasraa" "NA" "NA"
"PAN" 72015 "Panipenem" "Carbapenems" "NA" "NA" "carbenin,panipenemum,penipanem" "100056-1,53823-1"
"PAR" 165580 "Paromomycin" "Other antibacterials" "A07AA06,QA07AA06,QJ01GB92" "NA" "aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum" 3 "g" "51719-3,53824-9,55700-9,55701-7,55702-5"
"PAZ" 65957 "Pazufloxacin" "Fluoroquinolones" "J01MA18,QJ01MA18" "Quinolone antibacterials" "Fluoroquinolones" "NA" "pazufloxacine,pazufloxacino,pazufloxacinum" 1 "g" "NA"
"PEF" 51081 "Pefloxacin" "Fluoroquinolones" "J01MA03,QJ01MA03" "Quinolone antibacterials" "Fluoroquinolones" "pefl,perflo" "labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox" 0.8 "g" 0.8 "g" "18963-9,35828-3,390-5,3906-5,7040-9"
"PEF-S" "Pefloxacin screening test" "Fluoroquinolones" "NA" "pef screen" "NA" "NA"
"PNM" 10250769 "Penamecillin" "Beta-lactams/penicillins" "J01CE06,QJ01CE06" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum" 1.05 "g" "NA"
"PNO" "Penicillin/novobiocin" "Beta-lactams/penicillins" "NA" "pennov" "NA" "35872-1,35873-9,35874-7"
"PSU" "Penicillin/sulbactam" "Beta-lactams/penicillins" "NA" "NA" "NA" "NA"
"PNM1" 54686187 "Penimepicycline" "Tetracyclines" "J01AA10,QJ01AA10" "Tetracyclines" "Tetracyclines" "NA" "criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum" "NA"
"PIM" 65453 "Pentisomicin" "Aminoglycosides" "NA" "NA" "mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum" "NA"
"PTZ" 55250256 "Pentizidone" "Other" "NA" "NA" "pentizidona,pentizidonum" "NA"
"PEX" 16132253 "Pexiganan" "Other" "NA" "NA" "cytolex,mangainin" "NA"
"PHE" 272833 "Pheneticillin" "Penicillins,Beta-lactams" "J01CE05,QJ01CE05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "fene" "alfacillin,alticina,antibiocin,arcacil,arcasin,astracillin,bendralan,beromycin,brocsil,broxil,chemipen,cliacil,darcil,feneticilina,feneticillin,feneticillina,feneticilline,fenocin,icipen,isocillin,ispenoral,kavepenin,maxipen,optipen,oralopen,orapen,ospeneff,pedipen,penagen,pencompren,penemve,peniplus,penova,pensig,penvikal,phenethicilin,phenethicillin,phenethicillinum,pheneticilline,pheneticillinum,primcillin,priospen,roscopenin,semopen,suspen,synapen,syncillin,synerpenin,synthecillin,synthecilline,synthepen,triospen,vamosyn,veetids,vepen" 1 "g" "NA"
"PHN" 6869 "Phenoxymethylpenicillin" "Penicillins,Beta-lactams" "J01CE02,QJ01CE02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "fepe,peni v,penicillin v,phepen,pnv,pv" "apopen,calcipen,fenacilin,fenospen,meropenin,oracillin,oracilline,oratren,orocillin,ospen,phenocillin,phenomycilline,phenopenicillin,rocilin,stabicillin,vebecillin" 2 "g" "NA"
"PMR" 5284447 "Pimaricin" "Antifungals" "NA" "natamycin" "delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin" "NA"
"PTZ" 55250256 "Pentizidone" "Other antibacterials" "NA" "NA" "pentizidona,pentizidonum" "NA"
"PEX" 16132253 "Pexiganan" "Other antibacterials" "NA" "NA" "cytolex,mangainin" "NA"
"PHE" 272833 "Pheneticillin" "Beta-lactams/penicillins" "J01CE05,QJ01CE05" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "fene" "alfacillin,alticina,antibiocin,arcacil,arcasin,astracillin,bendralan,beromycin,brocsil,broxil,chemipen,cliacil,darcil,feneticilina,feneticillin,feneticillina,feneticilline,fenocin,icipen,isocillin,ispenoral,kavepenin,maxipen,optipen,oralopen,orapen,ospeneff,pedipen,penagen,pencompren,penemve,peniplus,penova,pensig,penvikal,phenethicilin,phenethicillin,phenethicillinum,pheneticilline,pheneticillinum,primcillin,priospen,roscopenin,semopen,suspen,synapen,syncillin,synerpenin,synthecillin,synthecilline,synthepen,triospen,vamosyn,veetids,vepen" 1 "g" "NA"
"PHN" 6869 "Phenoxymethylpenicillin" "Beta-lactams/penicillins" "J01CE02,QJ01CE02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "fepe,peni v,penicillin v,phepen,pnv,pv" "apopen,calcipen,fenacilin,fenospen,meropenin,oracillin,oracilline,oratren,orocillin,ospen,phenocillin,phenomycilline,phenopenicillin,rocilin,stabicillin,vebecillin" 2 "g" "NA"
"PMR" 5284447 "Pimaricin" "Antifungals/antimycotics" "NA" "natamycin" "delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin" "NA"
"PPA" 4831 "Pipemidic acid" "Quinolones" "J01MB04,QJ01MB04" "Quinolone antibacterials" "Other quinolones" "pipaci,pipz,pizu" "deblaston,dolcol,filtrax,karunomazin,memento,nuril,palin,pipedac,pipemid,pipemidate,pipemidic,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval" 0.8 "g" "NA"
"PIP" 43672 "Piperacillin" "Ureidopenicillins,Penicillins,Beta-lactams" "J01CA12,QJ01CA12" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pi,pip,pipc,pipe,pipera,pp" "penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,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" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "NA" "NA" "NA" 14 "g" "54197-9,54198-7,54199-5,55704-1"
"TZP" 461573 "Piperacillin/tazobactam" "Ureidopenicillins,Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR05,QJ01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp" "piptazobactam,tazonam,zobactin,zosyn" 14 "g" "101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
"PRC" 71978 "Piridicillin" "Penicillins,Beta-lactams" "NA" "NA" "NA" "NA"
"PRL" 157385 "Pirlimycin" "Lincosamides,Macrolides" "QJ51FF90" "pirlim" "pirlimycina,pirlimycine,pirlimycinum,pirsue" "35829-1,35830-9,35831-7"
"PIP" 43672 "Piperacillin" "Beta-lactams/penicillins" "J01CA12,QJ01CA12" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pi,pip,pipc,pipe,pipera,pp" "penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,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" "J01CR05,QJ01CR05" "NA" "NA" 14 "g" "54197-9,54198-7,54199-5,55704-1"
"TZP" 461573 "Piperacillin/tazobactam" "Beta-lactams/penicillins" "J01CR05,QJ01CR05" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp" "piptazobactam,tazonam,zobactin,zosyn" 14 "g" "101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
"PRC" 71978 "Piridicillin" "Beta-lactams/penicillins" "NA" "NA" "NA" "NA"
"PRL" 157385 "Pirlimycin" "Macrolides/lincosamides" "QJ51FF90" "pirlim" "pirlimycina,pirlimycine,pirlimycinum,pirsue" "35829-1,35830-9,35831-7"
"PIR" 4855 "Piromidic acid" "Quinolones" "J01MB03,QJ01MB03" "Quinolone antibacterials" "Other quinolones" "NA" "bactramyl,enterol,gastrurol,panacid,pirodal,piromidate,reelon,septural,urisept,uropir,zaomeal" 2 "g" "NA"
"PVM" 33478 "Pivampicillin" "Penicillins,Beta-lactams" "J01CA02,QJ01CA02" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "pivaloylampicillin,pivampicilina,pivampicilline,pivampicillinum" 1.05 "g" "18971-2,415-0,416-8,417-6,418-4"
"PME" 115163 "Pivmecillinam" "Penicillins,Beta-lactams" "J01CA08,QJ01CA08" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pivmec" "coactabs,melysin,pivamdinocillin,pivmecilinamo,pivmecillinamum,selexid" 0.6 "g" "NA"
"PVM" 33478 "Pivampicillin" "Beta-lactams/penicillins" "J01CA02,QJ01CA02" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "pivaloylampicillin,pivampicilina,pivampicilline,pivampicillinum" 1.05 "g" "18971-2,415-0,416-8,417-6,418-4"
"PME" 115163 "Pivmecillinam" "Beta-lactams/penicillins" "J01CA08,QJ01CA08" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "pivmec" "coactabs,melysin,pivamdinocillin,pivmecilinamo,pivmecillinamum,selexid" 0.6 "g" "NA"
"PLZ" 42613186 "Plazomicin" "Aminoglycosides" "J01GB14,QJ01GB14" "NA" "zemdri" "73592-8,73614-0,73637-1,92024-9,94719-2"
"PLB" 49800004 "Polymyxin B" "Polymyxins" "A07AA05,J01XB02,QA07AA05,QJ01XB02,QJ51XB02,QS01AA18,QS02AA11,QS03AA03,S01AA18,S02AA11,S03AA03" "Other antibacterials" "Polymyxins" "pb,pol,polb,poly,poly b,polyb,polymixin,polymixin b" "aerosporin" 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" "NA" "NA" "NA"
"POS" 468595 "Posaconazole" "Antifungals" "J02AC04,QJ02AC04" "Antimycotics for systemic use" "Triazole derivatives" "posa,posaco" "noxafil,schering,spriafil" 0.3 "g" 0.3 "g" "53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
"PRA" 9802884 "Pradofloxacin" "Fluoroquinolones,Quinolones" "QJ01MA97" "NA" "pudofloxacin,veraflox" "76148-6,87800-9"
"PRX" 71455 "Premafloxacin" "Fluoroquinolones,Quinolones" "NA" "premaf" "premafloxacine,premafloxacino" "73591-0,73613-2,73636-3"
"POS" 468595 "Posaconazole" "Antifungals/antimycotics" "J02AC04,QJ02AC04" "Antimycotics for systemic use" "Triazole derivatives" "posa,posaco" "noxafil,schering,spriafil" 0.3 "g" 0.3 "g" "53731-6,54186-2,54187-0,54188-8,54189-6,80545-7"
"PRA" 9802884 "Pradofloxacin" "Fluoroquinolones" "QJ01MA97" "NA" "pudofloxacin,veraflox" "76148-6,87800-9"
"PRX" 71455 "Premafloxacin" "Fluoroquinolones" "NA" "premaf" "premafloxacine,premafloxacino" "73591-0,73613-2,73636-3"
"PMD" 456199 "Pretomanid" "Antimycobacterials" "J04AK08,QJ04AK08" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" 0.2 "g" "93850-6"
"PRM" 6446787 "Primycin" "Macrolides" "NA" "NA" "chinopricin,debrycin,primicina,primycine" "NA"
"PRI" 11979535 "Pristinamycin" "Streptogramins" "J01FG01,QJ01FG01" "Macrolides, lincosamides and streptogramins" "Streptogramins" "pris,pristi" "eskalin,micamicina,mikamycin,mikamycine,mikamycinum,ostreogricina,ostreogrycine,ostreogrycinum,pristinamicina,pristinamycine,pristinamycinum,pyostacine,stafac,stafytracine,stajac,staphylomycin,stapyocine,starfac,virgimycin,virgimycine,virginiamicina,virginiamycin,virginiamycina,virginiamycinum" 2 "g" "32383-2,35833-3,35834-1,55709-0"
"PRB" 5903 "Procaine benzylpenicillin" "Penicillins,Beta-lactams" "J01CE09,QJ01CE09,QJ51CE09" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "afsillin,aquacilina,aquacillin,aquasuspen,avloprocil,cilicaine,crysticillin,depocillin,despacilina,distaquaine,duphapen,duracillin,hostacillin,hydracillin,kabipenin,ledercillin,millicillin,mylipen,neoproc,nopcaine,parencillin,premocillin,procanodia,prostabillin,retardillin,sharcillin,vetspen,vitablend,wycillin" 0.6 "g" "NA"
"PRP" 92879 "Propicillin" "Penicillins,Beta-lactams" "J01CE03,QJ01CE03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "baycillin,propicilina,propicilline,propicillinum" 0.9 "g" "NA"
"PRM" 6446787 "Primycin" "Macrolides/lincosamides" "NA" "NA" "chinopricin,debrycin,primicina,primycine" "NA"
"PRI" 11979535 "Pristinamycin" "Macrolides/lincosamides" "J01FG01,QJ01FG01" "Macrolides, lincosamides and streptogramins" "Streptogramins" "pris,pristi" "eskalin,micamicina,mikamycin,mikamycine,mikamycinum,ostreogricina,ostreogrycin,ostreogrycine,ostreogrycinum,pristinamicina,pristinamycine,pristinamycinum,pyostacine,stafac,stafytracine,stajac,staphylomycin,stapyocine,starfac,virgimycin,virgimycine,virginiamicina,virginiamycin,virginiamycina,virginiamycinum" 2 "g" "32383-2,35833-3,35834-1,55709-0"
"PRB" 5903 "Procaine benzylpenicillin" "Beta-lactams/penicillins" "J01CE09,QJ01CE09,QJ51CE09" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "afsillin,aquacilina,aquacillin,aquasuspen,avloprocil,cilicaine,crysticillin,depocillin,despacilina,distaquaine,duphapen,duracillin,hostacillin,hydracillin,kabipenin,ledercillin,millicillin,mylipen,neoproc,nopcaine,parencillin,premocillin,procanodia,prostabillin,retardillin,sharcillin,vetspen,vitablend,wycillin" 0.6 "g" "NA"
"PRP" 92879 "Propicillin" "Beta-lactams/penicillins" "J01CE03,QJ01CE03" "Beta-lactam antibacterials, penicillins" "Beta-lactamase sensitive penicillins" "NA" "baycillin,propicilina,propicilline,propicillinum" 0.9 "g" "NA"
"PKA" 9872451 "Propikacin" "Aminoglycosides" "NA" "NA" "propikacina,propikacine,propikacinum" "NA"
"PTH" 666418 "Protionamide" "Antimycobacterials" "J04AD01,QJ04AD01" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "prot" "ektebin,peteha,prothionamide,prothionamidum,protion,protionamid,protionamida,protionamidum,protionizina,tebeform,trevintix,tuberex" 0.75 "g" "NA"
"PRU" 65947 "Prulifloxacin" "Fluoroquinolones,Quinolones" "J01MA17,QJ01MA17" "Quinolone antibacterials" "Fluoroquinolones" "NA" "pruvel,quisnon,sword" 0.6 "g" "100058-7,76145-2"
"PRU" 65947 "Prulifloxacin" "Fluoroquinolones" "J01MA17,QJ01MA17" "Quinolone antibacterials" "Fluoroquinolones" "NA" "pruvel,quisnon,sword" 0.6 "g" "100058-7,76145-2"
"PZA" 1046 "Pyrazinamide" "Antimycobacterials" "J04AK01,QJ04AK01" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "pyra" "aldinamid,aldinamide,eprazin,farmizina,isopas,novamid,pezetamid,piraldina,pirazimida,pirazinamid,pirazinamida,pirazinamide,pirazinecarboxamide,pyrafat,pyrazide,pyrazinamdie,pyrazinamidum,pyrazineamide,pyrizinamide,rifafour,rozide,tebrazid,tisamid,unipyranamide" 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" "Streptogramins" "QJ01FG02" "Macrolides, lincosamides and streptogramins" "Streptogramins" "q/d,qda,qida,quda,rp,syn,synerc" "synercid" "23640-6,23641-4,33334-4,35835-8,58712-1"
"RAC" 56052 "Ractopamine" "Other" "NA" "NA" "bufenina,bufenine,buphenin,buphenine,bupheninum,luteonin,nilidrine,nylidrinum,optaflexx,paylean,prepar,ractopamina,ractopaminum,ritodrina,ritodrine,ritodrinium,tomax,utopar,yutopar" "NA"
"RAM" 16132338 "Ramoplanin" "Glycopeptides,Peptides" "NA" "ramopl" "NA" "41710-5,41711-3,41712-1,41737-8"
"RZM" 10993211 "Razupenem" "Carbapenems,Beta-lactams" "NA" "razupe" "NA" "73590-2,73612-4,73635-5"
"RTP" 6918462 "Retapamulin" "Pleuromutilins" "D06AX13,QD06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" "ret" "altabax,altargo,rebapamulin,retapamulina" "NA"
"QDA" 11979418 "Quinupristin/dalfopristin" "Macrolides/lincosamides" "QJ01FG02" "Macrolides, lincosamides and streptogramins" "Streptogramins" "q/d,qda,qida,quda,rp,syn,synerc" "synercid" "23640-6,23641-4,33334-4,35835-8,58712-1"
"RAC" 56052 "Ractopamine" "Other antibacterials" "NA" "NA" "bufenina,bufenine,buphenin,buphenine,bupheninum,luteonin,nilidrine,nylidrinum,optaflexx,paylean,prepar,ractopamina,ractopaminum,ritodrina,ritodrine,ritodrinium,tomax,utopar,yutopar" "NA"
"RAM" 16132338 "Ramoplanin" "Glycopeptides" "NA" "ramopl" "NA" "41710-5,41711-3,41712-1,41737-8"
"RZM" 10993211 "Razupenem" "Carbapenems" "NA" "razupe" "NA" "73590-2,73612-4,73635-5"
"RTP" 6918462 "Retapamulin" "Other antibacterials" "D06AX13,QD06AX13" "Antibiotics for topical use" "Other antibiotics for topical use" "ret" "altabax,altargo,rebapamulin,retapamulina" "NA"
"RZF" "Rezafungin" "Antifungals" "NA" "NA" "NA" "NA"
"RBC" 44631912 "Ribociclib" "Antifungals" "L01EF02,QL01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali" 0.45 "g" "NA"
"RBC" 44631912 "Ribociclib" "Antifungals/antimycotics" "L01EF02,QL01EF02" "Antimycotics for systemic use" "Triazole derivatives" "ribo" "kisqali" 0.45 "g" "NA"
"RST" 33042 "Ribostamycin" "Aminoglycosides" "J01GB10,QJ01GB10" "Aminoglycoside antibacterials" "Other aminoglycosides" "NA" "exaluren,hetangmycin,ribastamin,ribostamicina,ribostamycine,ribostamycinum,vistamycin,xylostatin" 1 "g" "NA"
"RID1" 16659285 "Ridinilazole" "Other" "NA" "NA" "ridinilazol" "NA"
"RIB" 135398743 "Rifabutin" "Rifamycins,Antimycobacterials" "J04AB04,QJ04AB04" "Drugs for treatment of tuberculosis" "Antibiotics" "ansamy,rfb,rifb" "alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,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" "Rifamycins,Antimycobacterials" "J04AB02,QJ04AB02,QJ54AB02" "Drugs for treatment of tuberculosis" "Antibiotics" "rifa,rifamp" "abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin" 0.6 "g" 0.6 "g" "NA"
"REI" 135483893 "Rifampicin/ethambutol/isoniazid" "Rifamycins,Antimycobacterials" "J04AM07,QJ04AM07" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "isonarif,rifamate,rifamazid" "NA"
"RFI" "Rifampicin/isoniazid" "Rifamycins,Antimycobacterials" "J04AM02,QJ04AM02" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RPEI" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Rifamycins,Antimycobacterials" "J04AM06,QJ04AM06" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RPI" "Rifampicin/pyrazinamide/isoniazid" "Rifamycins,Antimycobacterials" "J04AM05,QJ04AM05" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RFM" 6324616 "Rifamycin" "Rifamycins,Antimycobacterials" "A07AA13,D06AX15,J04AB03,QA07AA13,QD06AX15,QJ04AB03,QJ54AB03,QS01AA16,QS02AA12,S01AA16,S02AA12" "Drugs for treatment of tuberculosis" "Antibiotics" "rifmyc" "aemcolo,nacimycin,nancimycin,otofa,rifamastene,rifamicina,rifamycine,rifamycinum,rifocin,rifocyn,tuborin" 0.8 "g" 0.6 "g" "NA"
"RFP" 135403821 "Rifapentine" "Rifamycins,Antimycobacterials" "J04AB05,QJ04AB05" "Drugs for treatment of tuberculosis" "Antibiotics" "rifp,rpt" "prifitin,priftin,rifapentin,rifapentina,rifapentinum" 0.11 "g" "100059-5,76627-9"
"RFX" 6436173 "Rifaximin" "Other" "A07AA11,D06AX11,QA07AA11,QD06AX11,QG51AA06,QJ51XX01" "Intestinal antiinfectives" "Antibiotics" "NA" "fatroximin,flonorm,lormyx,lumenax,normix,rifacol,rifamixin,rifaxidin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan" 0.6 "g" "73589-4,73611-6,73634-8"
"RIT" 65633 "Ritipenem" "Carbapenems,Beta-lactams" "NA" "NA" "ritipenemsalt" "NA"
"RIA" 163692 "Ritipenem acoxil" "Carbapenems,Beta-lactams" "NA" "NA" "penemac" "NA"
"ROK" 5282211 "Rokitamycin" "Macrolides" "J01FA12,QJ01FA12" "Macrolides, lincosamides and streptogramins" "Macrolides" "rokita" "propionylleucomycin,ricamycin,rokicid,rokital,rokitamicina,rokitamycine,rokitamycinum" 0.8 "g" "NA"
"RID1" 16659285 "Ridinilazole" "Other antibacterials" "NA" "NA" "ridinilazol" "NA"
"RIB" 135398743 "Rifabutin" "Antimycobacterials" "J04AB04,QJ04AB04" "Drugs for treatment of tuberculosis" "Antibiotics" "ansamy,rifb" "alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,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,QJ04AB02,QJ54AB02" "Drugs for treatment of tuberculosis" "Antibiotics" "rifa,rifamp" "abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin" 0.6 "g" 0.6 "g" "NA"
"REI" 135483893 "Rifampicin/ethambutol/isoniazid" "Antimycobacterials" "J04AM07,QJ04AM07" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "isonarif,rifamate,rifamazid" "NA"
"RFI" "Rifampicin/isoniazid" "Antimycobacterials" "J04AM02,QJ04AM02" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RPEI" "Rifampicin/pyrazinamide/ethambutol/isoniazid" "Antimycobacterials" "J04AM06,QJ04AM06" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RPI" "Rifampicin/pyrazinamide/isoniazid" "Antimycobacterials" "J04AM05,QJ04AM05" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"RFM" 6324616 "Rifamycin" "Antimycobacterials" "A07AA13,D06AX15,J04AB03,QA07AA13,QD06AX15,QJ04AB03,QJ54AB03,QS01AA16,QS02AA12,S01AA16,S02AA12" "Drugs for treatment of tuberculosis" "Antibiotics" "rifmyc" "aemcolo,nacimycin,nancimycin,otofa,rifamastene,rifamicina,rifamycine,rifamycinum,rifocin,rifocyn,tuborin" 0.8 "g" 0.6 "g" "NA"
"RFP" 135403821 "Rifapentine" "Antimycobacterials" "J04AB05,QJ04AB05" "Drugs for treatment of tuberculosis" "Antibiotics" "rifp,rpt" "prifitin,priftin,rifapentin,rifapentina,rifapentinum" 0.11 "g" "100059-5,76627-9"
"RFX" 6436173 "Rifaximin" "Other antibacterials" "A07AA11,D06AX11,QA07AA11,QD06AX11,QG51AA06,QJ51XX01" "Intestinal antiinfectives" "Antibiotics" "NA" "fatroximin,flonorm,lormyx,lumenax,normix,rifacol,rifamixin,rifaxidin,rifaximina,rifaximine,rifaximinum,rifaxin,ritacol,spiraxin,xifaxan,xifaxsan" 0.6 "g" "73589-4,73611-6,73634-8"
"RIT" 65633 "Ritipenem" "Carbapenems" "NA" "NA" "ritipenemsalt" "NA"
"RIA" 163692 "Ritipenem acoxil" "Carbapenems" "NA" "NA" "penemac" "NA"
"ROK" 5282211 "Rokitamycin" "Macrolides/lincosamides" "J01FA12,QJ01FA12" "Macrolides, lincosamides and streptogramins" "Macrolides" "rokita" "propionylleucomycin,ricamycin,rokicid,rokital,rokitamicina,rokitamycine,rokitamycinum" 0.8 "g" "NA"
"RLT" 54682938 "Rolitetracycline" "Tetracyclines" "J01AA09,QJ01AA09" "Tetracyclines" "Tetracyclines" "NA" "bristacin,colbiocin,kinteto,reverin,revrin,rolitetraciclina,rolitetracyclinum,solvocillin,superciclin,synotodecin,synterin,syntetrex,syntetrin,tetraverin,transcycline,velacicline,velacycline" 0.35 "g" "18976-1,435-8,436-6,437-4,438-2"
"ROS" 287180 "Rosoxacin" "Quinolones" "J01MB01,QJ01MB01" "Quinolone antibacterials" "Other quinolones" "NA" "acrosoxacin,eracine,eradacil,eradacin,eradicin,rosoxacine,rosoxacino,rosoxacinum,roxadyl,winoxacin,winuron" 0.3 "g" "18977-9,439-0,440-8,441-6,442-4,55713-2"
"RXT" "Roxithromycin" "Macrolides" "J01FA06,QJ01FA06" "Macrolides, lincosamides and streptogramins" "Macrolides" "roxi,roxith" "NA" 0.3 "g" "18978-7,443-2,444-0,445-7,446-5,7046-6"
"RFL" 58258 "Rufloxacin" "Fluoroquinolones,Quinolones" "J01MA10,QJ01MA10" "Quinolone antibacterials" "Fluoroquinolones" "NA" "monos,rufloxacine,rufloxacino,rufloxacinum,tebraxin,uroflox" 0.2 "g" "NA"
"SAL" 3085092 "Salinomycin" "Ionophores" "QP51BB01" "salino" "coxistac,procoxacin,salinomicina,salinomycine,salinomycinum" "35836-6,35837-4,35838-2,87593-0"
"SAR" 56208 "Sarafloxacin" "Fluoroquinolones,Quinolones" "QJ01MA98" "sarafl" "difloxacino,difloxacinum,difloxcine,sarafin,saraflox,sarafloxacine,sarafloxacino,sarafloxacinum" "73588-6,73610-8,73633-0"
"RXT" "Roxithromycin" "Macrolides/lincosamides" "J01FA06,QJ01FA06" "Macrolides, lincosamides and streptogramins" "Macrolides" "roxi,roxith" "NA" 0.3 "g" "18978-7,443-2,444-0,445-7,446-5,7046-6"
"RFL" 58258 "Rufloxacin" "Fluoroquinolones" "J01MA10,QJ01MA10" "Quinolone antibacterials" "Fluoroquinolones" "NA" "monos,rufloxacine,rufloxacino,rufloxacinum,tebraxin,uroflox" 0.2 "g" "NA"
"SAL" 3085092 "Salinomycin" "Other antibacterials" "QP51BB01" "salino" "coxistac,procoxacin,salinomicina,salinomycine,salinomycinum" "35836-6,35837-4,35838-2,87593-0"
"SAR" 56208 "Sarafloxacin" "Fluoroquinolones" "QJ01MA98" "sarafl" "difloxacino,difloxacinum,difloxcine,sarafin,saraflox,sarafloxacine,sarafloxacino,sarafloxacinum" "73588-6,73610-8,73633-0"
"SRC" 54681908 "Sarecycline" "Tetracyclines" "J01AA14,QJ01AA14" "Tetracyclines" "Tetracyclines" "NA" "sareciclina,seysara" 0.1 "g" "NA"
"SRX" 9933415 "Sarmoxicillin" "Penicillins,Beta-lactams" "NA" "NA" "sarmoxillina,sarmoxilline,sarmoxillinum" "NA"
"SEC" 71815 "Secnidazole" "Other" "P01AB07" "NA" "flagentyl,secnidal,secnidazolum,secnil,sindose,solosec" 2 "g" "NA"
"SRX" 9933415 "Sarmoxicillin" "Beta-lactams/penicillins" "NA" "NA" "sarmoxillina,sarmoxilline,sarmoxillinum" "NA"
"SEC" 71815 "Secnidazole" "Other antibacterials" "P01AB07" "NA" "flagentyl,secnidal,secnidazolum,secnil,sindose,solosec" 2 "g" "NA"
"SMF" "Simvastatin/fenofibrate" "Antimycobacterials" "C10BA04,QC10BA04" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "simv" "NA" "NA"
"SIS" 36119 "Sisomicin" "Aminoglycosides" "J01GB08,QJ01GB08" "Aminoglycoside antibacterials" "Other aminoglycosides" "siso,sisomy" "rickamicin,salvamina,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" "Fluoroquinolones,Quinolones" "J01MA21,QJ01MA21" "sitafl" "gracevit" 0.1 "g" "NA"
"SIT" 461399 "Sitafloxacin" "Fluoroquinolones" "J01MA21,QJ01MA21" "sitafl" "gracevit" 0.1 "g" "NA"
"SDA" 2724368 "Sodium aminosalicylate" "Antimycobacterials" "J04AA02,QJ04AA02" "Drugs for treatment of tuberculosis" "Aminosalicylic acid and derivatives" "NA" "bactylan,lepasen,monopas,tubersan" 14 "g" 14 "g" "NA"
"SOL" 25242512 "Solithromycin" "Macrolides" "J01FA16,QJ01FA16" "NA" "solithera" "73587-8,73609-0,73632-2"
"SPX" 60464 "Sparfloxacin" "Fluoroquinolones,Quinolones" "J01MA09,QJ01MA09" "Quinolone antibacterials" "Fluoroquinolones" "spa,spar,sparfl" "esparfloxacino,parox,spara,sparfloxacine,sparfloxacinum,zagam" 0.2 "g" "20397-6,23610-9,23628-1,35839-0,7047-4"
"SPT" 15541 "Spectinomycin" "Other" "J01XX04,QJ01XX04" "Other antibacterials" "Other antibacterials" "sc,spe,spec,spect,spt" "actinospectacina,adspec,espectinomicina,prospec,spectam,spectinomicina,spectinomycine,spectinomycinhydrate,spectinomycinum,spectogard,stanilo,togamycin,trobicin" 3 "g" "18980-3,35840-8,451-5,452-3,453-1,454-9"
"SPI" 6419898 "Spiramycin" "Macrolides" "J01FA02,QJ01FA02,QJ51FA02" "Macrolides, lincosamides and streptogramins" "Macrolides" "sipram,spir,spiram" "formacidine" 3 "g" "18981-1,455-6,456-4,457-2,458-0,55715-7"
"SPM" "Spiramycin/metronidazole" "Other" "J01RA04,QJ01RA04" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"SOL" 25242512 "Solithromycin" "Macrolides/lincosamides" "J01FA16,QJ01FA16" "NA" "solithera" "73587-8,73609-0,73632-2"
"SPX" 60464 "Sparfloxacin" "Fluoroquinolones" "J01MA09,QJ01MA09" "Quinolone antibacterials" "Fluoroquinolones" "spa,spar,sparfl" "esparfloxacino,parox,spara,sparfloxacine,sparfloxacinum,zagam" 0.2 "g" "20397-6,23610-9,23628-1,35839-0,7047-4"
"SPT" 15541 "Spectinomycin" "Other antibacterials" "J01XX04,QJ01XX04" "Other antibacterials" "Other antibacterials" "sc,spe,spec,spect,spt" "actinospectacina,adspec,espectinomicina,prospec,spectam,spectinomicina,spectinomycine,spectinomycinhydrate,spectinomycinum,spectogard,stanilo,togamycin,trobicin" 3 "g" "18980-3,35840-8,451-5,452-3,453-1,454-9"
"SPI" 6419898 "Spiramycin" "Macrolides/lincosamides" "J01FA02,QJ01FA02,QJ51FA02" "Macrolides, lincosamides and streptogramins" "Macrolides" "sipram,spir,spiram" "formacidine" 3 "g" "18981-1,455-6,456-4,457-2,458-0,55715-7"
"SPM" "Spiramycin/metronidazole" "Other antibacterials" "J01RA04,QJ01RA04" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"STR" "Streptoduocin" "Aminoglycosides" "J01GA02,QJ01GA02" "Aminoglycoside antibacterials" "Streptomycins" "NA" "NA" 1 "g" "NA"
"STR1" 19649 "Streptomycin" "Aminoglycosides" "A07AA04,J01GA01,QA07AA04,QJ01GA01" "Aminoglycoside antibacterials" "Streptomycins" "s,st1000,st2000,stm,str,stre,strept" "agrept,agrimycin,chemform,estreptomicina,gerox,neodiestreptopab,strepcen,streptomicina,streptomycine,streptomycinum,streptomyzin" 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" "NA" "18983-7,35841-6,6933-6,7049-0"
"STI" "Streptomycin/isoniazid" "Antimycobacterials" "J04AM01,QJ04AM01" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"SUL" 130313 "Sulbactam" "Beta-lactamase inhibitors" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4"
"SBC" 20055036 "Sulbenicillin" "Penicillins,Beta-lactams" "J01CA16,QJ01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "sulben" "kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin" 15 "g" "NA"
"SUC" 5318 "Sulconazole" "Antifungals" "D01AC09,QD01AC09" "NA" "sulconazol,sulconazolum" "NA"
"SUP" 6634 "Sulfachlorpyridazine" "Sulfonamides" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA"
"SDI" 5215 "Sulfadiazine" "Trimethoprims,Sulfonamides" "J01EC02,QJ01EQ10" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "suldia" "codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine" 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,Sulfonamides" "J01EE06" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "berlocombin,cotetroxazine,potesept,trimerazine" "NA"
"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA"
"SUD" 5323 "Sulfadimethoxine" "Trimethoprims,Sulfonamides" "J01ED01,QJ01EQ09,QP51BA01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sdimet" "abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon" 0.5 "g" "87799-3,87803-3"
"SDM" 5327 "Sulfadimidine" "Trimethoprims,Sulfonamides" "J01EB03,QJ01EQ03,QP51AG01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "suldim" "azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin" 4 "g" "NA"
"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF" 5344 "Sulfafurazole" "Trimethoprims,Sulfonamides" "J01EB05,QJ01EQ05,QS01AB02,S01AB02" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfsz" "accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan" 4 "g" 4 "g" "NA"
"SLF1" 5343 "Sulfaisodimidine" "Trimethoprims,Sulfonamides" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine" 4 "g" 4 "g" "NA"
"SLF2" 9047 "Sulfalene" "Trimethoprims,Sulfonamides" "J01ED02,QJ01EQ19" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina" 0.1 "g" "NA"
"SZO" 187764 "Sulfamazone" "Trimethoprims,Sulfonamides" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA"
"SLF3" 5325 "Sulfamerazine" "Trimethoprims,Sulfonamides" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA"
"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SUM" "Sulfamethazine" "Sulfonamides" "NA" "NA" "NA" "87592-2"
"SLF4" 5328 "Sulfamethizole" "Trimethoprims,Sulfonamides" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3"
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims,Sulfonamides" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,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,Sulfonamides" "J01ED05,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA"
"SLF6" 19596 "Sulfametomidine" "Trimethoprims,Sulfonamides" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid" "NA"
"SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims,Sulfonamides" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" "NA"
"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA"
"SLF8" 12894 "Sulfamoxole" "Trimethoprims,Sulfonamides" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "NA" "enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide" 1 "g" 1 "g" "NA"
"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims,Sulfonamides" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF9" 5333 "Sulfanilamide" "Trimethoprims,Sulfonamides" "D06BA05,J01EB06,QD06BA05,QJ01EQ06" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder" "NA"
"SLF10" 68933 "Sulfaperin" "Trimethoprims,Sulfonamides" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum" 0.5 "g" "NA"
"SLF11" 5335 "Sulfaphenazole" "Trimethoprims,Sulfonamides" "J01ED08,QJ01EQ08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole" 1 "g" "NA"
"SLF12" 5336 "Sulfapyridine" "Trimethoprims,Sulfonamides" "J01EB04,QJ01EQ04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon" 1 "g" "14075-6,55580-5"
"SNA" 60582 "Sulfasuccinamide" "Sulfonamides" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA"
"SUT" 5340 "Sulfathiazole" "Trimethoprims,Sulfonamides" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7"
"SLF13" 3000579 "Sulfathiourea" "Trimethoprims,Sulfonamides" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA"
"SOX" "Sulfisoxazole" "Sulfonamides" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
"SSS" 86225 "Sulfonamide" "Sulfonamides" "NA" "sfna,sulami" "NA" "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" "NA" "sulope" "orlynvah" "55289-3,55290-1,55291-9"
"SLT6" 444022 "Sultamicillin" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA"
"SUR" 46700778 "Surotomycin" "Other" "NA" "NA" "surotomicina,surotomycine" "NA"
"TAL" 71447 "Talampicillin" "Penicillins,Beta-lactams" "J01CA15,QJ01CA15" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "aseocillin,phthalidyl,talampicilina,talampicilline,talampicillinum,talpen,yamacillin" 2 "g" "18988-6,479-6,480-4,481-2,482-0"
"TLP" 163307 "Talmetoprim" "Other" "NA" "NA" "NA" "NA"
"TAN" 76902493 "Taniborbactam" "Carbapenems,Beta-lactams,Beta-lactamase inhibitors" "NA" "vnrx-5133" "NA" "NA"
"TAZ" 123630 "Tazobactam" "Beta-lactamase inhibitors" "J01CG02,QJ01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo,tazoba" "exblifep,tazobactamsalt,tazobactamum,tazobactum" "41719-6,41720-4,41721-2,41740-2"
"TBP" 9800194 "Tebipenem" "Carbapenems,Beta-lactams" "NA" "NA" "NA" "NA"
"SUL" 130313 "Sulbactam" "Beta-lactams/penicillins" "J01CG01,QJ01CG01" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "sulbac" "betamaze,sulbactamum" 1 "g" "41716-2,41717-0,41718-8,41739-4"
"SBC" 20055036 "Sulbenicillin" "Beta-lactams/penicillins" "J01CA16,QJ01CA16" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "sulben" "kedacillin,kedacillina,sulbenicilina,sulbenicilline,sulbenicillinum,sulpelin" 15 "g" "NA"
"SUC" 5318 "Sulconazole" "Antifungals/antimycotics" "D01AC09,QD01AC09" "NA" "sulconazol,sulconazolum" "NA"
"SUP" 6634 "Sulfachlorpyridazine" "Other antibacterials" "QJ01EQ12" "sulchl" "cluricol,cosulid,cosumix,durasulf,nefrosul,nsulfanilamide,prinzone,solfaclorpiridazina,sonilyn,sulfacloropiridazina,sulfaclorpiridazina,vetisulid" "NA"
"SDI" 5215 "Sulfadiazine" "Trimethoprims" "J01EC02,QJ01EQ10" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "suldia" "codiazine,cremodiazine,cremotres,debenal,deltazina,dermazin,dermazine,diazolone,diazovit,eskadiazine,flamazine,geben,liquadiazine,microsulfon,neazine,neotrizine,palatrize,piridisir,pirimal,pyrimal,quadetts,quadramoid,sanodiazine,silbertone,sildaflo,silvadene,silvazine,silver,silveramide,sliverex,solfadiazina,spofadrizine,sterazine,sulfacombin,sulfadiazene,sulfadiazin,sulfadiazina,sulfadiazinum,sulfapirimidin,sulfapyrimidin,sulfapyrimidine,sulfatryl,sulfazine,sulfolex,sulfonsol,sulfose,sulphadiazine,terfonyl,theradiazine,thermazene,trifonamide,trisem,truozine" 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" "NA" "berlocombin,cotetroxazine,potesept,trimerazine" "NA"
"SLT1" 64932 "Sulfadiazine/trimethoprim" "Trimethoprims" "J01EE02,QJ01EW10,QJ51RE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "antastmon,astra,ditrim,ditrivet,sultrisan,triglobe,trimin,tucoprim,uniprim" "NA"
"SUD" 5323 "Sulfadimethoxine" "Trimethoprims" "J01ED01,QJ01EQ09,QP51BA01" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sdimet" "abcid,agribon,albon,arnosulfan,bactotril,bactrovet,deposul,diasulfa,diasulfyl,dimetazina,dinosol,dorisul,fuxal,lasibon,madribon,madrigid,madriqid,madroxin,madroxine,maxulvet,mecozine,memcozine,metoxidon,neostrepal,neostreptal,nsulfanilamidesalt,omnibon,persulfen,radonin,redifal,rofenaid,roscosulf,scandisil,solfadimetossina,sudine,suldixine,sulfabon,sulfadimethoxin,sulfadimethoxinesalt,sulfadimethoxinum,sulfadimetossina,sulfadimetoxin,sulfadimetoxina,sulfadimetoxine,sulfadimoxine,sulfastop,sulfoplan,sulforal,sulphadimethoxine,sulxin,sumbio,symbio,theracanzan,ultrasulfon" 0.5 "g" "87799-3,87803-3"
"SDM" 5327 "Sulfadimidine" "Trimethoprims" "J01EB03,QJ01EQ03,QP51AG01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "suldim" "azolmetazin,bovibol,calfspan,cremomethazine,diazil,diazilsulfadine,diazyl,dimezathine,intradine,kelametazine,mermeth,neasina,neazina,panazin,pirmazin,primazin,solfadimidina,spanbolet,sulfadimerazine,sulfadimesin,sulfadimesine,sulfadimethyldiazine,sulfadimezin,sulfadimezine,sulfadimezinum,sulfadimidin,sulfadimidina,sulfadimidinum,sulfadimidinun,sulfadine,sulfametazina,sulfametazyny,sulfamethiazine,sulfamezathine,sulfamidine,sulfodimesin,sulfodimezine,sulmet,sulphadimidine,sulphamethasine,sulphamethazine,sulphamezathine,sulphamidine,sulphodimezine,superseptil,superseptyl,vertolan,vesadin" 4 "g" "NA"
"SLT2" "Sulfadimidine/trimethoprim" "Trimethoprims" "J01EE05,QJ01EW03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF" 5344 "Sulfafurazole" "Trimethoprims" "J01EB05,QJ01EQ05,QS01AB02,S01AB02" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfsz" "accuzole,alphazole,amidoxal,astrazolo,azosulfizin,bactesulf,barazae,chemouag,cosoxazole,dorsulfan,entusil,entusul,ganda,gantrisin,gantrisine,gantrisona,gantrizin,gantrosan,isoxamin,neazolin,neoxazol,novazolo,novosaxazole,nsulphanilamide,pancid,pediazole,renosulfan,resoxol,roxosul,roxoxol,saxosozine,sodizole,solfafurazolo,sosol,soxamide,soxisol,soxitabs,soxomide,stansin,sulbio,sulfafurazol,sulfafurazolum,sulfagan,sulfagen,sulfaisoxazole,sulfalar,sulfapolar,sulfasol,sulfasoxazole,sulfasoxizole,sulfazin,sulfisin,sulfisonazole,sulfisoxasole,sulfisoxazol,sulfisoxazolum,sulfizin,sulfizol,sulfizole,sulfofurazole,sulfoxol,suloxsol,sulphafuraz,sulphafurazol,sulphafurazole,sulphafurazolum,sulphaisoxazole,sulphisoxazol,sulphisoxazole,sulphofurazole,sulsoxin,thiasin,unisulf,urisoxin,uritrisin,urogan" 4 "g" 4 "g" "NA"
"SLF1" 5343 "Sulfaisodimidine" "Trimethoprims" "J01EB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "aristamid,aristamide,aristogyn,domain,domian,elcosin,elcosine,elkosil,elkosin,elkosine,erycon,isosulf,mefenal,solfisomidina,sulfadimetine,sulfaisodimerazine,sulfaisodimidinum,sulfaisomidine,sulfasomidine,sulfisomidin,sulfisomidina,sulfisomidine,sulfisomidinum,sulphasomidine" 4 "g" 4 "g" "NA"
"SLF2" 9047 "Sulfalene" "Trimethoprims" "J01ED02,QJ01EQ19" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "dalysep,farmitalia,kelfizin,kelfizina,kelfizine,policydal,solfametopirazina,sulfalen,sulfaleno,sulfalenum,sulfamethopyrazine,sulfamethoxypyrazine,sulfametopyrazine,sulfametoxypyridazin,sulphalene,sulphametopyrazine,vetkelfizina" 0.1 "g" "NA"
"SZO" 187764 "Sulfamazone" "Trimethoprims" "J01ED09" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "sulfamazona,sulfamazonum,sulfenazone" 1.5 "g" "NA"
"SLF3" 5325 "Sulfamerazine" "Trimethoprims" "D06BA06,J01ED07,QD06BA06,QJ01EQ17" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "sulmet" "cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine" 3 "g" "NA"
"SLT3" "Sulfamerazine/trimethoprim" "Trimethoprims" "J01EE07,QJ01EW18" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SUM" 5327 "Sulfamethazine" "Other antibacterials" "NA" "NA" "NA" "87592-2"
"SLF4" 5328 "Sulfamethizole" "Trimethoprims" "B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sfmz" "aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin" 4 "g" "60175-7,60176-5,60177-3"
"SMX" 5329 "Sulfamethoxazole" "Trimethoprims" "J01EC01,QJ01EQ11" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "sfmx,sulf,sulfam" "septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,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,QJ01EQ15" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces" 0.5 "g" "NA"
"SLF6" 19596 "Sulfametomidine" "Trimethoprims" "J01ED03" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "duroprocin,methofadin,methofazine,solfametomidina,sulfametomidin,sulfametomidina,sulfametomidinum,telemid" "NA"
"SLF7" 5326 "Sulfametoxydiazine" "Trimethoprims" "J01ED04" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "bayrena,berlicid,dairena,durenat,juvoxin,kinecid,kirocid,kiron,longasulf,methoxypyrimal,solfametossidiazina,sulfameter,sulfametersalt,sulfamethorine,sulfamethoxine,sulfamethoxydiazin,sulfamethoxydiazine,sulfamethoxydin,sulfamethoxydine,sulfametin,sulfametinum,sulfametorine,sulfametorinum,sulfametoxidiazina,sulfametoxidine,sulfametoxydiazinum,sulla,sulphameter,sulphamethoxydiazine,supramid,ultrax" 0.5 "g" "NA"
"SLT4" "Sulfametrole/trimethoprim" "Trimethoprims" "J01EE03" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "trsm" "NA" "NA"
"SLF8" 12894 "Sulfamoxole" "Trimethoprims" "J01EC03" "Sulfonamides and trimethoprim" "Intermediate-acting sulfonamides" "NA" "enterocura,justamil,oxasulfa,solfaguanolo,solfamossolo,sulfadimethyloxazole,sulfaguanol,sulfaguanole,sulfaguanolum,sulfamoxol,sulfamoxolum,sulfano,sulfavigor,sulfmidil,sulfono,sulfune,sulfuno,sulphamoxole,tardamid,tardamide" 1 "g" 1 "g" "NA"
"SLT5" "Sulfamoxole/trimethoprim" "Trimethoprims" "J01EE04" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "NA" "NA" "NA"
"SLF9" 5333 "Sulfanilamide" "Trimethoprims" "D06BA05,J01EB06,QD06BA05,QJ01EQ06" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "albexan,albosal,ambeside,antistrept,astreptine,astrocid,bacteramid,bactesid,collomide,colsulanyde,copticide,deseptyl,dipron,ergaseptine,erysipan,estreptocida,exoseptoplix,fourneau,gerison,gombardol,hydroxysulfonamide,infepan,lusil,lysococcine,neococcyl,orgaseptine,prontalbin,prontylin,proseptal,proseptine,proseptol,pysococcine,sanamid,septanilam,septinal,septolix,septoplex,septoplix,solfanilamide,stramid,strepamide,strepsan,streptagol,streptamid,streptamin,streptasol,streptocid,streptocide,streptocidum,streptoclase,streptocom,strepton,streptopan,streptosil,streptozol,streptozone,streptrocide,sulfamidyl,sulfamine,sulfana,sulfanalone,sulfanidyl,sulfanil,sulfanilamida,sulfanilamidomethan,sulfanilamidum,sulfanimide,sulfocidin,sulfocidine,sulfonylamide,sulphanilamide,sulphanilamidum,sulphonamide,therapol,tolder" "NA"
"SLF10" 68933 "Sulfaperin" "Trimethoprims" "J01ED06" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "anastaf,archisulfa,archisulpha,avissul,chemiopen,demosulfan,demosulphan,durisan,isosulfamerazine,isosulphamerazine,methylsulfadiazin,methylsulfadiazine,methylsulphadiazine,novosul,orosulfan,pallidin,retardon,risulfasens,sulfaperina,sulfaperine,sulfaperinum,sulfatreis,sulfopirimidine,sulpenta,sulphaperin,sulphaperina,sulphaperinum" 0.5 "g" "NA"
"SLF11" 5335 "Sulfaphenazole" "Trimethoprims" "J01ED08,QJ01EQ08" "Sulfonamides and trimethoprim" "Long-acting sulfonamides" "NA" "depocid,depotsulfonamide,eftolon,firmazolo,inamil,isarol,merian,orisul,orisulf,paidazolo,phenylsulfapyrazole,plisulfan,raziosulfa,solfafenazolo,sulfabid,sulfafenazol,sulfafenazolo,sulfaphenazol,sulfaphenazolum,sulfaphenazon,sulfaphenylpipazol,sulfaphenylpyrazol,sulfaphenylpyrazole,sulfonylpyrazol,sulphaphenazole,sulphenazole" 1 "g" "NA"
"SLF12" 5336 "Sulfapyridine" "Trimethoprims" "J01EB04,QJ01EQ04" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "adiplon,coccoclase,dagenan,eubasin,eubasinum,haptocil,piridazol,plurazol,pyriamid,pyridazol,relbapiridina,ronin,septipulmon,solfapiridina,soludagenan,streptosilpyridine,sulfapiridina,sulfapyridin,sulfapyridinum,sulfidin,sulfidine,sulphapyridin,sulphapyridine,thioseptal,trianon" 1 "g" "14075-6,55580-5"
"SNA" 60582 "Sulfasuccinamide" "Other antibacterials" "NA" "NA" "sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum" "NA"
"SUT" 5340 "Sulfathiazole" "Trimethoprims" "D06BA02,J01EB07,QD06BA02,QJ01EQ07" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "sulthi" "azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole" "87591-4,87796-9,87797-7"
"SLF13" 3000579 "Sulfathiourea" "Trimethoprims" "J01EB08" "Sulfonamides and trimethoprim" "Short-acting sulfonamides" "NA" "badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea" 6 "g" "NA"
"SOX" 5344 "Sulfisoxazole" "Other antibacterials" "NA" "sulfiz" "NA" "11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
"SSS" 86225 "Sulfonamide" "Other antibacterials" "NA" "sfna,sulami" "NA" "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" "sulope" "orlynvah" "55289-3,55290-1,55291-9"
"SLT6" 444022 "Sultamicillin" "Beta-lactams/penicillins" "J01CR04,QJ01CR04" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "sultos" "combisid,sultamicilina,sultamicilline,sultamicillinum,unacid" 1.5 "g" "NA"
"SUR" 46700778 "Surotomycin" "Other antibacterials" "NA" "NA" "surotomicina,surotomycine" "NA"
"TAL" 71447 "Talampicillin" "Beta-lactams/penicillins" "J01CA15,QJ01CA15" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "NA" "aseocillin,phthalidyl,talampicilina,talampicilline,talampicillinum,talpen,yamacillin" 2 "g" "18988-6,479-6,480-4,481-2,482-0"
"TLP" 163307 "Talmetoprim" "Other antibacterials" "NA" "NA" "NA" "NA"
"TAZ" 123630 "Tazobactam" "Beta-lactams/penicillins" "J01CG02,QJ01CG02" "Beta-lactam antibacterials, penicillins" "Beta-lactamase inhibitors" "tazo,tazoba" "exblifep,tazobactamsalt,tazobactamum,tazobactum" "41719-6,41720-4,41721-2,41740-2"
"TBP" 9800194 "Tebipenem" "Carbapenems" "NA" "NA" "NA" "NA"
"TZD" 11234049 "Tedizolid" "Oxazolidinones" "J01XX11,QJ01XX11" "Other antibacterials" "Other antibacterials" "tedi" "torezolid" 0.2 "g" 0.2 "g" "73586-0,73608-2,73631-4"
"TEC" 16131923 "Teicoplanin" "Glycopeptides,Peptides" "J01XA02,QJ01XA02" "Other antibacterials" "Glycopeptide antibacterials" "tec,tei,teic,teicop,tp,tpl,tpn" "NA" 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,Peptides" "NA" "NA" "NA" "NA"
"TLV" 3081362 "Telavancin" "Lipoglycopeptides,Glycopeptides,Peptides" "J01XA03,QJ01XA03" "Other antibacterials" "Glycopeptide antibacterials" "tela,telava" "arbelic,nvancomycin,televancin" "72894-9,73630-6,85051-1,88886-7"
"TLT" 3002190 "Telithromycin" "Macrolides" "J01FA15,QJ01FA15" "Macrolides, lincosamides and streptogramins" "Macrolides" "teli,telith" "ketek,levviax" 0.8 "g" "35843-2,35844-0,35845-7,41722-0"
"TMX" 60021 "Temafloxacin" "Fluoroquinolones,Quinolones" "J01MA05,QJ01MA05" "Quinolone antibacterials" "Fluoroquinolones" "tema,temafl" "omniflox,temafloxacina,temafloxacine,temafloxacino,temafloxacinum" 0.8 "g" "18990-2,487-9,488-7,489-5,490-3"
"TEM" 171758 "Temocillin" "Penicillins,Beta-lactams" "J01CA17,QJ01CA17" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "temo,temoci" "negaban,temocilina,temocillina,temocilline,temocillinum" 4 "g" "18991-0,491-1,492-9,493-7,494-5,54190-4"
"TRB" 1549008 "Terbinafine" "Antifungals" "D01AE15,D01BA02,QD01AE15,QD01BA02" "Antifungals for systemic use" "Antifungals for systemic use" "terb" "afogan,bramazil,bramizil,corbinal,lamasil,lamisil,muzonal,shoprite,terbina,terbinafina,terbinafinum,terbine,terbinex,terbisil,zabel" 0.25 "g" "10720-1,10721-9,18992-8"
"TRC" 441383 "Terconazole" "Antifungals" "G01AG02,QG01AG02" "NA" "fungistat,panlomyc,terazol,terconazol,terconazolum,tercospor,tetrazol,triaconazole,zazole" "55196-0"
"TEC" 16131923 "Teicoplanin" "Glycopeptides" "J01XA02,QJ01XA02" "Other antibacterials" "Glycopeptide antibacterials" "tec,tei,teic,teicop,tp,tpl,tpn" "NA" 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" "NA" "NA" "NA"
"TLV" 3081362 "Telavancin" "Glycopeptides" "J01XA03,QJ01XA03" "Other antibacterials" "Glycopeptide antibacterials" "tela,telava" "arbelic,nvancomycin,televancin" "72894-9,73630-6,85051-1,88886-7"
"TLT" 3002190 "Telithromycin" "Macrolides/lincosamides" "J01FA15,QJ01FA15" "Macrolides, lincosamides and streptogramins" "Macrolides" "teli,telith" "ketek,levviax" 0.8 "g" "35843-2,35844-0,35845-7,41722-0"
"TMX" 60021 "Temafloxacin" "Fluoroquinolones" "J01MA05,QJ01MA05" "Quinolone antibacterials" "Fluoroquinolones" "tema,temafl" "omniflox,temafloxacina,temafloxacine,temafloxacino,temafloxacinum" 0.8 "g" "18990-2,487-9,488-7,489-5,490-3"
"TEM" 171758 "Temocillin" "Beta-lactams/penicillins" "J01CA17,QJ01CA17" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "temo,temoci" "negaban,temocilina,temocillina,temocilline,temocillinum" 4 "g" "18991-0,491-1,492-9,493-7,494-5,54190-4"
"TRB" 1549008 "Terbinafine" "Antifungals/antimycotics" "D01AE15,D01BA02,QD01AE15,QD01BA02" "Antifungals for systemic use" "Antifungals for systemic use" "terb" "afogan,bramazil,bramizil,corbinal,lamasil,lamisil,muzonal,shoprite,terbina,terbinafina,terbinafinum,terbine,terbinex,terbisil,zabel" 0.25 "g" "10720-1,10721-9,18992-8"
"TRC" 441383 "Terconazole" "Antifungals/antimycotics" "G01AG02,QG01AG02" "NA" "fungistat,panlomyc,terazol,terconazol,terconazolum,tercospor,tetrazol,triaconazole,zazole" "55196-0"
"TRZ" 65720 "Terizidone" "Antimycobacterials" "J04AK03,QJ04AK03" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "terivalidin,terizidona,terizidonum" "NA"
"TCY" 54675776 "Tetracycline" "Tetracyclines" "A01AB13,D06AA04,J01AA07,QA01AB13,QD06AA04,QG01AA90,QG51AA02,QJ01AA07,QJ51AA07,QS01AA09,QS02AA08,QS03AA02,S01AA09,S02AA08,S03AA02" "Tetracyclines" "Tetracyclines" "tc,te,tet,tetcyc,tetr,tetra" "abramycin,abricycline,agromicina,ambramicina,ambramycin,biocycline,brodspec,cefracycline,centet,ciclibion,copharlan,criseociclina,democracin,deschlorobiomycin,economycin,hostacyclin,lexacycline,limecycline,liquamycin,mericycline,micycline,neocycline,omegamycin,orlycycline,panmycin,purocyclina,roviciclina,solvocin,tetrabon,tetraciclina,tetracyclinehydrate,tetracyclinum,tetracyn,tetradecin,tetrafil,tetraverine,tetrazyklin,tsiklomistsin,tsiklomitsin,veracin,vetacyclinum" 1 "g" 1 "g" "101504-9,18993-6,25272-6,4045-1,495-2,496-0,497-8,498-6,7052-4,87590-6"
"TCY-S" "Tetracycline screening test" "Tetracyclines" "NA" "tcy screen" "NA" "NA"
"TOL" 54691494 "Tetracycline/oleandomycin" "Tetracyclines" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"TET" 65450 "Tetroxoprim" "Other" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA"
"TOL" 54691494 "Tetracycline/oleandomycin" "Other antibacterials" "J01RA08,QJ01RA08" "Combinations of antibacterials" "Combinations of antibacterials" "NA" "NA" "NA"
"TET" 65450 "Tetroxoprim" "Other antibacterials" "NA" "NA" "primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex" "NA"
"THA" 9568512 "Thiacetazone" "Oxazolidinones" "NA" "NA" "acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin" "32384-0,54184-7,54204-3"
"THI" 27200 "Thiamphenicol" "Phenicols" "J01BA02,QJ01BA02,QJ51BA02" "Amphenicols" "Amphenicols" "thiaph" "armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine" 1.5 "g" 1.5 "g" "41723-8,41724-6,41725-3,54169-8"
"TAT" "Thioacetazone" "Antimycobacterials" "J04AK07,QJ04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" "NA"
"TAT" 9568512 "Thioacetazone" "Antimycobacterials" "J04AK07,QJ04AK07" "Drugs for treatment of tuberculosis" "Other drugs for treatment of tuberculosis" "NA" "NA" "NA"
"THI1" "Thioacetazone/isoniazid" "Antimycobacterials" "J04AM04,QJ04AM04" "Drugs for treatment of tuberculosis" "Combinations of drugs for treatment of tuberculosis" "NA" "NA" "NA"
"THS" 16129666 "Thiostrepton" "Peptides" "NA" "NA" "alaninamide,bryamycin,gargon,pharmakon,prestwick,sporangiomycin,thiactin,tiostrepton" "NA"
"TIA" 656958 "Tiamulin" "Pleuromutilins" "QJ01XQ01" "tiamul" "denagard,thiamutilin,tiamulina,tiamuline,tiamulinum" "35846-5,35847-3,35848-1,87589-8"
"TIC" 36921 "Ticarcillin" "Penicillins,Beta-lactams" "J01CA13,QJ01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "tc,ti,tic,tica,ticarc" "ticar,ticarcilina,ticarcilline,ticarcillinum,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" "Penicillins,Beta-lactams,Beta-lactamase inhibitors" "J01CR03,QJ01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "t/c,tcc,ticcla,ticl,tim,tlc" "augpenin" 15 "g" "NA"
"TIA" 656958 "Tiamulin" "Other antibacterials" "QJ01XQ01" "tiamul" "denagard,thiamutilin,tiamulina,tiamuline,tiamulinum" "35846-5,35847-3,35848-1,87589-8"
"TIC" 36921 "Ticarcillin" "Beta-lactams/penicillins" "J01CA13,QJ01CA13" "Beta-lactam antibacterials, penicillins" "Penicillins with extended spectrum" "tc,ti,tic,tica,ticarc" "ticar,ticarcilina,ticarcilline,ticarcillinum,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,QJ01CR03" "Beta-lactam antibacterials, penicillins" "Combinations of penicillins, incl. beta-lactamase inhibitors" "t/c,tcc,ticcla,ticl,tim,tlc" "augpenin" 15 "g" "NA"
"TGC" 54686904 "Tigecycline" "Tetracyclines" "J01AA12,QJ01AA12" "Tetracyclines" "Tetracyclines" "tgc,tig,tige,tigecy" "tigeciclina,tigecyclin,tigecyclinehydrate,tigilcycline,tygacil" 0.1 "g" "101499-2,42354-1,42355-8,42356-6,42357-4,55158-0"
"TMN" "Tigemonam" "Monobactams,Beta-lactams" "NA" "NA" "NA" "NA"
"TBQ" 65592 "Tilbroquinol" "Fluoroquinolones,Quinolones" "P01AA05" "NA" "tilbroquinolum" "NA"
"TIP" 24860548 "Tildipirosin" "Macrolides" "QJ01FA96" "NA" "zuprevo" "100060-3,88375-1,88377-7"
"TIL" 5282521 "Tilmicosin" "Macrolides" "QJ01FA91" "tilmic" "micotil,pulmotil,tilmicosina,tilmicosine,tilmicosinum,tilmovet" "35849-9,35850-7,35851-5,87588-0"
"TIN" 5479 "Tinidazole" "Other" "G01AF21,J01XD02,P01AB02,QG01AF21,QJ01XD02,QP51AA02" "Other antibacterials" "Imidazole derivatives" "tini" "amtiba,bioshik,fasigin,fasigyn,glongyn,haisigyn,isotinidazole,pletil,protozol,simplotan,sorquetan,symplotan,tindamax,tindazole,tinidazolum,tricolam,trimonase" 2 "g" 1.5 "g" "54928-7,55720-7,55721-5,55722-3"
"TMN" "Tigemonam" "Monobactams" "NA" "NA" "NA" "NA"
"TBQ" 65592 "Tilbroquinol" "Fluoroquinolones" "P01AA05" "NA" "tilbroquinolum" "NA"
"TIP" 24860548 "Tildipirosin" "Macrolides/lincosamides" "QJ01FA96" "NA" "zuprevo" "100060-3,88375-1,88377-7"
"TIL" 5282521 "Tilmicosin" "Macrolides/lincosamides" "QJ01FA91" "tilmic" "micotil,pulmotil,tilmicosina,tilmicosine,tilmicosinum,tilmovet" "35849-9,35850-7,35851-5,87588-0"
"TIN" 5479 "Tinidazole" "Other antibacterials" "G01AF21,J01XD02,P01AB02,QG01AF21,QJ01XD02,QP51AA02" "Other antibacterials" "Imidazole derivatives" "tini" "amtiba,bioshik,fasigin,fasigyn,glongyn,haisigyn,isotinidazole,pletil,protozol,simplotan,sorquetan,symplotan,tindamax,tindazole,tinidazolum,tricolam,trimonase" 2 "g" 1.5 "g" "54928-7,55720-7,55721-5,55722-3"
"TCR" 3001386 "Tiocarlide" "Antimycobacterials" "J04AD02,QJ04AD02" "Drugs for treatment of tuberculosis" "Thiocarbamide derivatives" "NA" "aethoksid,aethoxydum,amixyl,datanil,disocarban,disoxyl,ethoxide,etocarlid,etocarlida,etocarlide,etocarlidum,etoksid,thiocarlide,tiocarlid,tiocarlida,tiocarlidum" 7 "g" "NA"
"TDC" 10247721 "Tiodonium chloride" "Other" "NA" "NA" "tiodonium" "NA"
"TXC" 65788 "Tioxacin" "Fluoroquinolones,Quinolones" "NA" "NA" "tioxacine,tioxacino,tioxacinum" "NA"
"TIZ" 394397 "Tizoxanide" "Other" "NA" "NA" "NA" "73585-2,73607-4,73629-8"
"TDC" 10247721 "Tiodonium chloride" "Other antibacterials" "NA" "NA" "tiodonium" "NA"
"TXC" 65788 "Tioxacin" "Fluoroquinolones" "NA" "NA" "tioxacine,tioxacino,tioxacinum" "NA"
"TIZ" 394397 "Tizoxanide" "Other antibacterials" "NA" "NA" "NA" "73585-2,73607-4,73629-8"
"TOB" 36294 "Tobramycin" "Aminoglycosides" "J01GB01,QJ01GB01,QS01AA12,S01AA12" "Aminoglycoside antibacterials" "Other aminoglycosides" "nn,tm,to,tob,tobr,tobram" "aktob,bethkis,distobram,gotabiotic,kitabis,nebcin,nebicin,nebramycin,tenebrimycin,tenemycin,tobacin,tobracin,tobradex,tobradistin,tobralex,tobramaxin,tobramicin,tobramicina,tobramitsetin,tobramycetin,tobramycine,tobramycinum,tobrased,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" "NA" "NA"
"TFX" 5517 "Tosufloxacin" "Fluoroquinolones,Quinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0"
"TFX" 5517 "Tosufloxacin" "Fluoroquinolones" "J01MA22,QJ01MA22,QS01AE09,S01AE09" "tosufl" "NA" 0.45 "g" "100061-1,76146-0"
"TMP" 5578 "Trimethoprim" "Trimethoprims" "J01EA01,QJ01EA01,QJ51EA01" "Sulfonamides and trimethoprim" "Trimethoprim and derivatives" "t,tmp,tr,tri,trim,w" "abaprim,anitrim,antrima,antrimox,bacdan,bacidal,bacide,bacin,bacterial,bacticel,bactifor,bactoprim,bactramin,bencole,bethaprim,biosulten,briscotrim,chemotrin,colizole,conprim,cotrimel,deprim,dosulfin,duocide,esbesul,espectrin,euctrim,exbesul,fermagex,fortrim,futin,ikaprim,infectotrimet,instalac,kombinax,lagatrim,lastrim,lescot,monoprim,monotrim,monotrimin,novotrimel,omstat,pancidim,proloprim,protrin,purbal,resprim,roubac,roubal,salvatrim,setprin,sinotrim,stopan,streptoplus,sugaprim,sulfamar,sulfoxaprim,sulthrim,sultrex,syraprim,tiempe,trimethioprim,trimethoprime,trimethoprimum,trimethopriom,trimetoprim,trimetoprima,trimexol,trimezol,trimogal,trimono,trimopan,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,Sulfonamides" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "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" "J01FA08,QJ01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3"
"TRO" 55886 "Trospectomycin" "Other" "NA" "trospe" "trospectinomycin,trospectomicina,trospectomycine,trospectomycinum" "NA"
"TVA" 62959 "Trovafloxacin" "Fluoroquinolones,Quinolones" "J01MA13,QJ01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov,trovaf" "trovan,turvel" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1"
"TUL" 9832301 "Tulathromycin" "Macrolides" "QJ01FA94" "tulath" "arovyn,draxxin,increxxa,macrosyn,tulieve,tulissin" "76149-4,87798-5"
"TYL" 5280440 "Tylosin" "Macrolides" "QJ01FA90,QJ51FA90" "tylo" "fradizine,tilosina,tylan,tylocine,tylosine,tylosinum,vubityl" "35856-4,35857-2,35858-0,87587-2"
"TYL1" 6441094 "Tylvalosin" "Macrolides" "QJ01FA92" "tvn" "aivlosin" "101526-2,87586-4"
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other" "NA" "NA" "NA" "NA"
"VAN" 14969 "Vancomycin" "Glycopeptides,Peptides" "A07AA09,J01XA01,QA07AA09,QJ01XA01,QS01AA28,S01AA28" "Other antibacterials" "Glycopeptide antibacterials" "va,van,vanc,vancom" "vancocin,vancoled,vancomicina,vancomycine,vancomycinum" 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,Peptides" "NA" "NA" "NA" "NA"
"SXT" 358641 "Trimethoprim/sulfamethoxazole" "Trimethoprims" "J01EE01" "Sulfonamides and trimethoprim" "Combinations of sulfonamides and trimethoprim, incl. derivatives" "cot,cotrim,sxt,t/s,tms,trisul,trsu,trsx,ts" "abacin,abactrim,agoprim,alfatrim,aposulfatrim,bacteral,bactilen,bactiver,bacton,bactoreduct,bactrim,bactrizol,bactromin,bactropin,baktar,benzenesulfonamide,berlocid,bibacrim,biseptol,centran,centrin,chemitrim,chemotrim,ciplin,comox,cotribene,cotrim,cotrimhexal,cotrimoxazol,cotrimoxazole,cotrimstada,cotriver,dibaprim,drylin,duratrimet,eltrianyl,escoprim,eslectin,esteprim,eusaprim,fectrim,gamazole,gantanol,gantaprim,gantaprin,gantrim,groprim,helveprim,imexim,insozalin,jenamoxazol,kemoprim,kepinol,laratrim,linaris,maxtrim,metoxal,microtrim,mikrosid,momentol,nopil,oecotrim,omsat,oriprim,oxaprim,pantoprim,potrox,primazole,radonil,septra,septrim,servitrim,sigaprim,sigaprin,sulfatrim,sulfotrim,sulfotrimin,sulmeprim,sulprim,sumetrolim,supracombin,suprim,tacumil,teleprim,teleprin,thiocuran,tribakin,trifen,trigonyl,trimedin,trimesulf,trimethoprimsulfa,trimetoger,trimexazol,trimezole,trimforte,trimosulfa,uroplus" "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,QJ01FA08" "Macrolides, lincosamides and streptogramins" "Macrolides" "NA" "aovine,cyclamycin,evramicina,matromicina,oleandocetin,oleandocetine,tekmisin,treolmicina,tribiocillina,triocetin,triolan,troleandomicina,troleandomycine,troleandomycinum,viamicina,wytrion" 1 "g" "18999-3,519-9,520-7,521-5,522-3"
"TRO" 55886 "Trospectomycin" "Other antibacterials" "NA" "trospe" "trospectinomycin,trospectomicina,trospectomycine,trospectomycinum" "NA"
"TVA" 62959 "Trovafloxacin" "Fluoroquinolones" "J01MA13,QJ01MA13" "Quinolone antibacterials" "Fluoroquinolones" "trov,trovaf" "trovan,turvel" 0.2 "g" 0.2 "g" "23642-2,23643-0,35855-6,7058-1"
"TUL" 9832301 "Tulathromycin" "Macrolides/lincosamides" "QJ01FA94" "tulath" "arovyn,draxxin,increxxa,macrosyn,tulieve,tulissin" "76149-4,87798-5"
"TYL" 5280440 "Tylosin" "Macrolides/lincosamides" "QJ01FA90,QJ51FA90" "tylo" "fradizine,tilosina,tylan,tylocine,tylosine,tylosinum,vubityl" "35856-4,35857-2,35858-0,87587-2"
"TYL1" 6441094 "Tylvalosin" "Macrolides/lincosamides" "QJ01FA92" "tvn" "aivlosin" "101526-2,87586-4"
"PRU1" 124225 "Ulifloxacin (Prulifloxacin)" "Other antibacterials" "NA" "NA" "NA" "NA"
"VAN" 14969 "Vancomycin" "Glycopeptides" "A07AA09,J01XA01,QA07AA09,QJ01XA01,QS01AA28,S01AA28" "Other antibacterials" "Glycopeptide antibacterials" "va,van,vanc,vancom" "vancocin,vancoled,vancomicina,vancomycine,vancomycinum" 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" "NA" "NA" "NA"
"VIO" 135398671 "Viomycin" "Antimycobacterials" "NA" "NA" "florimycin,floromycin,vioactane,viocin,viomicin,viomicina,viomycine,viomycinum" "19001-7,23616-6,527-2,528-0,529-8,530-6"
"VIR" "Virginiamycine" "Streptogramins" "NA" "NA" "NA" "NA"
"VOR" 71616 "Voriconazole" "Antifungals" "J02AC03,QJ02AC03" "Antimycotics for systemic use" "Triazole derivatives" "vori,vorico,vrc" "vfend,voriconazol,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"
"XER" 140830474 "Xeruborbactam" "Beta-lactamase inhibitors" "NA" "NA" "benzo,borate" "NA"
"XBR" 72144 "Xibornol" "Other" "J01XX02,QJ01XX02" "Other antibacterials" "Other antibacterials" "NA" "bactacine,bracen,nanbacine,xibornolo,xibornolum" "NA"
"ZID" 77846445 "Zidebactam" "Beta-lactamase inhibitors" "NA" "NA" "zidebactamsalt" "NA"
"ZFD" 76685216 "Zoliflodacin" "Spiropyrimidinetriones" "NA" "zol" "nuzolvence,spiro,zoliflodacina,zoliflodacine" "NA"
"ZOR" 70697970 "Zorbamycin" "Glycopeptides,Peptides" "NA" "NA" "bleomycetin,boanmycin,nbleomycinamide,pingyangmycin" "NA"
"VIR" 11979535 "Virginiamycine" "Other antibacterials" "NA" "NA" "NA" "NA"
"VOR" 71616 "Voriconazole" "Antifungals/antimycotics" "J02AC03,QJ02AC03" "Antimycotics for systemic use" "Triazole derivatives" "vori,vorico,vrc" "vfend,voriconazol,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,QJ01XX02" "Other antibacterials" "Other antibacterials" "NA" "bactacine,bracen,nanbacine,xibornolo,xibornolum" "NA"
"ZID" 77846445 "Zidebactam" "Other antibacterials" "NA" "NA" "zidebactamsalt" "NA"
"ZFD" "Zoliflodacin" "NA" "NA" "NA" "NA"
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pattern regular_expr case_sensitive affect_ab_name affect_mo_name en ar bn zh cs da nl fi fr de el hi id it ja ko no pl pt ro ru es sw sv tr uk ur vi
language name English FALSE FALSE FALSE FALSE English Arabic Bengali Chinese Czech Danish Dutch Finnish French German Greek Hindi Indonesian Italian Japanese Korean Norwegian Polish Portuguese Romanian Russian Spanish Swahili Swedish Turkish Ukrainian Urdu Vietnamese
language name FALSE FALSE FALSE FALSE English العربية ইংরেজি 汉语 Čeština Dansk Nederlands Suomi Français Deutsch Ελληνικά हिन्दी Inggris Italiano 日本語 영어 Norsk Polski Português Română Русский Español Kiswahili Svenska Türkçe Українська انگریزی Tiếng Anh
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Coagulase-negative Staphylococcus المكورات العنقودية سالبة التخثر কোয়াগুলেজ-নেগেটিভ স্ট্যাফিলোকক্কাস 凝固酶阴性葡萄球菌 Koaguláza-negativní stafylokok Koagulase-negative stafylokokker Coagulase-negatieve Staphylococcus Koagulaasinegatiivinen stafylokokki Staphylococcus à coagulase négative Koagulase-negative Staphylococcus Σταφυλόκοκκος με αρνητική πηκτικότητα कोएगुलेज़-ऩेगेटिव स्टैफिलोकोकस Stafilokokus koagulase-negatif Stafilococco coagulasi-negativo コアグラーゼ陰性ブドウ球菌 코아귤라제 음성 포도상구균 Koagulase-negative stafylokokker Staphylococcus koagulazoujemny Staphylococcus coagulase negativo Stafilococ coagulazo-negativ Коагулазоотрицательный стафилококк Staphylococcus coagulasa negativo Staphylococcus wasiokuwa na coagulase Koagulasnegativa stafylokocker Koagülaz-negatif Stafilokok Коагулазонегативний стафілокок کواگولیز منفی اسٹیفیلوکوکس Staphylococcus âm tính với coagulase
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Coagulase-positive Staphylococcus المكورات العنقودية موجبة التخثر কোয়াগুলেজ-পজিটিভ স্ট্যাফিলোকক্কাস 凝固酶阳性葡萄球菌 Koagulázopozitivní stafylokok Koagulase-positive stafylokokker Coagulase-positieve Staphylococcus Koagulaasipositiivinen stafylokokki Staphylococcus à coagulase positif Koagulase-positive Staphylococcus Σταφυλόκοκκος θετικός στην πήξη कोएगुलेज़-पॉज़िटिव स्टैफिलोकोकस Stafilokokus koagulase-positif Stafilococco coagulasi-positivo コアグラーゼ陽性ブドウ球菌 코아귤라제 양성 포도상구균 Koagulase-positive stafylokokker Staphylococcus koagulazo-dodatni Staphylococcus coagulase positivo Stafilococul coagulazo-pozitiv Коагулазоположительный стафилококк Staphylococcus coagulasa positivo Staphylococcus wenye coagulase Koagulaspositiva stafylokocker Koagülaz-pozitif Stafilokok Коагулазопозитивний стафілокок کواگولیز مثبت اسٹیفیلوکوکس Staphylococcus dương tính với coagulase
Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Coagulase-negative Staphylococcus المكورات العنقودية سالبة التخثر কোয়াগুলেজ-নেগেটিভ স্ট্যাফিলোকক্কাস 凝固酶阴性葡萄球菌 Koaguláza-negativní stafylokok Koagulase-negative stafylokokker Coagulase-negatieve Staphylococcus Koagulaasinegatiivinen stafylokokki Staphylococcus à coagulase négative Koagulase-negative Staphylococcus Σταφυλόκοκκος με αρνητική πηκτικότητα कोएगुलेज़-ऩेगेटिव स्टैफिलोकोकस Stafilokokus koagulase-negatif Staphylococcus negativo coagulasi コアグラーゼ陰性ブドウ球菌 코아귤라제 음성 포도상구균 Koagulase-negative stafylokokker Staphylococcus koagulazoujemny Staphylococcus coagulase negativo Stafilococ coagulazo-negativ Коагулазоотрицательный стафилококк Staphylococcus coagulasa negativo Staphylococcus wasiokuwa na coagulase Koagulasnegativa stafylokocker Koagülaz-negatif Stafilokok Коагулазонегативний стафілокок کواگولیز منفی اسٹیفیلوکوکس Staphylococcus âm tính với coagulase
Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Coagulase-positive Staphylococcus المكورات العنقودية موجبة التخثر কোয়াগুলেজ-পজিটিভ স্ট্যাফিলোকক্কাস 凝固酶阳性葡萄球菌 Koagulázopozitivní stafylokok Koagulase-positive stafylokokker Coagulase-positieve Staphylococcus Koagulaasipositiivinen stafylokokki Staphylococcus à coagulase positif Koagulase-positive Staphylococcus Σταφυλόκοκκος θετικός στην πήξη कोएगुलेज़-पॉज़िटिव स्टैफिलोकोकस Stafilokokus koagulase-positif Staphylococcus positivo coagulasi コアグラーゼ陽性ブドウ球菌 코아귤라제 양성 포도상구균 Koagulase-positive stafylokokker Staphylococcus koagulazo-dodatni Staphylococcus coagulase positivo Stafilococul coagulazo-pozitiv Коагулазоположительный стафилококк Staphylococcus coagulasa positivo Staphylococcus wenye coagulase Koagulaspositiva stafylokocker Koagülaz-pozitif Stafilokok Коагулазопозитивний стафілокок کواگولیز مثبت اسٹیفیلوکوکس Staphylococcus dương tính với coagulase
Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-haemolytic Streptococcus العقديات الحالة للدم من النوع بيتا বিটা-হেমোলাইটিক স্ট্রেপটোকক্কাস β-溶血性链球菌 Beta-hemolytický streptokok Beta-haemolytiske streptokokker Beta-hemolytische Streptococcus Beeta-hemolyyttinen streptokokki Streptococcus Bêta-hémolytique Beta-hämolytischer Streptococcus Β-αιμολυτικός στρεπτόκοκκος बीटा-हीमोलिटिक स्ट्रेप्टोकोकस Streptokokus beta-hemolitik Streptococcus Beta-emolitico ベータ溶血性レンサ球菌 베타 용혈성 연쇄상구균 Beta-hemolytiske streptokokker Streptococcus beta-hemolityczny Streptococcus Beta-hemolítico Streptococ beta-hemolitic Бета-гемолитический стрептококк Streptococcus Beta-hemolítico Streptococcus wa beta-hemolitiki Beta-hemolytiska streptokocker Beta-hemolitik Streptokok Бета-гемолітичний стрептокок بیٹا ہیمولائٹک اسٹریپٹوکوکس Streptococcus tan máu beta
unknown Gram-negatives TRUE TRUE FALSE TRUE unknown Gram-negatives سالبة الجرام غير معروفة অজানা গ্রাম-নেগেটিভ 不明革兰氏阴性菌 neznámé gramnegativní ukendte Gram-negative onbekende Gram-negatieven tuntemattomat gramnegatiiviset Gram négatifs inconnus unbekannte Gramnegativen άγνωστοι αρνητικοί κατά Gram अज्ञात ग्राम-ऩेगेटिव्स Gram negatif tidak diketahui Gram negativi sconosciuti 不明なグラム陰性菌 알 수 없는 그람 음성균 ukjent Gram-negative Nieznane bakterie Gram-ujemne Gram negativos desconhecidos Gram-negative necunoscute неизвестные грамотрицательные Gram negativos desconocidos Gram hasi wasiojulikana okända gramnegativa bakterier bilinmeyen Gram-negatifler невідомі грамнегативні نامعلوم گرام منفی Gram âm chưa xác định
unknown Gram-positives TRUE TRUE FALSE TRUE unknown Gram-positives موجبة الجرام غير معروفة অজানা গ্রাম-পজিটিভ 不明革兰氏阳性菌 neznámé grampozitivní ukendte Gram-positive onbekende Gram-positieven tuntemattomat grampositiiviset Gram positifs inconnus unbekannte Grampositiven άγνωστοι θετικοί κατά Gram अज्ञात ग्राम-पॉज़िटिव्स Gram positif tidak diketahui Gram positivi sconosciuti 未知のグラム陽性菌 알 수 없는 그람 양성균 ukjent Gram-positive Nieznane bakterie Gram-dodatnie Gram positivos desconhecidos Gram-pozitive necunoscute неизвестные грамположительные Gram positivos desconocidos Gram chanya wasiojulikana okända Gram-positiva bilinmeyen Gram-pozitifler невідомі грампозитивні نامعلوم گرام مثبت Gram dương chưa xác định
@@ -280,8 +280,7 @@ Antifungals FALSE TRUE TRUE FALSE Antifungals مضادات الفطريات অ
Antifungals/antimycotics FALSE TRUE TRUE FALSE Antifungals/antimycotics مضادات الفطريات/الفطريات المُمرِضة অ্যান্টিফাঙ্গালস/অ্যান্টিমাইকোটিকস 抗真菌药/抗真菌药 Antimykotika/antimykotika Antimykotika/antimykotika Antifungica/antimycotica Sienilääkkeet/antimykootit Antifongiques/antimycotiques Antimykotika/Antimykotika Αντιμυκητιασικά/αντιμυκητιασικά प्रतिफफूंद/प्रतिमाइकोटिक्स Antijamur/antimikotik Antifungini/antimicotici 抗真菌剤／抗真菌剤 항진균제/항진균성약물 Soppdrepende midler/antimykotika Środki przeciwgrzybicze/przeciwmikotyczne Antifúngicos/antimicóticos Antifungice/antimicrotice Противогрибковые препараты/антимикотики Antifúngicos/antimicóticos Dawa za kuua kuvu/antimaikoti Antimykotika/antimykotika Antifungaller/antimikotikler Протигрибкові засоби/антимікотики فنگس/اینٹی مائیکوٹک Thuốc chống nấm/kháng nấm
Antimycobacterials FALSE TRUE TRUE FALSE Antimycobacterials مضادات الفطريات الحمضية المقاومة অ্যান্টিমাইকোব্যাকটেরিয়ালস 抗霉菌素类 Antimykobakteriální látky Antimycobakterier Antimycobacteriele middelen Antimykobakteerit Antimycobactériens Antimykobakterielle Mittel Αντιμυκοβακτηριακά प्रतिमाइकोबैक्टीरियल्स Antimikobakteri Antimicobatterici 抗マイコバクテリア薬 항항산균제 Antimykobakterielle midler Środki przeciwgrzybicze Antimycobacterials Antimicobacteriene Антимикобактериальные препараты Antimicrobianos Dawa dhidi ya mykobakteria Antimykobakterier Antimikobakteriyeller Засоби, що діють на мікобактерії اینٹی مائیکوبیکٹیریل Thuốc chống trực khuẩn kháng axit
Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-lactams/penicillins البيتا-لاكتامات/البنسلينات বেটা-ল্যাকটামস/পেনিসিলিনস β-内酰胺类/青霉素类 Beta-laktamy/peniciliny Beta-lactamer/penicilliner Beta-lactams/penicillines Beetalaktaamit/penisilliinit Bêta-lactamines/pénicillines Beta-Lactame/Penicilline Β-λακτάμες/πενικιλλίνες बीटा-लैक्टाम्स/पेनिसिलिन्स Beta-laktam/penisilin Beta-lattami/penicilline β-ラクタム系／ペニシリン系抗菌薬 베타-락탐/페니실린 Betalaktamer/penicilliner Beta-laktamy/penicyliny Beta-lactâmicas/penicilinas Beta-lactame/peniciline Бета-лактамы/пенициллины Beta-lactámicos/penicilinas Betalaktamu/penisilini Beta-laktamer/penicilliner Beta-laktamlar/penisilinler Бета-лактами/пеніциліни بیٹا لیکٹمز/پینسلنز Beta-lactam/penicillin
Beta-lactams FALSE TRUE TRUE FALSE Betalactams البيتا-لاكتامات বেটা-ল্যাকটামস β-内酰胺类 Beta-laktamy Beta-lactamer Beta-lactams Beetalaktaamit Bêta-lactamines Beta-Lactame Β-λακτάμες बीटा-लैक्टाम्स Beta-laktam Beta-lattami β-ラクタム系抗菌薬 베타-락탐 Betalaktamer Beta-laktamy Beta-lactâmicas Beta-lactame Бета-лактамы Beta-lactámicos Betalaktamu Betalaktamer Beta-laktamlar Бета-лактами بیٹا لیکٹمز Beta-lactam
Beta-lactamase inhibitors FALSE TRUE TRUE FALSE Beta-lactamase inhibitors مثبطات بيتا-لاكتاماز বেটা-ল্যাকটামেজ ইনহিবিটরস β-内酰胺酶抑制剂 Inhibitory beta-laktamázy Beta-laktamasehæmmere Beta-lactamaseremmers Beetalaktamaasin estäjät Inhibiteurs de bêta-lactamase Beta-Laktamase-Inhibitoren Αναστολείς β-λακταμάσης बीटा-लैक्टामेज़ अवरोधक Inhibitor beta-laktamase Inibitori delle beta-lattamasi β-ラクタマーゼ阻害薬 베타-락타마제 억제제 Beta-laktamasehemmere Inhibitory beta-laktamaz Inibidores da beta-lactamase Inhibitori de beta-lactamază Ингибиторы бета-лактамаз Inhibidores de beta-lactamasa Vizuizi vya beta-laktamasi Beta-laktamashämmare Beta-laktamaz inhibitörleri Інгібітори бета-лактамаз بیٹا لیکٹامیز انہیبیٹرز Chất ức chế beta-lactamase
Betalactams FALSE TRUE TRUE FALSE Betalactams البيتا-لاكتامات বেটা-ল্যাকটামস β-内酰胺类 Beta-laktamy Beta-lactamer Beta-lactams Beetalaktaamit Bêta-lactamines Beta-Lactame Β-λακτάμες बीटा-लैक्टाम्स Beta-laktam Beta-lattami β-ラクタム系抗菌薬 베타-락탐 Betalaktamer Beta-laktamy Beta-lactâmicas Beta-lactame Бета-лактамы Beta-lactámicos Betalaktamu Betalaktamer Beta-laktamlar Бета-лактами بیٹا لیکٹمز Beta-lactam
Carbapenems FALSE TRUE TRUE FALSE Carbapenems الكاربابينيمات কার্বাপেনেমস 碳青霉烯类 Karbapenemy Carbapenemer Carbapenems Karbapeneemit Carbapénèmes Carbapeneme Καρβαπενέμες कार्बापेनेम्स Karbapenem Carbapenemi カルバペネム系抗生物質 카르바페넴 Carbapenemer Karbapenemy Carbapenêmicos Carbapeneme Карбапенемы Carbapenémicos Karbapenemu Carbapenemer Karbapenemler Карбапенеми کارباپینیمز Carbapenem
Cephalosporins FALSE TRUE TRUE FALSE Cephalosporins السيفالوسبورينات সেফালোসপরিনস 头孢菌素类 Cefalosporiny Cefalosporiner Cefalosporines Kefalosporiinit Céphalosporines Cephalosporine Κεφαλοσπορίνες सेफालोस्पोरिन्स Sefalosporin Cefalosporine セファロスポリン 세팔로스포린 Cefalosporiner Cefalosporyny Cefalosporinas Cefalosporine Цефалоспорины Cefalosporinas Sefalosporini Kefalosporiner Sefalosporinler Цефалоспорини سیفالوسپورنز Cephalosporin
Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporins (1st gen.) السيفالوسبورينات (الجيل الأول) সেফালোসপরিনস (১ম প্রজন্ম) 头孢菌素类（第一代） Cefalosporiny (1. gen.) Cefalosporiner (1. gen.) Cefalosporines (1e gen.) Kefalosporiinit (1. suk.) Céphalosporines (1ère génération) Cephalosporine (1. Gen.) Κεφαλοσπορίνες (1ου γένους) सेफालोस्पोरिन्स (प्रथम पीढ़ी) Sefalosporin (generasi 1) Cefalosporine (1° gen.) セファロスポリン系抗生物質（第1世代） 세팔로스포린 (1세대) Cefalosporiner (1. generasjon) Cefalosporyny (1. gen.) Cefalosporinas (1º género) Cefalosporine (prima generație) Цефалоспорины (1-го пок.) Cefalosporinas (1er gen.) Sefalosporini (kizazi cha 1) Kefalosporiner (första gen.) Sefalosporinler (1. kuşak) Цефалоспорини (1 пок.) سیفالوسپورنز (پہلی نسل) Cephalosporin (thế hệ 1)
@@ -303,7 +302,6 @@ Other antibacterials FALSE TRUE TRUE FALSE Other antibacterials مضادات ب
Oxazolidinones FALSE TRUE TRUE FALSE Oxazolidinones الأوكسازوليدينونات অক্সাজোলিডিনোনস 恶唑烷酮类 Oxazolidinone Oxazolidinones Oxazolidinonen Oxazolidinonit Oxazolidinones Oxazolidinone Οξαζολιδινόνες ऑक्साज़ोलिडिनोन्स Oksazolidinon Oxazolidinonas オキサゾリジノン 옥사졸리디논 Oxazolidinones Oksazolidynony Oxazolidinonas Oxazolidinone Оксазолидиноны Oxazolidinonas Oxazolidinoni Oxazolidinones Oxazolidinonlar Оксазолідинони اوکسا زولڈی نونز Oxazolidinone
Penicillins FALSE TRUE TRUE FALSE Penicillins البنسلينات পেনিসিলিনস 青霉素类 Пенициллины Penicillins Penicillines Penisilliinit Pénicillines Penicillins Πενικιλίνες पेनिसिलिन्स Penisilin Penicilinas ペニシリン 페니실린 Penicillins Penicyliny Penicilinas Peniciline Пенициллины Penicilinas Penisilini Penicillins Penisilinler Пеніциліни پینسلن Penicillin
Phenicols FALSE TRUE TRUE FALSE Phenicols الفينيكولات ফেনিকলস 酚类抗生素 Phenikoly Fenicoler Fenicols Fenikolit Phénicols Phenicol Φαινικόλες फेनिकोल्स Fenikol Fenicoli フェニコール 페니콜 Fenicoler Fenikole Fenicóis Fenicoli Фениколы Fenicoles Fenikoli Fenicoler Fenikoller Фенікони فینیکولز Phenicols
Phosphonics FALSE TRUE TRUE FALSE Phosphonics الفوسفونيّات ফসফোনিকস 膦酸类 Phosphonáty Fosfonater Fosfonaten Fosfonaatit Phosphoniques Phosphonates Φωσφονικά फॉस्फ़ोनिक्स Fosfonik Fosfonici ホスホン酸系抗菌薬 포스포닉계 Fosfonater Fosfoniany Fosfônicos Fosfonați Фосфоники Fosfónicos Fosfoniki Fosfonater Fosfonikler Фосфоніки فاسفونکس Các hợp chất phosphonic
Polymyxins FALSE TRUE TRUE FALSE Polymyxins البوليميكسينات পলিমিক্সিনস 多粘菌素类 Polymyxiny Polymyxiner Polymyxines Polymysiinit Polymyxines Polymyxine Πολυμυξίνες पॉलीमिक्सिन्स Polimiksin Polimixine ポリミキシン 폴리믹신 Polymyxiner Polimyksyny Polimixinas Polimixine Полимиксины Polimixinas Polimiksini Polymyxiner Polimiksinler Поліміксини پولی مائکسینز Polymyxin
Quinolones FALSE TRUE TRUE FALSE Quinolones الكوينولونات কুইনোলোনস 喹诺酮类 Chinolony Kinoloner Quinolonen Kinolonit Quinolones Quinolone Κινολόνες क्विनोलोन्स Kuinalon Chinoloni キノロン 퀴놀론 Kinoloner Quinolony Quinolones Quinolone Хинолоны Quinolonas Kinoloni Kinoloner Kinolonlar Хінолони کوئنولونز Quinolone
Rifamycins FALSE TRUE TRUE FALSE Rifamycins الريفاميسينات রিফামাইসিনস 利福霉素类 Rifamycine Rifamycins Rifamycinen Rifamysiinit Rifamycines Rifamycine Ριφαμυκίνες रिफामाइसिन्स Rifamisin Rifamicinas リファマイシン 리팜이신 Rifamycins Rifamycyny Rifamycinas Rifamicine Рифамицины Rifamicinas Rifamasini Rifamycins Rifamisinler Рифаміцини ریفامائسنز Rifamycin
1 pattern regular_expr case_sensitive affect_ab_name affect_mo_name en ar bn zh cs da nl fi fr de el hi id it ja ko no pl pt ro ru es sw sv tr uk ur vi
2 language name English FALSE FALSE FALSE FALSE English Arabic Bengali Chinese Czech Danish Dutch Finnish French German Greek Hindi Indonesian Italian Japanese Korean Norwegian Polish Portuguese Romanian Russian Spanish Swahili Swedish Turkish Ukrainian Urdu Vietnamese
3 language name FALSE FALSE FALSE FALSE English العربية ইংরেজি 汉语 Čeština Dansk Nederlands Suomi Français Deutsch Ελληνικά हिन्दी Inggris Italiano 日本語 영어 Norsk Polski Português Română Русский Español Kiswahili Svenska Türkçe Українська انگریزی Tiếng Anh
4 Coagulase-negative Staphylococcus TRUE TRUE FALSE TRUE Coagulase-negative Staphylococcus المكورات العنقودية سالبة التخثر কোয়াগুলেজ-নেগেটিভ স্ট্যাফিলোকক্কাস 凝固酶阴性葡萄球菌 Koaguláza-negativní stafylokok Koagulase-negative stafylokokker Coagulase-negatieve Staphylococcus Koagulaasinegatiivinen stafylokokki Staphylococcus à coagulase négative Koagulase-negative Staphylococcus Σταφυλόκοκκος με αρνητική πηκτικότητα कोएगुलेज़-ऩेगेटिव स्टैफिलोकोकस Stafilokokus koagulase-negatif Stafilococco coagulasi-negativo Staphylococcus negativo coagulasi コアグラーゼ陰性ブドウ球菌 코아귤라제 음성 포도상구균 Koagulase-negative stafylokokker Staphylococcus koagulazoujemny Staphylococcus coagulase negativo Stafilococ coagulazo-negativ Коагулазоотрицательный стафилококк Staphylococcus coagulasa negativo Staphylococcus wasiokuwa na coagulase Koagulasnegativa stafylokocker Koagülaz-negatif Stafilokok Коагулазонегативний стафілокок کواگولیز منفی اسٹیفیلوکوکس Staphylococcus âm tính với coagulase
5 Coagulase-positive Staphylococcus TRUE TRUE FALSE TRUE Coagulase-positive Staphylococcus المكورات العنقودية موجبة التخثر কোয়াগুলেজ-পজিটিভ স্ট্যাফিলোকক্কাস 凝固酶阳性葡萄球菌 Koagulázopozitivní stafylokok Koagulase-positive stafylokokker Coagulase-positieve Staphylococcus Koagulaasipositiivinen stafylokokki Staphylococcus à coagulase positif Koagulase-positive Staphylococcus Σταφυλόκοκκος θετικός στην πήξη कोएगुलेज़-पॉज़िटिव स्टैफिलोकोकस Stafilokokus koagulase-positif Stafilococco coagulasi-positivo Staphylococcus positivo coagulasi コアグラーゼ陽性ブドウ球菌 코아귤라제 양성 포도상구균 Koagulase-positive stafylokokker Staphylococcus koagulazo-dodatni Staphylococcus coagulase positivo Stafilococul coagulazo-pozitiv Коагулазоположительный стафилококк Staphylococcus coagulasa positivo Staphylococcus wenye coagulase Koagulaspositiva stafylokocker Koagülaz-pozitif Stafilokok Коагулазопозитивний стафілокок کواگولیز مثبت اسٹیفیلوکوکس Staphylococcus dương tính với coagulase
6 Beta-haemolytic Streptococcus TRUE TRUE FALSE TRUE Beta-haemolytic Streptococcus العقديات الحالة للدم من النوع بيتا বিটা-হেমোলাইটিক স্ট্রেপটোকক্কাস β-溶血性链球菌 Beta-hemolytický streptokok Beta-haemolytiske streptokokker Beta-hemolytische Streptococcus Beeta-hemolyyttinen streptokokki Streptococcus Bêta-hémolytique Beta-hämolytischer Streptococcus Β-αιμολυτικός στρεπτόκοκκος बीटा-हीमोलिटिक स्ट्रेप्टोकोकस Streptokokus beta-hemolitik Streptococcus Beta-emolitico ベータ溶血性レンサ球菌 베타 용혈성 연쇄상구균 Beta-hemolytiske streptokokker Streptococcus beta-hemolityczny Streptococcus Beta-hemolítico Streptococ beta-hemolitic Бета-гемолитический стрептококк Streptococcus Beta-hemolítico Streptococcus wa beta-hemolitiki Beta-hemolytiska streptokocker Beta-hemolitik Streptokok Бета-гемолітичний стрептокок بیٹا ہیمولائٹک اسٹریپٹوکوکس Streptococcus tan máu beta
7 unknown Gram-negatives TRUE TRUE FALSE TRUE unknown Gram-negatives سالبة الجرام غير معروفة অজানা গ্রাম-নেগেটিভ 不明革兰氏阴性菌 neznámé gramnegativní ukendte Gram-negative onbekende Gram-negatieven tuntemattomat gramnegatiiviset Gram négatifs inconnus unbekannte Gramnegativen άγνωστοι αρνητικοί κατά Gram अज्ञात ग्राम-ऩेगेटिव्स Gram negatif tidak diketahui Gram negativi sconosciuti 不明なグラム陰性菌 알 수 없는 그람 음성균 ukjent Gram-negative Nieznane bakterie Gram-ujemne Gram negativos desconhecidos Gram-negative necunoscute неизвестные грамотрицательные Gram negativos desconocidos Gram hasi wasiojulikana okända gramnegativa bakterier bilinmeyen Gram-negatifler невідомі грамнегативні نامعلوم گرام منفی Gram âm chưa xác định
8 unknown Gram-positives TRUE TRUE FALSE TRUE unknown Gram-positives موجبة الجرام غير معروفة অজানা গ্রাম-পজিটিভ 不明革兰氏阳性菌 neznámé grampozitivní ukendte Gram-positive onbekende Gram-positieven tuntemattomat grampositiiviset Gram positifs inconnus unbekannte Grampositiven άγνωστοι θετικοί κατά Gram अज्ञात ग्राम-पॉज़िटिव्स Gram positif tidak diketahui Gram positivi sconosciuti 未知のグラム陽性菌 알 수 없는 그람 양성균 ukjent Gram-positive Nieznane bakterie Gram-dodatnie Gram positivos desconhecidos Gram-pozitive necunoscute неизвестные грамположительные Gram positivos desconocidos Gram chanya wasiojulikana okända Gram-positiva bilinmeyen Gram-pozitifler невідомі грампозитивні نامعلوم گرام مثبت Gram dương chưa xác định
280 Antifungals/antimycotics FALSE TRUE TRUE FALSE Antifungals/antimycotics مضادات الفطريات/الفطريات المُمرِضة অ্যান্টিফাঙ্গালস/অ্যান্টিমাইকোটিকস 抗真菌药/抗真菌药 Antimykotika/antimykotika Antimykotika/antimykotika Antifungica/antimycotica Sienilääkkeet/antimykootit Antifongiques/antimycotiques Antimykotika/Antimykotika Αντιμυκητιασικά/αντιμυκητιασικά प्रतिफफूंद/प्रतिमाइकोटिक्स Antijamur/antimikotik Antifungini/antimicotici 抗真菌剤／抗真菌剤 항진균제/항진균성약물 Soppdrepende midler/antimykotika Środki przeciwgrzybicze/przeciwmikotyczne Antifúngicos/antimicóticos Antifungice/antimicrotice Противогрибковые препараты/антимикотики Antifúngicos/antimicóticos Dawa za kuua kuvu/antimaikoti Antimykotika/antimykotika Antifungaller/antimikotikler Протигрибкові засоби/антимікотики فنگس/اینٹی مائیکوٹک Thuốc chống nấm/kháng nấm
281 Antimycobacterials FALSE TRUE TRUE FALSE Antimycobacterials مضادات الفطريات الحمضية المقاومة অ্যান্টিমাইকোব্যাকটেরিয়ালস 抗霉菌素类 Antimykobakteriální látky Antimycobakterier Antimycobacteriele middelen Antimykobakteerit Antimycobactériens Antimykobakterielle Mittel Αντιμυκοβακτηριακά प्रतिमाइकोबैक्टीरियल्स Antimikobakteri Antimicobatterici 抗マイコバクテリア薬 항항산균제 Antimykobakterielle midler Środki przeciwgrzybicze Antimycobacterials Antimicobacteriene Антимикобактериальные препараты Antimicrobianos Dawa dhidi ya mykobakteria Antimykobakterier Antimikobakteriyeller Засоби, що діють на мікобактерії اینٹی مائیکوبیکٹیریل Thuốc chống trực khuẩn kháng axit
282 Beta-lactams/penicillins FALSE TRUE TRUE FALSE Beta-lactams/penicillins البيتا-لاكتامات/البنسلينات বেটা-ল্যাকটামস/পেনিসিলিনস β-内酰胺类/青霉素类 Beta-laktamy/peniciliny Beta-lactamer/penicilliner Beta-lactams/penicillines Beetalaktaamit/penisilliinit Bêta-lactamines/pénicillines Beta-Lactame/Penicilline Β-λακτάμες/πενικιλλίνες बीटा-लैक्टाम्स/पेनिसिलिन्स Beta-laktam/penisilin Beta-lattami/penicilline β-ラクタム系／ペニシリン系抗菌薬 베타-락탐/페니실린 Betalaktamer/penicilliner Beta-laktamy/penicyliny Beta-lactâmicas/penicilinas Beta-lactame/peniciline Бета-лактамы/пенициллины Beta-lactámicos/penicilinas Betalaktamu/penisilini Beta-laktamer/penicilliner Beta-laktamlar/penisilinler Бета-лактами/пеніциліни بیٹا لیکٹمز/پینسلنز Beta-lactam/penicillin
283 Beta-lactams Betalactams FALSE TRUE TRUE FALSE Betalactams البيتا-لاكتامات বেটা-ল্যাকটামস β-内酰胺类 Beta-laktamy Beta-lactamer Beta-lactams Beetalaktaamit Bêta-lactamines Beta-Lactame Β-λακτάμες बीटा-लैक्टाम्स Beta-laktam Beta-lattami β-ラクタム系抗菌薬 베타-락탐 Betalaktamer Beta-laktamy Beta-lactâmicas Beta-lactame Бета-лактамы Beta-lactámicos Betalaktamu Betalaktamer Beta-laktamlar Бета-лактами بیٹا لیکٹمز Beta-lactam
Beta-lactamase inhibitors FALSE TRUE TRUE FALSE Beta-lactamase inhibitors مثبطات بيتا-لاكتاماز বেটা-ল্যাকটামেজ ইনহিবিটরস β-内酰胺酶抑制剂 Inhibitory beta-laktamázy Beta-laktamasehæmmere Beta-lactamaseremmers Beetalaktamaasin estäjät Inhibiteurs de bêta-lactamase Beta-Laktamase-Inhibitoren Αναστολείς β-λακταμάσης बीटा-लैक्टामेज़ अवरोधक Inhibitor beta-laktamase Inibitori delle beta-lattamasi β-ラクタマーゼ阻害薬 베타-락타마제 억제제 Beta-laktamasehemmere Inhibitory beta-laktamaz Inibidores da beta-lactamase Inhibitori de beta-lactamază Ингибиторы бета-лактамаз Inhibidores de beta-lactamasa Vizuizi vya beta-laktamasi Beta-laktamashämmare Beta-laktamaz inhibitörleri Інгібітори бета-лактамаз بیٹا لیکٹامیز انہیبیٹرز Chất ức chế beta-lactamase
284 Carbapenems FALSE TRUE TRUE FALSE Carbapenems الكاربابينيمات কার্বাপেনেমস 碳青霉烯类 Karbapenemy Carbapenemer Carbapenems Karbapeneemit Carbapénèmes Carbapeneme Καρβαπενέμες कार्बापेनेम्स Karbapenem Carbapenemi カルバペネム系抗生物質 카르바페넴 Carbapenemer Karbapenemy Carbapenêmicos Carbapeneme Карбапенемы Carbapenémicos Karbapenemu Carbapenemer Karbapenemler Карбапенеми کارباپینیمز Carbapenem
285 Cephalosporins FALSE TRUE TRUE FALSE Cephalosporins السيفالوسبورينات সেফালোসপরিনস 头孢菌素类 Cefalosporiny Cefalosporiner Cefalosporines Kefalosporiinit Céphalosporines Cephalosporine Κεφαλοσπορίνες सेफालोस्पोरिन्स Sefalosporin Cefalosporine セファロスポリン 세팔로스포린 Cefalosporiner Cefalosporyny Cefalosporinas Cefalosporine Цефалоспорины Cefalosporinas Sefalosporini Kefalosporiner Sefalosporinler Цефалоспорини سیفالوسپورنز Cephalosporin
286 Cephalosporins (1st gen.) FALSE TRUE TRUE FALSE Cephalosporins (1st gen.) السيفالوسبورينات (الجيل الأول) সেফালোসপরিনস (১ম প্রজন্ম) 头孢菌素类（第一代） Cefalosporiny (1. gen.) Cefalosporiner (1. gen.) Cefalosporines (1e gen.) Kefalosporiinit (1. suk.) Céphalosporines (1ère génération) Cephalosporine (1. Gen.) Κεφαλοσπορίνες (1ου γένους) सेफालोस्पोरिन्स (प्रथम पीढ़ी) Sefalosporin (generasi 1) Cefalosporine (1° gen.) セファロスポリン系抗生物質（第1世代） 세팔로스포린 (1세대) Cefalosporiner (1. generasjon) Cefalosporyny (1. gen.) Cefalosporinas (1º género) Cefalosporine (prima generație) Цефалоспорины (1-го пок.) Cefalosporinas (1er gen.) Sefalosporini (kizazi cha 1) Kefalosporiner (första gen.) Sefalosporinler (1. kuşak) Цефалоспорини (1 пок.) سیفالوسپورنز (پہلی نسل) Cephalosporin (thế hệ 1)
302 Oxazolidinones FALSE TRUE TRUE FALSE Oxazolidinones الأوكسازوليدينونات অক্সাজোলিডিনোনস 恶唑烷酮类 Oxazolidinone Oxazolidinones Oxazolidinonen Oxazolidinonit Oxazolidinones Oxazolidinone Οξαζολιδινόνες ऑक्साज़ोलिडिनोन्स Oksazolidinon Oxazolidinonas オキサゾリジノン 옥사졸리디논 Oxazolidinones Oksazolidynony Oxazolidinonas Oxazolidinone Оксазолидиноны Oxazolidinonas Oxazolidinoni Oxazolidinones Oxazolidinonlar Оксазолідинони اوکسا زولڈی نونز Oxazolidinone
303 Penicillins FALSE TRUE TRUE FALSE Penicillins البنسلينات পেনিসিলিনস 青霉素类 Пенициллины Penicillins Penicillines Penisilliinit Pénicillines Penicillins Πενικιλίνες पेनिसिलिन्स Penisilin Penicilinas ペニシリン 페니실린 Penicillins Penicyliny Penicilinas Peniciline Пенициллины Penicilinas Penisilini Penicillins Penisilinler Пеніциліни پینسلن Penicillin
304 Phenicols FALSE TRUE TRUE FALSE Phenicols الفينيكولات ফেনিকলস 酚类抗生素 Phenikoly Fenicoler Fenicols Fenikolit Phénicols Phenicol Φαινικόλες फेनिकोल्स Fenikol Fenicoli フェニコール 페니콜 Fenicoler Fenikole Fenicóis Fenicoli Фениколы Fenicoles Fenikoli Fenicoler Fenikoller Фенікони فینیکولز Phenicols
Phosphonics FALSE TRUE TRUE FALSE Phosphonics الفوسفونيّات ফসফোনিকস 膦酸类 Phosphonáty Fosfonater Fosfonaten Fosfonaatit Phosphoniques Phosphonates Φωσφονικά फॉस्फ़ोनिक्स Fosfonik Fosfonici ホスホン酸系抗菌薬 포스포닉계 Fosfonater Fosfoniany Fosfônicos Fosfonați Фосфоники Fosfónicos Fosfoniki Fosfonater Fosfonikler Фосфоніки فاسفونکس Các hợp chất phosphonic
305 Polymyxins FALSE TRUE TRUE FALSE Polymyxins البوليميكسينات পলিমিক্সিনস 多粘菌素类 Polymyxiny Polymyxiner Polymyxines Polymysiinit Polymyxines Polymyxine Πολυμυξίνες पॉलीमिक्सिन्स Polimiksin Polimixine ポリミキシン 폴리믹신 Polymyxiner Polimyksyny Polimixinas Polimixine Полимиксины Polimixinas Polimiksini Polymyxiner Polimiksinler Поліміксини پولی مائکسینز Polymyxin
306 Quinolones FALSE TRUE TRUE FALSE Quinolones الكوينولونات কুইনোলোনস 喹诺酮类 Chinolony Kinoloner Quinolonen Kinolonit Quinolones Quinolone Κινολόνες क्विनोलोन्स Kuinalon Chinoloni キノロン 퀴놀론 Kinoloner Quinolony Quinolones Quinolone Хинолоны Quinolonas Kinoloni Kinoloner Kinolonlar Хінолони کوئنولونز Quinolone
307 Rifamycins FALSE TRUE TRUE FALSE Rifamycins الريفاميسينات রিফামাইসিনস 利福霉素类 Rifamycine Rifamycins Rifamycinen Rifamysiinit Rifamycines Rifamycine Ριφαμυκίνες रिफामाइसिन्स Rifamisin Rifamicinas リファマイシン 리팜이신 Rifamycins Rifamycyny Rifamycinas Rifamicine Рифамицины Rifamicinas Rifamasini Rifamycins Rifamisinler Рифаміцини ریفامائسنز Rifamycin
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index.md
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@@ -318,10 +318,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB),
list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
#> category susceptible. Set the `guideline` argument or the `AMR_guideline`
#> option to either "CLSI" or "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr>
man/AMR-options.Rd
+4 -13
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@@ -4,27 +4,18 @@
\alias{AMR-options}
\title{Options for the AMR package}
\description{
This is an overview of all the package-specific options you can set in the \code{AMR} package. Set them using the \code{\link[=options]{options()}} function, e.g.:
\code{options(AMR_guideline = "CLSI")}
This is an overview of all the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
}
\section{Options (alphabetical order)}{
\section{Options}{
\itemize{
\item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-22) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use.
\item \code{AMR_breakpoint_type} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate which breakpoint type to use. This must be either "ECOFF", "animal", or "human".
\item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"none"}, \code{"conservative"}, \code{"standard"}, or \code{"lenient"} - the default is \code{"conservative"}.
\item \code{AMR_capped_mic_handling} \cr A \link{character} to use in \code{\link[=as.sir]{as.sir()}}, to indicate how capped MIC values (\code{<}, \code{<=}, \code{>}, \code{>=}) should be interpreted. Must be one of \code{"standard"}, \code{"strict"}, \code{"relaxed"}, or \code{"inverse"} - the default is \code{"standard"}.
\item \code{AMR_cleaning_regex} \cr A \link[base:regex]{regular expression} (case-insensitive) to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to clean the user input. The default is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".
\item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
\item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
\item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).
\itemize{
\item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.
\item For \code{\link[=resistance]{resistance()}} and \code{\link[=susceptibility]{susceptibility()}}, this setting determines how the \code{"I"} (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, \code{"I"} is considered \emph{resistant} in susceptibility calculations; under EUCAST, \code{"I"} is considered \emph{susceptible} in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
\item For \code{\link[=interpretive_rules]{interpretive_rules()}}, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
\item For many plotting functions (e.g., for MIC or disk diffusion values), supplying \code{mo} and \code{ab} enables automatic SIR-based interpretative colouring. These colours are derived from \code{\link[=as.sir]{as.sir()}} in the background and therefore depend on the active \code{guideline} setting, which again uses EUCAST 2025 if not set explicitly.
}
\item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2025"}. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
\item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
\item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
@@ -52,7 +43,7 @@ In this file, you can set options such as...
...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with \code{\link[=as.sir]{as.sir()}}.
\subsection{Share Options Within Team}{
For a more collaborative 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:
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:
\enumerate{
\item Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
\item For each user, open the \code{.Rprofile} file using \code{utils::file.edit("~/.Rprofile")} and put in there:
man/AMR.Rd
+2 -2
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@@ -83,10 +83,10 @@ Other contributors:
\item Judith M. Fonville [contributor]
\item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
\item Matthew Saab (\href{https://orcid.org/0009-0008-6626-7919}{ORCID}) [contributor]
\item Matthew Saab [contributor]
\item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
\item Rogier P. Schade (\href{https://orcid.org/0000-0002-9487-4467}{ORCID}) [contributor]
\item Rogier P. Schade [contributor]
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
\item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
man/ab_property.Rd
+2 -5
View File
@@ -27,7 +27,7 @@ ab_synonyms(x, ...)
ab_tradenames(x, ...)
ab_group(x, language = get_AMR_locale(), all_groups = FALSE, ...)
ab_group(x, language = get_AMR_locale(), ...)
ab_atc(x, only_first = FALSE, ...)
@@ -59,8 +59,6 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
\item{...}{In case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}.}
\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most specific group name.}
\item{only_first}{A \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).}
\item{administration}{Way of administration, either \code{"oral"} or \code{"iv"}.}
@@ -96,7 +94,7 @@ The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column ren
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://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
}
\section{Download Our Reference Data}{
@@ -116,7 +114,6 @@ ab_cid("AMX")
ab_synonyms("AMX")
ab_tradenames("AMX")
ab_group("AMX")
ab_group("AMX", all_groups = TRUE) # most specific to most general
ab_atc_group1("AMX")
ab_atc_group2("AMX")
ab_url("AMX")
man/amr-tidymodels.Rd
+10 -23
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@@ -2,27 +2,21 @@
% Please edit documentation in R/tidymodels.R
\name{amr-tidymodels}
\alias{amr-tidymodels}
\alias{all_sir}
\alias{all_sir_predictors}
\alias{all_mic}
\alias{all_mic_predictors}
\alias{all_disk}
\alias{all_disk_predictors}
\alias{all_sir}
\alias{all_sir_predictors}
\alias{step_mic_log2}
\alias{step_sir_numeric}
\title{AMR Extensions for Tidymodels}
\usage{
all_sir()
all_sir_predictors()
all_mic()
all_mic_predictors()
all_disk()
all_sir()
all_disk_predictors()
all_sir_predictors()
step_mic_log2(recipe, ..., role = NA, trained = FALSE, columns = NULL,
skip = FALSE, id = recipes::rand_id("mic_log2"))
@@ -51,22 +45,21 @@ may affect the computations for subsequent operations.}
\item{id}{A character string that is unique to this step to identify it.}
}
\description{
This family of functions allows using AMR-specific data types such as \verb{<sir>} and \verb{<mic>} inside \code{tidymodels} pipelines.
This family of functions allows using AMR-specific data types such as \verb{<mic>} and \verb{<sir>} inside \code{tidymodels} pipelines.
}
\details{
You can read more in our online \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{AMR with tidymodels introduction}.
Tidyselect helpers include:
\itemize{
\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \code{\link[=as.sir]{<sir>}} columns
\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \code{\link[=as.mic]{<mic>}} columns
\item \code{\link[=all_disk]{all_disk()}} and \code{\link[=all_disk_predictors]{all_disk_predictors()}} to select \code{\link[=as.disk]{<disk>}} columns
\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \verb{<mic>} columns
\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \verb{<sir>} columns
}
Pre-processing pipeline steps include:
\itemize{
\item \code{\link[=step_sir_numeric]{step_sir_numeric()}} to convert SIR columns to numeric (via \code{as.numeric()}), to be used with \code{\link[=all_sir_predictors]{all_sir_predictors()}}: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. Keep this in mind for further processing, especially if the model does not allow for \code{NA} values.
\item \code{\link[=step_mic_log2]{step_mic_log2()}} to convert MIC columns to numeric (via \code{as.numeric()}) and apply a log2 transform, to be used with \code{\link[=all_mic_predictors]{all_mic_predictors()}}
\item \code{\link[=step_sir_numeric]{step_sir_numeric()}} to convert SIR columns to numeric (via \code{as.numeric()}), to be used with \code{\link[=all_sir_predictors]{all_sir_predictors()}}: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. Keep this in mind for further processing, especially if the model does not allow for \code{NA} values.
}
These steps integrate with \code{recipes::recipe()} and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
@@ -119,13 +112,7 @@ if (require("tidymodels")) {
bind_cols(out_testing)
# Evaluate predictions using standard classification metrics
our_metrics <- metric_set(accuracy,
recall,
precision,
sensitivity,
specificity,
ppv,
npv)
our_metrics <- metric_set(accuracy, kap, ppv, npv)
metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
# Show performance
@@ -133,6 +120,6 @@ if (require("tidymodels")) {
}
}
\seealso{
\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.sir]{as.sir()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}}
\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.sir]{as.sir()}}
}
\keyword{internal}
man/amr_course.Rd
-36
View File
@@ -1,36 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/amr_course.R
\name{amr_course}
\alias{amr_course}
\title{Download and Unpack an AMR Course Repository}
\usage{
amr_course(github_repo, branch = "main", ...)
}
\arguments{
\item{github_repo}{A character string specifying the GitHub repository with username and repo name, e.g. \code{"https://github.com/username/repo"}.}
\item{branch}{A character string specifying the branch to download. Defaults to \code{"main"}.}
\item{...}{Additional arguments passed on to \code{\link[usethis:zip-utils]{usethis::use_course()}}.}
}
\value{
Called for its side effect. \code{\link[usethis:zip-utils]{usethis::use_course()}} will prompt the user to choose a destination and open the extracted project. Returns invisibly whatever \code{\link[usethis:zip-utils]{usethis::use_course()}} returns.
}
\description{
Downloads and unpacks a GitHub repository containing course materials, using \code{\link[usethis:zip-utils]{usethis::use_course()}}. This is a convenience wrapper intended for use in educational settings, such as workshops or tutorials associated with the AMR package.
}
\details{
This function constructs a ZIP archive URL from the provided \code{github_repo} and \code{branch}, then delegates to \code{\link[usethis:zip-utils]{usethis::use_course()}} to handle the download and extraction.
The function is designed for interactive use in course or workshop settings and is not intended for use in non-interactive or automated pipelines.
}
\examples{
\dontrun{
# Let this run by users, e.g., webinar participants
amr_course("https://github.com/my_user_name/our_AMR_course")
}
}
\seealso{
\code{\link[usethis:zip-utils]{usethis::use_course()}}
}
man/antibiogram.Rd
+2 -2
View File
@@ -72,7 +72,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item{ab_transform}{A character to transform antimicrobial input - must be one of the column names of the \link{antimicrobials} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case-and-replace-when]{case_when()}}. See \emph{Examples}.}
\item{syndromic_group}{A column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
\item{add_total_n}{\emph{(deprecated in favour of \code{formatting_type})} A \link{logical} to indicate whether \code{n_tested} available numbers per pathogen should be added to the table (default is \code{TRUE}). This will add the lowest and highest number of available isolates per antimicrobial (e.g, if for \emph{E. coli} 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200"). This option is unavailable when \code{wisca = TRUE}; in that case, use \code{\link[=retrieve_wisca_parameters]{retrieve_wisca_parameters()}} to get the parameters used for WISCA.}
@@ -209,7 +209,7 @@ wisca(your_data,
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"))
}\if{html}{\out{</div>}}
WISCA uses a sophisticated Bayesian decision model to combine both local and pooled antimicrobial resistance data. This approach not only evaluates local patterns but can also draw on multi-centre data sets to improve regimen accuracy, even in low-incidence infections like paediatric bloodstream infections (BSIs).
WISCA uses a sophisticated Bayesian decision model to combine both local and pooled antimicrobial resistance data. This approach not only evaluates local patterns but can also draw on multi-centre datasets to improve regimen accuracy, even in low-incidence infections like paediatric bloodstream infections (BSIs).
}
}
man/antimicrobial_selectors.Rd
+18 -34
View File
@@ -17,7 +17,6 @@
\alias{cephalosporins_5th}
\alias{fluoroquinolones}
\alias{glycopeptides}
\alias{ionophores}
\alias{isoxazolylpenicillins}
\alias{lincosamides}
\alias{lipoglycopeptides}
@@ -26,13 +25,10 @@
\alias{nitrofurans}
\alias{oxazolidinones}
\alias{penicillins}
\alias{peptides}
\alias{phenicols}
\alias{phosphonics}
\alias{polymyxins}
\alias{quinolones}
\alias{rifamycins}
\alias{spiropyrimidinetriones}
\alias{streptogramins}
\alias{sulfonamides}
\alias{tetracyclines}
@@ -82,8 +78,6 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@@ -102,12 +96,8 @@ oxazolidinones(only_sir_columns = FALSE, return_all = TRUE, ...)
penicillins(only_sir_columns = FALSE, return_all = TRUE, ...)
peptides(only_sir_columns = FALSE, return_all = TRUE, ...)
phenicols(only_sir_columns = FALSE, return_all = TRUE, ...)
phosphonics(only_sir_columns = FALSE, return_all = TRUE, ...)
polymyxins(only_sir_columns = FALSE, only_treatable = TRUE,
return_all = TRUE, ...)
@@ -116,8 +106,6 @@ quinolones(only_sir_columns = FALSE, only_treatable = TRUE,
rifamycins(only_sir_columns = FALSE, return_all = TRUE, ...)
spiropyrimidinetriones(only_sir_columns = FALSE, return_all = TRUE, ...)
streptogramins(only_sir_columns = FALSE, return_all = TRUE, ...)
sulfonamides(only_sir_columns = FALSE, return_all = TRUE, ...)
@@ -185,46 +173,42 @@ The \code{\link[=administrable_per_os]{administrable_per_os()}} and \code{\link[
The \code{\link[=amr_selector]{amr_selector()}} function can be used to internally filter the \link{antimicrobials} data set on any results, see \emph{Examples}. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of \emph{E. coli} and \emph{K. pneumoniae} and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies \href{https://www.eucast.org/expert_rules_and_expected_phenotypes}{'EUCAST Expected Resistant Phenotypes' v1.2} (2023) to determine intrinsic resistance, using the \code{\link[=eucast_rules]{eucast_rules()}} function internally. Because of this determination, this function is quite slow in terms of performance.
}
\section{Full list of supported (antimicrobial) classes}{
\itemize{
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), kasugamycin (KAS), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), and ampicillin (AMP)
\item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
\item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
\item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), taniborbactam (TAN), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftibuten/avibactam (CTA), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), taniborbactam (TAN), and tebipenem (TBP)
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
\item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
\item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
\item \code{\link[=cephalosporins]{cephalosporins()}} can select: \cr cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), and loracarbef (LOR)
\item \code{\link[=cephalosporins_1st]{cephalosporins_1st()}} can select: \cr cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), and cephradine (CED)
\item \code{\link[=cephalosporins_2nd]{cephalosporins_2nd()}} can select: \cr cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), and loracarbef (LOR)
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftibuten/avibactam (CTA), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/taniborbactam (FTA), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
\item \code{\link[=cephalosporins_3rd]{cephalosporins_3rd()}} can select: \cr cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), and latamoxef (LTM)
\item \code{\link[=cephalosporins_4th]{cephalosporins_4th()}} can select: \cr cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), and cefquinome (CEQ)
\item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
\item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)
\item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), and vancomycin-macromethod (VAM)
\item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
\item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), lincomycin (LIN), and pirlimycin (PRL)
\item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), clindamycin inducible screening test (CLI-S), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
\item \code{\link[=macrolides]{macrolides()}} can select: \cr acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), and tylvalosin (TYL1)
\item \code{\link[=monobactams]{monobactams()}} can select: \cr aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), carumonam (CAR), and tigemonam (TMN)
\item \code{\link[=nitrofurans]{nitrofurans()}} can select: \cr furazidin (FUR), furazolidone (FRZ), nifurtoinol (NFR), nitrofurantoin (NIT), and nitrofurazone (NIZ)
\item \code{\link[=oxazolidinones]{oxazolidinones()}} can select: \cr cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), and thiacetazone (THA)
\item \code{\link[=penicillins]{penicillins()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), carbenicillin (CRB), carindacillin (CRN), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), temocillin (TEM), ticarcillin (TIC), and ticarcillin/clavulanic acid (TCC)
\item \code{\link[=peptides]{peptides()}} can select: \cr avoparcin (AVO), bacitracin (BAC), bleomycin (BLM), dalbavancin (DAL), daptomycin (DAP), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), thiostrepton (THS), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
\item \code{\link[=phenicols]{phenicols()}} can select: \cr chloramphenicol (CHL), florfenicol (FLR), and thiamphenicol (THI)
\item \code{\link[=phosphonics]{phosphonics()}} can select: \cr amikacin/fosfomycin (AKF) and fosfomycin (FOS)
\item \code{\link[=polymyxins]{polymyxins()}} can select: \cr colistin (COL), polymyxin B (PLB), and polymyxin B/polysorbate 80 (POP)
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), ozenoxacin (OZN), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
\item \code{\link[=quinolones]{quinolones()}} can select: \cr besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nalidixic acid screening test (NAL-S), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
\item \code{\link[=rifamycins]{rifamycins()}} can select: \cr rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), and rifapentine (RFP)
\item \code{\link[=spiropyrimidinetriones]{spiropyrimidinetriones()}} can select: \cr zoliflodacin (ZFD)
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr ostreogrycin (OST), pristinamycin (PRI), quinupristin/dalfopristin (QDA), and virginiamycine (VIR)
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfachlorpyridazine (SUP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethazine (SUM), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfasuccinamide (SNA), sulfathiazole (SUT), sulfathiourea (SLF13), sulfisoxazole (SOX), sulfonamide (SSS), and trimethoprim/sulfamethoxazole (SXT)
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), tetracycline/oleandomycin (TOL), and tigecycline (TGC)
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), iclaprim (ICL), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), ormetroprim/sulfamethoxazole (ORS), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
\item \code{\link[=streptogramins]{streptogramins()}} can select: \cr pristinamycin (PRI) and quinupristin/dalfopristin (QDA)
\item \code{\link[=sulfonamides]{sulfonamides()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfamoxole (SLF8), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), and sulfathiourea (SLF13)
\item \code{\link[=tetracyclines]{tetracyclines()}} can select: \cr cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tetracycline screening test (TCY-S), and tigecycline (TGC)
\item \code{\link[=trimethoprims]{trimethoprims()}} can select: \cr brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), and trimethoprim/sulfamethoxazole (SXT)
\item \code{\link[=ureidopenicillins]{ureidopenicillins()}} can select: \cr azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), and piperacillin/tazobactam (TZP)
}
}
man/antimicrobials.Rd
+4 -4
View File
@@ -5,14 +5,14 @@
\alias{antimicrobials}
\alias{antibiotics}
\alias{antivirals}
\title{Data Sets with 625 Antimicrobial Drugs}
\title{Data Sets with 617 Antimicrobial Drugs}
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 505 observations and 14 variables:}{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 497 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{\strong{This is a unique identifier.}}
\item \code{group}\cr One or more short and concise group names, based on WHONET and WHOCC definitions
\item \code{group}\cr A short and concise group name, based on WHONET and WHOCC definitions
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02} (last updated May 4th, 2025):
\item \code{atc_group1}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}
\item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
@@ -50,7 +50,7 @@ LOINC:
}
}
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 505 rows and 14 columns.
An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
}
man/as.ab.Rd
+1 -8
View File
@@ -1,12 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ab.R
\docType{data}
\name{as.ab}
\alias{as.ab}
\alias{ab}
\alias{is.ab}
\alias{ab_reset_session}
\alias{NA_ab_}
\title{Transform Input to an Antibiotic ID}
\usage{
as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
@@ -15,8 +13,6 @@ as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
is.ab(x)
ab_reset_session()
NA_ab_
}
\arguments{
\item{x}{A \link{character} vector to determine to antibiotic ID.}
@@ -51,14 +47,12 @@ Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on th
Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
\code{NA_ab_} is a missing value of the new \code{ab} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
}
\section{Source}{
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://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
}
\section{WHOCC}{
@@ -117,4 +111,3 @@ if (require("dplyr")) {
\item \code{\link[=ab_from_text]{ab_from_text()}} for a function to retrieve antimicrobial drugs from clinical text (from health care records)
}
}
\keyword{datasets}
man/as.av.Rd
+1 -1
View File
@@ -44,7 +44,7 @@ Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} fun
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://health.ec.europa.eu/documents/community-register/html/reg_hum_atc.htm}
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
}
\section{WHOCC}{
man/as.mic.Rd
+3 -11
View File
@@ -12,15 +12,13 @@
\alias{droplevels.mic}
\title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
\usage{
as.mic(x, na.rm = FALSE, keep_operators = "all",
round_to_next_log2 = FALSE)
as.mic(x, na.rm = FALSE, keep_operators = "all")
is.mic(x)
NA_mic_
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE,
round_to_next_log2 = FALSE)
rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
mic_p50(x, na.rm = FALSE, ...)
@@ -35,8 +33,6 @@ mic_p90(x, na.rm = FALSE, ...)
\item{keep_operators}{A \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{round_to_next_log2}{A \link{logical} to round up all values to the next log2 level, that are not either 0.0001, 0.0002, 0.0005, 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, 2048, or 4096. Values that are already in this list (with or without operators), are left unchanged (including any operators).}
\item{mic_range}{A manual range to rescale the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to prevent rescaling on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{as.mic}{A \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{TRUE} for \code{\link[=rescale_mic]{rescale_mic()}} and \code{FALSE} for \code{\link[=droplevels]{droplevels()}}. When setting this to \code{FALSE} in \code{\link[=rescale_mic]{rescale_mic()}}, the output will have factor levels that acknowledge \code{mic_range}.}
@@ -110,7 +106,7 @@ is.mic(mic_data)
# this can also coerce combined MIC/SIR values:
as.mic("<=0.002; S")
# mathematical processing treats MICs as, and returns, numeric values
# mathematical processing treats MICs as numeric values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)
@@ -118,10 +114,6 @@ all(mic_data < 512)
# rescale MICs using rescale_mic()
rescale_mic(mic_data, mic_range = c(4, 16))
# round up to nearest log2 level, e.g. for CLSI breakpoint interpretation:
c(1:8)
as.mic(c(1:8), round_to_next_log2 = TRUE)
# interpret MIC values
as.sir(
x = as.mic(2),
man/as.mo.Rd
+3 -12
View File
@@ -1,6 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R
\docType{data}
\name{as.mo}
\alias{as.mo}
\alias{mo}
@@ -10,7 +9,6 @@
\alias{mo_failures}
\alias{mo_reset_session}
\alias{mo_cleaning_regex}
\alias{NA_mo_}
\title{Transform Arbitrary Input to Valid Microbial Taxonomy}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE,
@@ -33,8 +31,6 @@ mo_failures()
mo_reset_session()
mo_cleaning_regex()
NA_mo_
}
\arguments{
\item{x}{A \link{character} vector or a \link{data.frame} with one or two columns.}
@@ -49,9 +45,7 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
\item{minimum_matching_score}{A numeric value to set as the lower limit for the \link[=mo_matching_score]{MO matching score}. When left blank, this will be determined automatically based on the character length of \code{x}, its \link[=microorganisms]{taxonomic kingdom} and \link[=mo_matching_score]{human pathogenicity}.}
\item{keep_synonyms}{A \link{logical} to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of \emph{S. pyogenes}. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
The default is \code{FALSE}, which will return a note if outdated taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{keep_synonyms}{A \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
\item{reference_df}{A \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
@@ -63,7 +57,7 @@ The default is \code{FALSE}, which will return a note if outdated taxonomic name
\item{language}{Language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}
\item{info}{A \link{logical} to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with outdated taxonomic names. The default is \code{TRUE} only in interactive mode.}
\item{info}{A \link{logical} to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is \code{TRUE} only in interactive mode.}
\item{...}{Other arguments passed on to functions.}
}
@@ -106,7 +100,7 @@ There are three helper functions that can be run after using the \code{\link[=as
\itemize{
\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \link{data.frame} that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see \emph{Matching Score for Microorganisms} below).
\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \link{character} \link{vector} with all values that could not be coerced to a valid value.
\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \link{data.frame} with all values that could be coerced based on outdated, previously accepted taxonomic names.
\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \link{data.frame} with all values that could be coerced based on old, previously accepted taxonomic names.
}
}
@@ -157,8 +151,6 @@ This is based on:
\item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
}
}
\code{NA_mo_} is a missing value of the new \code{mo} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
}
\section{Source}{
@@ -268,4 +260,3 @@ mo_is_intrinsic_resistant("ESCCOL", ab = "vanco")
The \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}) to get properties based on the returned code.
}
\keyword{datasets}

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